Maximum residue number is 9000. Maximum number of atoms is 96000. Restrictions on the number of symmetry operations allowed in IMOL and AUTO modes, present in older versions, have been eased.
( PARAMETER (MXATOM=96000,MXRES=9000,MXSYMM=230) ) MXSYMM is: maximum number of symm. operations + 27
The possible keywords are:
AMODE, ANGLE, ATYPE, FROM, BIGSEARCH, HEXCLUDE, HOH, LIMITS, METAL, MODE, NOLIST, SOURCE, SPACEGROUP, SYMM, SYMTIT, TARGET, TITLE, TO
- for all interatomic distances for chosen residues.
- for interresidual contacts for chosen residues. It is similar to 'ALL' except that distances between atoms of different residues only will be computed, and distances between main-chain atoms from adjacent residues are also suppressed.
- for intersubunit contacts (subunits must have different chain names in the Brookhaven file).
- for intermolecular contacts. This mode requires symmetry information, see keywords SYMM and SPACEGROUP. The program looks for contacts using the supplied symmetry operations. If the symmetry operators are supplied via a spacegroup specification, then the identity operator is removed. The identity operator can be specified explicitly using a SYMM card.
Main-chain to main-chain and side-chain to side-chain contacts are suppressed if the atoms are on the same or adjacent residues and the target symmetry operation is the identity.
- as IMOL, but additional (primitive) lattice translations are generated automatically and combined with the supplied space-group symmetry in a search for intermolecular contacts. The identity operator is suppressed for lattice translations equal to (0,0,0), so that contacts within the same asymmetric unit are not listed.
The default is to use only single translations (e.g. +A ,-A, +A-B ...etc), which works well if the molecule is reasonably positioned within the cell (not outside). To extend the search to a larger volume (up to two lattice translations in all directions) you must also specify the BIGSEARCH keyword.
Additional output for MODE AUTO
(as in the original contact.f the default is do SOURCE = all input atoms to TARGET = all input atoms)
contact xyzin /homes/henrick/pdb/pdb4ins.ent <<eof MODE AUTO ATYPE ALL LIMITS 2 3.66 eofgives for LIMITS 2 3.66 Angstrom for PDB file 4ins
Sorted summation for Number of Contacts for atoms between symmetry related molecules Excluding water molecules
Num contacts TransSymm Symmetry ================================================= 995 555 002 2: -X+Y, -X, Z 818 555 001 1: -Y, X-Y, Z 337 554 007 7: -Y+1/3, X-Y+2/3, Z+2/3 331 455 005 5: -X+Y+2/3, -X+1/3, Z+1/3 179 554 002 2: -X+Y, -X, Z 145 554 009 9: X, Y, Z 143 556 009 9: X, Y, Z 76 556 001 1: -Y, X-Y, Z 9 554 008 8: -X+Y+1/3, -X+2/3, Z+2/3 9 555 004 4: -Y+2/3, X-Y+1/3, Z+1/3 4 555 008 8: -X+Y+1/3, -X+2/3, Z+2/3 3 555 007 7: -Y+1/3, X-Y+2/3, Z+2/3 3 454 005 5: -X+Y+2/3, -X+1/3, Z+1/3 2 554 004 4: -Y+2/3, X-Y+1/3, Z+1/3Note: The 2 Zinc insulin dodecamer requires the symmetry operations (in addition to identity) -X+Y, -X, Z and -Y, X-Y, Z, hence in the above table of contacts the cutoff at 6Ang for a significant oligomer is clear.
For LIMITS 2 3.66 Angstrom one gets Sorted summation for Number of Contacts for atoms between symmetry related molecules Excluding water molecules
Num contacts TransSymm Symmetry ================================================= 49 555 002 2: -X+Y, -X, Z 39 555 001 1: -Y, X-Y, Z 10 554 007 7: -Y+1/3, X-Y+2/3, Z+2/3 9 554 009 9: X, Y, Z 9 556 009 9: X, Y, Z 9 554 002 2: -X+Y, -X, Z 8 455 005 5: -X+Y+2/3, -X+1/3, Z+1/3Again the cutoff is clear.
Note: The summation of all atom contacts between symmetry related molecules excludes water molecules, but includes any other HETATM labelled atoms.
Again if there is no spacegroup name on the CRYST1 record of the input PDB file then the keyword SPACEGROUP can be used.
- all types of atoms will be used in computations.
- carbon atoms omitted.
If SYMTIT cards are not supplied, the symmetry description will be : symmetry 1, symmetry 2, etc...
If spacegroup symmetry operations are required, and have not been supplied by the SPACEGROUP or SYMM cards, then they will be taken from the input PDB file CRYST1 line if they are there. SYMMTitles are automatically generated in this case.
