Contacts of the strand formed by residues 13 - 18 (chain B) in PDB entry 2E7A


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 VAL 13 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  SER*     4.9     1.1    -      -       -      +
     11B  MET      3.6    11.2    -      -       -      +
     12B  PRO*     1.3    75.1    -      -       -      +
     14B  ALA*     1.3    70.7    +      -       -      +
     36B  LEU*     4.1    20.2    -      -       +      -
     37B  LEU*     3.5     0.5    -      -       -      -
     38B  ALA*     2.9    42.3    +      -       +      +
     39B  ASN*     4.2     8.7    -      -       -      +
     41B  VAL*     3.4     7.7    -      -       -      +
    154B  ILE      3.3    13.9    -      -       -      +
    155B  ILE*     4.0    18.6    -      -       +      -
     55C  LEU*     3.9    19.5    -      -       +      -
    123C  VAL*     4.0    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 14 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  VAL*     1.3    80.7    -      -       -      +
     15B  HIS*     1.3    61.5    +      -       -      +
     16B  VAL*     4.7     1.1    -      -       +      -
     36B  LEU*     3.1    14.8    -      -       -      +
     37B  LEU*     3.8     8.5    -      -       +      -
     41B  VAL*     3.7    23.3    -      -       +      -
     48B  LEU*     4.0    15.0    -      -       +      -
     59B  TYR*     4.0     2.4    +      -       -      -
    153B  GLY*     3.0     3.4    -      -       -      -
    154B  ILE*     2.8    39.1    +      -       +      +
    123C  VAL*     5.4     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 15 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  ALA*     1.3    74.7    -      -       -      +
     16B  VAL*     1.3    60.6    +      -       -      +
     17B  VAL*     4.2    11.8    -      -       +      +
     34B  ASN      3.6    19.7    -      -       -      -
     35B  ALA*     3.2    11.2    -      -       -      +
     36B  LEU*     2.7    38.6    +      -       +      +
     59B  TYR*     2.6    26.5    +      +       -      +
    151B  TYR*     3.7    42.7    -      +       +      +
    152B  PHE      3.5     4.0    +      -       -      -
     93C  LEU      4.9     2.2    +      -       -      -
    122C  GLY*     4.4     0.9    -      -       -      -
    123C  VAL*     3.7    18.6    +      -       +      +
    124C  PHE*     3.6    28.3    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 16 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  ALA*     4.7     0.9    -      -       +      -
     15B  HIS*     1.3    77.0    -      -       -      +
     17B  VAL*     1.3    66.3    +      -       -      +
     28B  TRP*     3.6    23.9    -      -       +      -
     29B  LEU      3.3    19.5    -      -       -      +
     30B  ASN*     4.0    19.1    -      -       +      -
     36B  LEU      4.0     6.1    -      -       -      +
     37B  LEU*     4.8     2.5    -      -       +      -
     43B  LEU*     4.6     7.6    -      -       +      -
     48B  LEU*     4.3    21.8    -      -       +      -
    151B  TYR*     3.3     4.5    -      -       -      +
    152B  PHE*     2.7    60.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 17 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  HIS*     4.2    23.3    -      -       +      +
     16B  VAL*     1.3    79.3    -      -       -      +
     18B  ALA*     1.3    73.1    +      -       -      +
     28B  TRP*     3.5     6.8    -      -       -      -
     29B  LEU*     2.8    40.3    +      -       +      +
     32B  ARG*     4.0    28.5    -      -       +      +
     34B  ASN      5.1     2.2    -      -       -      +
     35B  ALA*     4.6     7.6    -      -       +      -
    148B  GLY*     6.1     5.4    -      -       -      +
    150B  VAL      3.5    12.8    -      -       -      +
    151B  TYR*     4.4     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 18 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  VAL*     1.3    84.6    -      -       -      +
     19B  ASN*     1.3    59.7    +      -       -      +
     20B  PRO*     3.0    14.6    -      -       -      +
     26B  LEU*     4.1     8.7    -      -       +      -
     27B  GLN      3.7     6.3    -      -       -      +
     28B  TRP*     3.8     5.8    -      -       -      -
    144B  PHE*     3.9    28.4    -      -       +      +
    150B  VAL*     3.3    38.7    +      -       +      +
----------------------------------------------------------
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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