Contacts of the strand formed by residues 1240 - 1243 (chain A) in PDB entry 3H0G


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 ILE1240 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1168A  GLU*     3.3    11.9    -      -       -      +
   1170A  LYS*     2.6    53.3    -      -       +      +
   1197A  ARG*     3.6    36.1    -      -       +      +
   1198A  LEU      3.3    24.2    -      -       -      +
   1199A  GLU*     4.9    11.7    -      -       +      -
   1212A  MET*     4.2     0.2    -      -       -      +
   1230A  ILE      4.0     1.8    -      -       -      +
   1231A  TRP*     3.7    12.5    -      -       -      -
   1232A  SER*     3.9    11.7    +      -       -      -
   1236A  ALA*     5.5     0.2    -      -       -      +
   1238A  LYS*     3.9     9.0    -      -       +      +
   1239A  LEU*     1.3    77.5    -      -       -      +
   1241A  ILE*     1.3    80.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1196A  LEU      3.9     0.7    -      -       -      +
   1197A  ARG*     3.8     2.1    -      -       -      -
   1198A  LEU*     3.4    38.5    +      -       +      +
   1200A  LEU*     4.0    18.2    -      -       +      -
   1212A  MET*     3.5    32.1    -      -       +      +
   1215A  VAL*     4.4     4.5    -      -       +      -
   1216A  ALA*     3.9    25.8    -      -       +      -
   1219A  ILE*     5.5     0.2    -      -       +      -
   1229A  THR*     4.0     3.1    -      -       -      -
   1230A  ILE      3.6    15.7    -      -       -      +
   1231A  TRP*     3.5    22.0    -      -       +      +
   1240A  ILE*     1.3    86.7    -      -       -      +
   1242A  ARG*     1.3    76.0    +      -       -      +
   1243A  CYS*     4.6     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG1242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1162A  GLN*     5.6     1.2    -      -       -      +
   1163A  ASP      3.6     4.8    +      -       -      -
   1164A  THR*     3.0    25.5    -      -       -      +
   1166A  ILE*     5.7     1.0    -      -       -      +
   1174A  GLU*     2.3    51.9    +      -       +      +
   1195A  LEU*     2.6    46.1    -      -       +      +
   1196A  LEU      3.6     3.1    -      -       -      -
   1197A  ARG*     3.7    27.6    -      -       +      +
   1228A  PHE      4.0     4.5    -      -       -      +
   1229A  THR*     3.3    18.2    -      -       -      -
   1230A  ILE*     3.4    24.0    +      -       +      +
   1241A  ILE*     1.3    74.8    -      -       -      +
   1243A  CYS*     1.3    76.6    +      -       -      +
   1244A  ARG*     3.0    30.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS1243 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1194A  TRP      4.0     3.1    -      -       -      +
   1195A  LEU*     4.3     0.8    -      -       -      +
   1196A  LEU*     3.2    37.8    +      -       +      +
   1198A  LEU*     3.8    28.0    -      -       +      -
   1219A  ILE*     4.7     8.3    -      -       -      -
   1227A  LEU*     4.1    22.4    -      -       +      +
   1228A  PHE      3.7     7.4    -      -       -      +
   1229A  THR*     4.1    14.4    -      -       +      -
   1241A  ILE*     4.2     5.2    -      -       -      -
   1242A  ARG*     1.3    97.8    -      -       -      +
   1244A  ARG*     1.3    66.3    +      -       -      +
----------------------------------------------------------
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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