When using the ANGLE option, the program calculates the hydrogen position for those target nitrogen atoms where the hydrogen position is unambiguous (i.e., excluding NZ on Lys and N terminus). The angle O...H...N is calculated and printed. For source...oxygen hydrogen bonds, the angle source...O__Bonded carbon is calculated. Limits on both these angles (ANGH and ANGO) must be supplied, and bonds with angles less than these limits are rejected. Suitable values are 120 and 90 degrees.
The ANGLE option can be used to search for hydrogen bonds within the protein, and the bond angles will be calculated as described above. Note that mainchain-mainchain and sidechain-sidechain contacts within one residue or to an immediately adjacent residue are suppressed in this mode. The minimum bond length (DMIN) for bonds to be included and the maximum number of bonds (MAXNB) are read from the same card, in free format, as is the MAXIMUM temperature factor for a source atom to be included in contact search and water analysis (BMAX).
An analysis of all water-protein and water-water hydrogen bonds and the bond angles at the water oxygen is also given. Note: water residue name should be WAT and the water atom name must be O (NOT O1 or OW etc) when using this option.
The ANGLE option may be used in conjunction with all modes, but to ensure the numbers are correct (especially the number of waters in the first and second hydration shells) the IMOL (or even better AUTO) mode should always be used, and identity (symm x,y,z) included to generate all lattice contacts for analysis of water interactions (only water molecules should be selected as the SOURCE range in this case).
The ANGLE operation in this version should be the same as the original with the exception except perhaps as I am not certain about the original all waters with occupancy less that 1.0 are excluded from water analysis in this version.
In addition both residue names for waters of HOH or WAT are allowed.
- the minimum distance between atoms to be included in the printout
- the maximum distance to be printed out. Because of the bricking algorithm (see DESCRIPTION section above) some contacts may be missed if <dmax> is greater than 6.0 A.
- n1, n2
- range of source residues. You may input as many SOURCE cards as you like (within array limits). The maximum residue number allowed is 9000. If the range is made of just one residue only n1 is required.
- n1, n2
- range of target residues. You may input as many TARGET cards as you like (within array limits). The maximum residue number allowed is 9000 (MXRES). If the range is made of just one residue only n1 is required.
(i) based on atom numbers FROM ATOM 1 TO 561 TO ATOM 1 TO 561 (ii) based on residue numbers but now allowing for chain names FROM RESIDUE ALL CHAIN A 1 to 125 TO RESIDUE ALL CHAIN W 1 to 256The general input expression is:
FROM [ [ ATOM <inat0> [TO] <inat1> ] | [ RESIDUE <ires0> [TO] <ires1> ]] ... [ CHAIN <chainid> ALL | ONS | CA ] TO [ [ ATOM <jnat0> [TO] <jnat1> ] | [ RESIDUE <jres0> [TO] <jres1> ]] ... [ CHAIN <chainid> ALL | ONS | CA ]If ATOM is specified it is followed by <inat0> and <inat1>, respectively the first and last target atoms checked. I.e. FROM atoms <inat0> to <inat1> are checked against TO atoms <jnat0> to <jnat1>. (Atoms are numbered 1 to NAT, in the order read, but the residue order can be varied without restriction. Beware: atoms with occ=0.0 are not counted.)
If RESIDUE is specified it is followed by <jres0> and <jres1>, respectively the first and last target residues checked, and optionally subsidiary keywords:
CHAIN <chainid> ALL | ONS | CA ALL (default) will select all atoms in the requested residues. ONs will select just the oxygen and nitrogen atoms. CA will select just the CA atoms.i.e. FROM residues <ires0> to <ires1> are checked against TO residues <jres0> to <jres1> for the appropriate class of atoms.
will give just source CHAIN A to TARGET CHAIN B contact xyzin /homes/henrick/pdb/pdb4ins.ent <<eof LIMITS 2 3.66 FROM RESIDUE ALL CHAIN A 1 to 21 TO RESIDUE ALL CHAIN B 1 to 30 eof
If MODE is not specified elsewhere then the use of the METAL keyword will automatically set the MODE to AUTO, and look for contacts with symmetry related atoms - in this case the symmetry operations must be specified in some manner; see the MODE keyword for more details.
<metal-ligand distance> defaults to a value of 2.35 Å, if not explicitly specified. Pairs of atoms which are less than this distance apart will be marked with a "***" symbol (see Comments on output). Use the LIMITS keyword to set the closest and furthest distance for finding contacts, though note that METAL will automatically set a closest distance of at least 0.25 Å, overriding that set by LIMITS if it is smaller.
