Contacts of the strand formed by residues 1257 - 1263 (chain A) in PDB entry 3CMT


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with GLN1257 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1046A  SER      4.7     1.2    -      -       -      +
   1050A  ALA*     3.9     9.0    -      -       -      +
   1243A  ARG*     3.3    34.7    +      -       +      +
   1244A  VAL      3.3    13.0    -      -       -      +
   1245A  LYS*     3.4    38.3    -      -       +      +
   1255A  PHE      5.2     4.3    +      -       -      +
   1256A  LYS*     1.3    77.4    -      -       -      +
   1258A  ALA*     1.3    63.1    +      -       -      +
   1259A  GLU*     4.3     4.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA1258 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1046A  SER*     3.4    26.9    -      -       -      +
   1047A  LEU*     3.5    32.8    -      -       +      +
   1050A  ALA*     4.2     2.4    -      -       +      +
   1242A  THR      3.9     0.3    -      -       -      +
   1243A  ARG*     3.3     3.0    -      -       -      +
   1244A  VAL*     2.8    39.3    +      -       +      +
   1257A  GLN*     1.3    75.8    -      -       -      +
   1259A  GLU*     1.3    62.2    +      -       -      +
   1260A  PHE*     4.3     6.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU1259 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1046A  SER*     3.5    12.0    +      -       -      -
   1228A  ILE*     4.0    12.5    -      -       +      +
   1241A  GLU*     5.6     2.9    -      -       +      +
   1242A  THR      3.2     7.2    -      -       -      +
   1243A  ARG*     2.4    50.8    +      -       +      +
   1257A  GLN*     4.3     5.7    -      -       +      +
   1258A  ALA*     1.3    77.3    -      -       -      +
   1260A  PHE*     1.3    64.2    +      -       -      +
   1273A  GLU*     4.4     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE1260 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1044A  SER*     3.3    25.4    -      -       -      -
   1046A  SER*     4.1     3.4    -      -       -      -
   1047A  LEU*     4.8     2.2    -      -       +      -
   1075A  LEU*     3.9    17.5    -      -       +      -
   1225A  ILE*     4.7     0.4    -      -       +      -
   1241A  GLU*     3.7     6.6    +      -       -      +
   1242A  THR*     2.7    62.5    +      -       +      +
   1244A  VAL*     3.7    26.9    -      -       +      -
   1258A  ALA*     4.3     8.1    -      -       +      -
   1259A  GLU*     1.3    78.6    -      -       -      +
   1261A  GLN*     1.3    73.3    +      -       -      +
   1262A  ILE*     3.8    17.0    -      -       +      -
   1268A  ILE*     3.8    19.7    -      -       +      -
   1269A  ASN      5.1     0.4    -      -       -      +
   1273A  GLU*     3.5    25.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN1261 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1231A  VAL*     3.5    26.2    -      -       +      +
   1240A  SER      3.6     3.4    -      -       -      -
   1241A  GLU*     3.2    34.7    +      -       -      +
   1260A  PHE*     1.3    78.2    -      -       -      +
   1262A  ILE*     1.3    61.0    +      -       -      +
   1263A  LEU*     3.8    15.0    -      -       +      +
   1268A  ILE*     3.3     4.3    -      -       -      -
   1269A  ASN*     2.7    64.9    +      -       +      +
   1302A  LYS*     5.4    12.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1262 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1070A  SER      4.3     2.5    -      -       -      +
   1071A  GLY*     4.0    28.7    -      -       -      +
   1074A  THR*     3.8    28.9    -      -       +      +
   1075A  LEU*     5.4     1.1    -      -       +      +
   1103A  TYR*     4.9     2.9    -      -       -      +
   1225A  ILE*     4.8     2.0    -      -       +      -
   1239A  GLY*     3.1     2.3    -      -       -      -
   1240A  SER*     2.7    46.8    +      -       -      +
   1242A  THR*     3.7    20.2    -      -       +      +
   1260A  PHE*     3.8    20.0    -      -       +      -
   1261A  GLN*     1.3    72.6    -      -       -      +
   1263A  LEU*     1.3    68.3    +      -       -      +
   1264A  TYR*     3.6     5.0    +      -       +      -
   1267A  GLY*     3.5     9.0    -      -       -      +
   1268A  ILE*     4.5     7.0    -      -       +      -
   1502A  ADP      4.6    15.3    -      -       -      +
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Residues in contact with LEU1263 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1103A  TYR*     4.7     0.3    +      -       -      -
   1231A  VAL*     4.0    26.7    -      -       +      -
   1238A  VAL*     3.8    16.8    -      -       +      +
   1239A  GLY*     4.5     1.6    -      -       -      -
   1261A  GLN*     4.0    12.3    -      -       +      +
   1262A  ILE*     1.3    76.7    -      -       -      +
   1264A  TYR*     1.3    65.6    +      -       -      +
   1266A  GLU*     3.0    34.3    +      -       +      +
   1267A  GLY*     2.8    41.9    +      -       -      +
   1269A  ASN*     4.1    33.0    -      -       +      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il