Contacts of the strand formed by residues 1088 - 1091 (chain E) in PDB entry 2X4Y


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 LEU1088 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1086E  LEU      3.8     2.0    +      -       -      +
   1087E  ASP*     1.3    75.7    -      -       -      +
   1089E  VAL*     1.3    66.2    +      -       -      +
   1101E  ALA      3.5     2.0    -      -       -      +
   1102E  LEU*     4.0    13.9    -      -       +      -
   1148E  PHE*     3.5    36.8    -      -       +      -
   1164E  PRO*     3.7     3.5    -      -       -      +
   1165E  LEU*     3.0    48.8    +      -       +      +
   1195E  ALA*     3.6    23.3    -      -       +      +
   1196E  LEU*     4.7     2.2    -      -       +      -
   1198E  HIS*     4.1     9.4    -      -       +      -
   1199E  ARG*     3.9    31.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL1089 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1083E  LEU*     4.1    16.6    -      -       +      -
   1087E  ASP*     4.3     4.9    -      -       +      +
   1088E  LEU*     1.3    80.6    -      -       -      +
   1090E  TRP*     1.3    64.6    +      -       -      +
   1091E  ALA*     4.3     1.8    -      -       +      -
   1100E  PRO*     3.5     4.2    -      -       -      +
   1101E  ALA*     2.9    53.1    +      -       +      +
   1103E  ILE*     3.8    35.0    -      -       +      -
   1145E  VAL*     4.4     2.9    -      -       +      -
   1162E  LEU*     4.1    23.1    -      -       +      -
   1163E  VAL      3.2    13.7    -      -       -      +
   1164E  PRO*     4.4     4.3    -      -       +      -
   1165E  LEU*     3.6     9.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP1090 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1089E  VAL*     1.3    72.0    -      -       -      +
   1091E  ALA*     1.3    59.8    +      -       -      +
   1098E  SER*     3.7    24.7    -      -       -      -
   1099E  TYR      3.7     4.7    -      -       -      -
   1100E  PRO*     3.7    15.7    -      -       +      -
   1161E  LYS      3.5     1.6    -      -       -      +
   1162E  LEU*     3.2     7.1    -      -       -      +
   1163E  VAL*     2.7    41.0    +      -       +      +
   1164E  PRO      3.8     8.3    -      -       -      -
   1165E  LEU*     3.6    23.1    -      -       +      +
   1171E  LEU*     3.9    14.8    -      -       +      +
   1172E  ASP*     2.8    35.3    +      -       -      -
   1175E  LYS*     3.6    32.1    -      -       +      -
   1176E  MET*     3.5    25.1    -      -       +      -
   1188E  VAL*     3.7    22.0    -      -       +      -
   1192E  TYR*     3.6    28.7    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA1091 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1089E  VAL*     4.3     1.3    -      -       +      -
   1090E  TRP*     1.3    74.8    -      -       -      +
   1092E  LYS*     1.3    61.9    +      -       -      +
   1093E  CYS*     3.9     2.1    +      -       -      -
   1097E  PRO      4.3     0.5    -      -       -      +
   1098E  SER*     3.7     1.1    -      -       -      -
   1099E  TYR*     2.8    39.3    +      -       -      +
   1101E  ALA*     4.0    13.0    -      -       +      -
   1145E  VAL*     4.2     3.1    -      -       +      -
   1147E  PHE*     3.7    16.9    -      -       +      -
   1157E  LEU*     3.6    20.9    -      -       +      -
   1161E  LYS      3.5     4.3    -      -       -      -
   1162E  LEU*     3.7    11.0    -      -       +      -
----------------------------------------------------------
 Back to top of page


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