The output consists of a list of metal-ligand contacts; for each metal atom a table of angles is also printed for all those atoms closer than <metal-ligand distance>. These are the angles at the metal position formed by each pair of contacting atoms.
contact xyzin /homes/henrick/pdb/pdb4ins.ent <<eof METAL ZN 2.35 eofExample 2:
If there is no spacegroup name on the CRYST1 line in the input PDB file use (or you can still select individual symmetry operations with SYMMETRY keyword as in the original contact.f)
contact xyzin /homes/henrick/pdb/pdb4ins.ent <<eof METAL ZN 2.35 SPACEGROUP R3 eofThis gives the output:
zn 1 ZN His 10B CD2 ... 3.08 [ ] 1: -Y, X-Y, Z His 10B CE1 ... 3.02 [ ] 9: X, Y, Z His 10B CE1 ... 3.02 [ ] 1: -Y, X-Y, Z His 10B NE2 ... 2.11 ***[ ] 9: X, Y, Z His 10B NE2 ... 2.10 ***[ ] 1: -Y, X-Y, Z His 10B NE2 ... 2.11 ***[ ] 2: -X+Y, -X, Z Wat 201 O ... 2.19 ***[ ] 1: -Y, X-Y, Z Wat 201 O ... 2.19 ***[ ] 2: -X+Y, -X, Z Wat 251 O ... 3.32 [ ] 9: X, Y, Z Wat 251 O ... 3.32 [ ] 1: -Y, X-Y, Z Wat 251 O ... 3.32 [ ] 2: -X+Y, -X, Z His 10B CD2 ... 3.09 [ ] 9: X, Y, Z His 10B CD2 ... 3.09 [ ] 2: -X+Y, -X, Z His 10B CE1 ... 3.02 [ ] 2: -X+Y, -X, Z Wat 201 O ... 2.19 ***[ ] 9: X, Y, Z zn 2 ZN His 10D CD2 ... 3.14 [ ] 1: -Y, X-Y, Z His 10D CD2 ... 3.14 [ ] 2: -X+Y, -X, Z His 10D CE1 ... 2.96 [ ] 1: -Y, X-Y, Z His 10D CE1 ... 2.96 [ ] 2: -X+Y, -X, Z His 10D NE2 ... 2.08 ***[ ] 1: -Y, X-Y, Z His 10D NE2 ... 2.08 ***[ ] 2: -X+Y, -X, Z Wat 513 O ... 2.32 ***[ -C] 9: X, Y, Z Wat 513 O ... 2.32 ***[ -C] 2: -X+Y, -X, Z His 10D CD2 ... 3.14 [ ] 9: X, Y, Z His 10D CE1 ... 2.96 [ ] 9: X, Y, Z His 10D NE2 ... 2.08 ***[ ] 9: X, Y, Z Wat 513 O ... 2.32 ***[ -C] 1: -Y, X-Y, Z for Metal atom ZN ZN 1 ============================================ 1 His 10B NE2 2 His 10B NE2 98.9 3 His 10B NE2 98.7 98.8 4 Wat 201 O 93.9 90.4 163.0 5 Wat 201 O 163.1 93.9 90.2 74.9 6 Wat 201 O 90.2 163.2 93.7 74.8 74.8 1 2 3 4 5 for Metal atom ZN ZN 2 ============================================ 1 His 10D NE2 2 His 10D NE2 103.4 3 Wat 513 O 154.0 96.6 4 Wat 513 O 96.6 87.7 67.5 5 His 10D NE2 103.4 103.4 87.7 154.0 6 Wat 513 O 87.7 154.0 67.5 67.5 96.6 1 2 3 4 5Example 3:
METAL AL 2.25For pdb entry 1kdn the aluminium to ligand contacts are within the same residue, not between residues, nor are symmetry related contacts involved. Note that the order of the atoms in the input file is important in this case:
--- this will work HETATM 1150 AL AF3 A 157 69.404 29.227 2.379 1.00 22.45 HETATM 1151 F1 AF3 A 157 69.611 30.838 3.207 1.00 23.32 HETATM 1152 F2 AF3 A 157 68.410 27.856 3.138 1.00 23.97 HETATM 1153 F3 AF3 A 157 69.936 28.691 0.589 1.00 19.15 --- this will fail HETATM 1151 F1 AF3 A 157 69.611 30.838 3.207 1.00 23.32 HETATM 1152 F2 AF3 A 157 68.410 27.856 3.138 1.00 23.97 HETATM 1153 F3 AF3 A 157 69.936 28.691 0.589 1.00 19.15 HETATM 1150 AL AF3 A 157 69.404 29.227 2.379 1.00 22.45
The main output of the program is a list of the contacts. The information is arranged in columns as follows:
First three columns: describe the "source" atom 1 - residue name 2 - residue number 3 - atom name Second three columns: describe the "target" atom 4 - residue name 5 - residue number 6 - atom nameIn MODEs ALL, IRES and ISUB the target atoms are simply taken from those listed in the input pdb file (limited by the TARGET keyword, if present). In these modes, the next three columns are:
7 - distance between target and source (angstroms) 8 - hydrogen bond angle (if ANGLE keyword is present) 9 - "***", " *" or " " (i.e. blank)See the comments for keyword ANGLE above for more details of the contents of column 8; it will be empty if ANGLE is not specified. In column 9, "***" indicates the strong possibly of a hydrogen bond at this contact (distance < 3.3 A), " *" indicates a weak possibility (distance > 3.3 A). Blank indicates that the program considers there is no possibility of a hydrogen bond. (Nb: when using the METAL keyword, column 9 instead marks those contacts which lie within the <metal-ligand distance>.)
