Contacts of the strand formed by residues 1164 - 1168 (chain A) in PDB entry 2H7C


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 VAL1164 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1121A  ILE*     3.8    22.9    -      -       +      -
   1122A  TYR      3.4    10.1    -      -       -      +
   1123A  THR*     3.6    23.3    -      -       -      +
   1133A  LEU*     4.2    11.2    -      -       +      -
   1134A  PRO      2.9    11.1    +      -       -      +
   1135A  VAL*     3.4     8.7    -      -       +      +
   1136A  MET*     2.7    33.1    +      -       -      +
   1163A  VAL*     1.3    74.6    -      -       -      +
   1165A  VAL*     1.3    57.9    +      -       -      +
   1166A  VAL*     4.4     4.3    -      -       +      -
   1205A  ILE*     4.1    18.8    -      -       +      -
   1208A  PHE      4.0     4.3    -      -       -      +
   1209A  GLY      4.1     5.4    -      -       -      +
   1210A  GLY*     3.9    22.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL1165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1121A  ILE*     3.5     1.0    -      -       -      -
   1122A  TYR*     2.8    53.6    +      -       +      +
   1136A  MET*     3.4     9.4    -      -       +      +
   1138A  TRP*     5.3     0.2    -      -       +      -
   1154A  GLY*     3.9    31.0    -      -       -      +
   1157A  LEU*     3.8    30.3    -      -       +      -
   1158A  ALA*     3.9     8.7    -      -       +      +
   1163A  VAL*     4.0     7.9    -      -       +      -
   1164A  VAL*     1.3    73.7    -      -       -      +
   1166A  VAL*     1.3    63.0    +      -       -      +
   1167A  THR*     4.3    16.2    -      -       +      -
   1218A  PHE*     5.0     4.0    -      -       +      -
   1476A  PHE*     4.5    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1119A  LEU*     4.2    21.8    -      -       +      -
   1120A  ASN      3.3     9.6    -      -       -      +
   1121A  ILE*     4.2     9.0    -      -       +      -
   1135A  VAL*     4.0    23.1    -      -       +      -
   1136A  MET      2.9     8.9    +      -       -      +
   1137A  VAL*     3.2    13.9    -      -       +      +
   1138A  TRP*     2.7    32.6    +      -       -      +
   1164A  VAL*     4.4     3.1    -      -       +      -
   1165A  VAL*     1.3    77.2    -      -       -      +
   1167A  THR*     1.3    58.2    +      -       -      +
   1168A  ILE*     3.9    20.6    -      -       +      -
   1201A  VAL*     4.3    10.3    -      -       +      -
   1205A  ILE*     4.0    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR1167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1119A  LEU*     3.2     3.5    -      -       -      +
   1120A  ASN*     2.9    52.1    +      -       -      +
   1122A  TYR*     4.3     7.0    -      -       +      -
   1138A  TRP*     3.7    27.4    -      -       +      -
   1149A  ALA*     3.6    20.6    +      -       -      +
   1152A  TYR*     3.8    22.1    +      -       +      +
   1154A  GLY      5.2     0.2    -      -       -      +
   1165A  VAL*     4.3    13.9    -      -       +      -
   1166A  VAL*     1.3    75.4    -      -       -      +
   1168A  ILE*     1.3    61.8    +      -       -      +
   1476A  PHE*     4.8     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE1168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1055A  PHE*     4.8     0.2    -      -       +      -
   1118A  TYR      4.0     3.6    -      -       -      -
   1119A  LEU*     4.0     7.4    -      -       +      -
   1137A  VAL*     3.7    25.4    -      -       +      -
   1138A  TRP      3.2    17.9    +      -       -      +
   1139A  ILE*     4.0    24.2    -      -       +      -
   1140A  HIS*     3.5    15.1    +      -       -      -
   1149A  ALA*     3.5     8.8    -      -       -      +
   1166A  VAL*     3.9    13.9    -      -       +      -
   1167A  THR*     1.3    78.2    -      -       -      +
   1169A  GLN*     1.3    68.2    +      -       -      +
   1170A  TYR*     4.4     1.9    -      -       +      -
   1194A  GLN*     4.0    27.4    -      -       +      +
   1197A  ALA*     3.9    33.4    -      -       +      -
   1198A  LEU*     5.8     1.1    -      -       +      -
   1201A  VAL*     5.7     0.2    -      -       +      -
----------------------------------------------------------
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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