Contacts of the strand formed by residues 965 - 969 (chain A) in PDB entry 3I8E


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 PHE 965 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    921A  ILE*     4.8     3.6    -      -       +      -
    923A  VAL*     4.8    18.2    -      -       +      -
    930A  VAL*     5.5     6.0    -      -       +      +
    931A  LEU      5.6     0.4    -      -       -      -
    932A  LEU*     3.3    46.9    -      -       +      -
    957A  VAL*     5.9     0.9    -      -       +      -
    958A  GLU      3.9     4.3    -      -       -      +
    959A  ILE*     3.7    37.2    -      -       +      -
    961A  ASP      3.7    10.1    -      -       -      -
    962A  ASP      4.0    14.4    -      -       -      -
    963A  ASP*     3.7    16.6    -      -       -      -
    964A  ASN*     1.3    77.4    -      -       -      +
    966A  LEU*     1.3    62.1    +      -       -      +
    967A  GLY      3.8     1.0    +      -       -      -
    975A  PHE*     5.5     0.9    -      -       -      -
    976A  VAL*     3.3     5.5    -      -       -      +
    977A  CYS*     2.7    49.6    +      -       +      +
    978A  GLN*     5.2     0.7    -      -       -      -
    979A  LYS*     5.2     2.7    -      -       +      -
    992A  LEU*     4.0    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 966 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    956A  ALA      4.1     0.2    -      -       -      +
    957A  VAL*     3.6     6.4    -      -       -      +
    958A  GLU*     2.9    41.6    +      -       +      +
    960A  LEU*     3.9    29.4    -      -       +      -
    964A  ASN      4.0     1.2    +      -       -      -
    965A  PHE*     1.3    72.0    -      -       -      +
    967A  GLY*     1.3    78.1    +      -       -      +
    974A  LEU*     4.3    16.4    -      -       +      -
    975A  PHE      3.5    13.9    -      -       -      +
    976A  VAL*     4.4    11.9    -      -       +      -
   1007A  PHE*     3.7    40.7    -      -       +      -
   1028A  VAL*     4.7     2.7    -      -       +      -
   1040A  VAL*     3.9    25.4    -      -       +      -
   1088A  PHE*     4.9     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 967 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    930A  VAL*     5.5     1.1    -      -       -      -
    954A  MET*     3.9     8.1    -      -       -      -
    956A  ALA      3.5     6.5    -      -       -      -
    957A  VAL*     4.7     1.3    -      -       -      -
    965A  PHE      3.8     2.0    +      -       -      -
    966A  LEU*     1.3    82.6    -      -       -      +
    968A  ALA*     1.3    59.5    +      -       -      -
    974A  LEU*     3.6     0.7    -      -       -      -
    975A  PHE*     2.9    57.0    +      -       -      +
   1007A  PHE*     4.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 968 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    954A  MET*     3.5     6.4    -      -       -      +
    955A  SER*     2.9    28.7    +      -       -      +
    956A  ALA*     2.9    19.8    +      -       +      +
    967A  GLY*     1.3    75.0    -      -       -      -
    969A  GLU*     1.3    66.8    +      -       -      +
    973A  ASN      3.7     5.6    -      -       -      -
    974A  LEU*     3.8    12.6    -      -       +      -
    975A  PHE*     4.6     0.4    -      -       -      -
   1004A  VAL*     3.6    31.4    -      -       +      -
   1007A  PHE*     3.9     4.3    -      -       +      -
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Residues in contact with GLU 969 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    951A  PRO      5.1     0.3    -      -       -      +
    952A  ASN*     3.5    31.1    -      -       +      +
    953A  TRP*     3.3    30.0    +      -       +      +
    954A  MET*     4.3     1.1    -      -       -      -
    955A  SER*     3.7     6.8    +      -       -      -
    968A  ALA*     1.3    80.0    -      -       -      +
    970A  ASN*     1.3    56.2    +      -       +      +
    971A  ALA*     2.5    34.5    +      -       -      +
    972A  PHE*     2.7    17.2    +      -       -      -
    973A  ASN*     3.1    37.7    +      -       -      +
    975A  PHE*     4.6     5.6    -      -       +      -
   1003A  PHE*     5.8     2.1    -      -       -      -
   1004A  VAL*     5.6     1.7    -      -       -      +
   1076A  PHE*     4.0    12.7    -      -       -      -
   1078A  THR*     4.1     9.0    -      -       -      +
----------------------------------------------------------
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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