Contacts of the strand formed by residues 7 - 15 (chain B) in PDB entry 6QPA


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 7 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  ASN      4.9     2.9    -      -       -      +
      6B  PRO*     1.3    77.9    -      -       -      +
      8B  ILE*     1.3    61.9    +      -       -      +
     80B  THR      4.0     0.2    -      -       -      +
     81B  VAL*     3.5     2.4    -      -       -      +
     82B  TRP*     2.9    48.9    +      -       +      +
     83B  LYS      4.7     2.2    +      -       -      +
     84B  ASP*     3.6    35.7    -      -       -      +
     85B  VAL*     3.9     5.6    -      -       +      +
    118B  TYR*     3.5    37.2    -      -       +      -
    119B  PHE      3.6     8.5    -      -       -      +
    120B  GLU*     5.2     4.9    -      -       +      -
    202B  PHE*     4.1    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 8 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  PRO*     4.8     0.4    -      -       +      +
      7B  ILE*     1.3    78.8    -      -       -      +
      9B  ALA*     1.3    64.8    +      -       -      +
     10B  ILE*     3.8    23.8    -      -       +      -
     79B  TYR*     4.0    19.1    -      -       +      -
     80B  THR      3.5     6.7    -      -       -      +
     81B  VAL*     4.1    14.6    -      -       +      -
    118B  TYR*     3.5     1.9    -      -       -      -
    119B  PHE*     2.7    48.6    +      -       +      +
    121B  VAL*     3.8    17.0    -      -       +      -
    197B  MET*     3.8    37.0    -      -       +      -
    199B  MET*     4.1     5.4    -      -       -      -
    308B  TRP*     4.2    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 9 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  ILE*     4.2     1.2    +      -       -      +
      8B  ILE*     1.3    71.5    -      -       -      +
     10B  ILE*     1.3    61.1    +      -       -      +
     11B  ASN      3.9     0.4    -      -       -      -
     78B  GLN      3.4     2.6    -      -       -      +
     79B  TYR*     3.4     2.3    -      -       -      -
     80B  THR*     2.9    48.7    +      -       -      +
     82B  TRP*     4.4     2.8    -      -       +      +
     88B  HIS*     4.0    14.4    -      -       +      +
    116B  GLU*     3.8    22.4    -      -       +      +
    117B  PRO      3.3     7.0    -      -       -      +
    118B  TYR*     4.1    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 10 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  ILE*     3.8    14.1    -      -       +      -
      9B  ALA*     1.3    73.9    -      -       -      +
     11B  ASN*     1.3    61.6    +      -       -      +
     12B  MET*     3.3    20.2    +      -       +      +
     77B  PHE*     3.8    22.7    -      -       +      -
     78B  GLN      3.5     2.7    -      -       -      +
     79B  TYR*     3.7    30.1    -      -       +      -
    115B  TRP      3.3     0.7    -      -       -      +
    116B  GLU*     3.3     3.2    -      -       -      -
    117B  PRO*     3.0    33.0    +      -       -      +
    119B  PHE*     3.7    31.2    -      -       +      -
    199B  MET*     3.8    25.1    -      -       +      -
    254B  LEU*     3.8     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 11 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  ALA      3.9     0.4    -      -       -      -
     10B  ILE*     1.3    70.1    -      -       -      +
     12B  MET*     1.3    60.9    +      -       -      +
     13B  ALA*     4.5     5.0    -      -       -      +
     76B  MET      3.4     2.9    -      -       -      +
     77B  PHE*     3.4     4.3    -      -       -      -
     78B  GLN*     2.9    57.0    +      -       +      +
     92B  HIS*     6.0     1.6    -      -       -      -
    114B  PRO*     3.3    24.7    -      -       -      +
    115B  TRP      3.8     0.4    -      -       -      -
    116B  GLU*     3.7    25.3    +      -       -      +
    208B  GLY*     3.4    24.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 12 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  ILE*     3.7    24.9    -      -       +      +
     11B  ASN*     1.3    71.6    +      -       -      +
     13B  ALA*     1.3    60.1    +      -       -      +
     76B  MET      3.9     2.9    -      -       -      -
     77B  PHE*     3.8    33.0    -      -       +      -
    113B  GLY*     3.9     2.4    -      -       -      -
    114B  PRO*     3.2     4.9    -      -       -      +
    115B  TRP*     2.8    46.9    +      -       +      +
    117B  PRO*     4.1    16.4    -      -       +      -
    119B  PHE*     4.1    14.6    -      -       +      -
    252B  GLN*     4.7     8.1    -      -       -      +
    254B  LEU*     3.6    32.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 13 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  ASN*     4.5     6.5    -      -       -      +
     12B  MET*     1.3    75.0    -      -       -      +
     14B  LYS*     1.3    63.2    +      -       -      +
     15B  ILE*     4.2    14.8    -      -       +      -
     75B  GLY*     3.5     3.5    -      -       -      -
     76B  MET*     2.8    44.2    +      -       +      +
     77B  PHE*     4.6     3.6    -      -       -      -
    110B  VAL*     5.1     7.6    -      -       +      -
    112B  GLU      3.3    13.2    -      -       -      +
    113B  GLY      4.9     0.4    -      -       -      -
    114B  PRO*     4.4    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 14 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  ALA*     1.3    78.5    -      -       -      +
     15B  ILE*     1.3    61.8    +      -       -      +
     50B  GLN*     4.7     5.9    +      -       -      -
     73B  PRO*     3.7    30.4    +      -       +      +
     74B  MET      3.4     4.9    -      -       -      +
     75B  GLY*     4.4     6.5    -      -       -      +
     77B  PHE*     5.8     3.2    -      -       +      -
    110B  VAL*     3.8     0.9    -      -       -      -
    111B  ILE*     2.8    25.5    +      -       -      -
    112B  GLU*     2.8    48.2    +      -       +      +
    297B  MET*     4.5    20.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 15 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  ALA*     4.4    10.5    -      -       +      -
     14B  LYS*     1.3    80.0    -      -       -      +
     16B  ALA*     1.3    69.1    +      -       -      +
     21B  SER*     4.6     2.2    -      -       -      -
     25B  MET*     4.0    23.1    -      -       +      -
     49B  LEU*     4.2     7.9    -      -       +      -
     73B  PRO*     3.2     6.2    -      -       -      +
     74B  MET*     2.8    48.6    +      -       +      +
     76B  MET*     3.9    37.5    -      -       +      -
    109B  MET*     3.2    39.5    -      -       +      +
    110B  VAL*     4.6     7.0    -      -       +      -
    111B  ILE*     4.3     1.1    -      -       -      +
----------------------------------------------------------
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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