The final three columns will be empty except in MODE IMOL or AUTO. In these cases, the target atoms are generated from those in the pdb file by a combination of a symmetry operation followed by a lattice translation. These columns give information about the operations used to create these "symmetry related" atoms:
10 - lattice translations 11 - number identifying symmetry operation 12 - name identifying symmetry operationSee the SYMM, SYMTIT and SPACEGROUP keywords for more details of the number (col. 11) and name (col. 12) of the symmetry operators. Column 10 will contain output of the form
e.g. [ +B-C] or [+A ].Here A, B and C refer to the primitive lattice vectors a, b and c respectively, which are generated from the CRYST1 card in the pdb file. So in these two modes, target atoms may seem to appear more than once - but they will be distinguished by having different associated symmetry and/or translation operations, which means they are symmetry related to the atom listed in columns 4-6 but are at different physical positions.
contact xyzin holo9c4.brk <<eof TITLE INTER-MOLECULAR CONTACTS FOR HOLO-GAPDH ATYPE ALL MODE IMOL limits 0.0 3.9 symtit +A symm 1+X,Y,Z symtit +C symm X,Y,1+Z symtit 21 symm -X,1/2+Y,-Z eof2) Intermolecular contacts (AUTO mode). Default symmetry labels.
contact xyzin xisomerase.brk << eof mode auto symm -Y,X-Y,1/3+Z symm Y-X,-X,2/3+Z symm Y,X,-Z symm -X,Y-X,1/3-Z symm X-Y,-Y,2/3-Z eof3)Contacts between specified parts of the molecule:
contact xyzin holo9c4.brk << eof TITLE NAD-WATER CONTACTS limits 0.0 3.9 SOURCE 336 TARGET 337 1000 eof4)Bond lengths in NAD molecule (residue number 336):
contact xyzin holo9c4.brk << eof TITLE NAD BONDS mode ALL limits 0.0 1.9 SOURCE 336 TARGET 336 eof5)Intersubunit contacts for a fragment of the chain. Subunits must have different chain names in the Brookhaven data file.
contact xyzin holo9c4.brk << eof title INTERSUBUNIT CONTACTS mode ISUB limits 0.0 3.9 source 180 210 eof6) Analysis of water hydrogen bonding (all water contacts)
contact xyzin holo9c4.brk << eof TITLE WATER CONTACTS mode auto angle symm x,y,z symm -X,1/2+Y,-Z SOURCE 340 1000 !water molecules eof7) Hydrogen bonds and angles for a piece of chain
contact xyzin holo9c4.brk << eof ANGLE LIMITS 0.0 3.4 SOURCE 33 88 TARGET 1 334 eof8) For MODE AUTO with TO and FROM keywords
contact xyzin /homes/henrick/pdb/pdb4ins.ent <<eof MODE AUTO LIMITS 2 3.66 FROM RESIDUE ALL CHAIN A 1 to 21 TO RESIDUE ALL CHAIN D 1 to 30 eofwill give all symmetry related chain D atoms to identity chain A atoms, i.e.
Thr 8A O His 5D CD2 ... 3.00 +C1: -Y, X-Y, Z Ser 9A C His 5D NE2 ... 3.45 +C1: -Y, X-Y, Z Ser 9A O His 5D CD2 ... 3.39 +C1: -Y, X-Y, Z His 5D CE1 ... 3.62 +C1: -Y, X-Y, Z His 5D NE2 ... 2.60 *** +C1: -Y, X-Y, Z Gln 15A CG Phe 25D CE2 ... 3.57 -A 5: -X+Y+2/3,-X+1/3,Z+1/3 Asn 18A CG Thr 27D OG1 ... 3.64 -A 5: -X+Y+2/3,-X+1/3,Z+1/3 Asn 18A OD1 Thr 27D OG1 ... 2.75 *** -A 5: -X+Y+2/3,-X+1/3,Z+1/39) Combining selection TO/FROM with AUTO and ANGLE
contact xyzin /homes/henrick/pdb/pdb4ins.ent <<eof MODE AUTO LIMITS 2 3.66 FROM RESIDUE ALL CHAIN A 1 to 21 TO RESIDUE ALL CHAIN D 1 to 30 ANGLE eof