Contacts of the strand formed by residues 61 - 67 (chain B) 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 ILE 61 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  ASN*     5.1     8.1    +      -       -      +
     34B  ALA*     3.9    27.4    -      -       +      -
     35B  LYS      5.0     4.5    -      -       -      +
     36B  ASN*     2.8    23.6    +      -       -      +
     37B  THR      4.3     3.4    -      -       -      -
     38B  ARG      3.5    31.2    -      -       -      +
     39B  LEU*     4.6     4.5    -      -       +      -
     57B  MET*     4.4    17.5    -      -       +      -
     59B  GLY      3.3     5.4    +      -       -      +
     60B  LYS*     1.3    70.8    -      -       -      +
     62B  ALA*     1.3    59.9    +      -       -      +
     63B  VAL      3.9    12.1    -      -       -      +
     64B  MET*     4.1     6.3    -      -       +      -
     79B  ILE*     3.9    34.3    -      -       +      -
     80B  LEU      4.0     4.5    -      -       -      +
     81B  THR*     4.8     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 62 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  LYS      3.3     6.0    +      -       -      +
     61B  ILE*     1.3    74.5    -      -       -      +
     63B  VAL*     1.3    65.1    +      -       +      +
     80B  LEU      3.0    11.7    +      -       -      +
     82B  ALA*     4.2     8.1    -      -       +      +
    120B  ILE*     3.6    38.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 63 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61B  ILE*     3.9     6.2    -      -       -      +
     62B  ALA*     1.3    84.2    -      -       -      +
     64B  MET*     1.3    64.9    +      -       -      +
     65B  GLU*     4.1    20.0    -      -       +      +
     78B  PHE*     4.3    11.4    -      -       +      -
     79B  ILE*     3.5     5.0    -      -       -      -
     80B  LEU*     3.1    57.9    +      -       +      -
    120B  ILE*     3.7    16.6    -      -       +      -
    121B  ILE*     5.4     0.4    -      -       -      -
    122B  GLY*     3.6    32.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 64 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  GLY*     3.7    17.7    -      -       -      -
     18B  CYS*     3.7     9.0    -      -       -      +
     19B  VAL*     4.3    14.8    -      -       +      +
     32B  LEU*     3.2    34.1    -      -       -      +
     34B  ALA*     3.3    26.9    -      -       +      +
     39B  LEU*     3.6    27.1    -      -       -      -
     61B  ILE*     4.1    10.3    -      -       +      -
     63B  VAL*     1.3    77.4    -      -       -      +
     65B  GLU*     1.3    73.2    +      -       -      +
     77B  LEU*     3.8    18.2    -      -       +      -
     78B  PHE      3.4     4.0    -      -       -      -
     79B  ILE*     4.2     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 65 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  VAL*     4.5     9.1    -      -       -      +
     63B  VAL*     4.1    19.1    -      -       +      +
     64B  MET*     1.3    85.0    +      -       -      +
     66B  LEU*     1.3    61.9    +      -       -      +
     67B  PHE*     4.1     0.4    +      -       -      -
     76B  LEU      3.8     0.3    -      -       -      +
     77B  LEU*     3.2     8.9    -      -       -      +
     78B  PHE*     2.9    39.3    +      -       +      +
    122B  GLY      3.9    18.3    -      -       -      +
    123B  ILE*     5.4     3.3    -      -       -      +
    124B  ILE*     3.7    29.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 66 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  VAL*     4.2    24.7    -      -       +      +
     20B  THR      3.4    34.1    -      -       -      +
     21B  GLY*     3.7    14.6    -      -       -      +
     22B  HIS      4.5     0.9    -      -       -      +
     23B  PHE*     3.4    37.0    -      -       +      -
     30B  ASN*     5.6     0.2    -      -       +      -
     32B  LEU*     4.2    11.4    -      -       +      -
     65B  GLU*     1.3    77.2    +      -       -      +
     67B  PHE*     1.3    61.2    +      -       -      +
     75B  ASP*     3.9    20.7    -      -       +      +
     76B  LEU      3.4    13.9    -      -       -      +
     77B  LEU*     4.2     6.7    -      -       +      -
    124B  ILE*     5.0     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 67 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66B  LEU*     1.3    77.3    -      -       -      +
     68B  ARG*     1.3    62.7    +      -       -      +
     69B  PRO*     4.2    14.8    -      -       +      +
     75B  ASP*     3.6     4.2    +      -       -      -
     76B  LEU*     2.9    52.1    +      -       +      +
     77B  LEU      4.2     1.8    -      -       -      -
     78B  PHE*     3.7    27.4    -      +       +      -
     88B  ILE*     3.8    35.0    -      -       +      -
    124B  ILE*     3.6    39.5    -      -       +      -
    128B  CYS*     4.0    15.5    -      -       -      -
    131B  ILE*     4.8     1.3    -      -       +      -
    145B  LEU*     3.6    26.9    -      -       +      -
----------------------------------------------------------
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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