Contacts of the strand formed by residues 506 - 514 (chain A) in PDB entry 2W7P


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 LEU 506 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    422A  PHE*     3.7     9.2    -      -       +      -
    424A  GLU*     3.4     9.9    -      -       -      -
    425A  ILE*     3.2    32.7    +      -       +      +
    431A  GLN*     3.2    13.2    -      -       +      +
    460A  LEU*     3.4    38.1    -      -       +      -
    461A  LYS      3.7     7.2    -      -       -      +
    462A  ASN*     4.8     0.7    -      -       -      +
    463A  VAL*     3.9     2.0    -      -       -      +
    492A  LEU*     5.3     0.2    -      -       +      -
    504A  LEU*     2.9    56.5    +      -       +      +
    505A  ARG*     1.3    73.5    -      -       -      +
    507A  ARG*     1.3    61.3    +      -       -      +
    508A  LEU      3.9    14.1    -      -       -      +
    509A  MET*     3.6    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 507 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    421A  THR*     2.8    44.4    -      -       +      +
    422A  PHE*     3.1    30.4    +      -       -      +
    424A  GLU*     5.3     1.3    -      -       -      +
    461A  LYS*     2.8    19.7    +      -       +      +
    462A  ASN      3.4    17.0    -      -       -      +
    463A  VAL*     3.9    23.8    -      -       +      +
    465A  PHE*     2.8    41.6    -      -       -      -
    506A  LEU*     1.3    73.2    -      -       -      +
    508A  LEU*     1.3    60.5    +      -       +      +
      4T    C      3.2    34.6    +      -       -      -
      5T  8OG      3.0    24.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 508 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    419A  GLU*     3.6    21.8    -      -       -      +
    420A  ARG      2.9    43.1    -      -       -      +
    421A  THR*     3.8    13.0    -      -       +      +
    422A  PHE*     3.7     6.3    -      -       -      -
    459A  LYS*     3.9    20.6    -      -       +      +
    460A  LEU*     3.8     2.3    -      -       -      -
    461A  LYS*     3.0    62.0    +      -       +      +
    506A  LEU*     3.9     5.9    -      -       -      +
    507A  ARG*     1.3    83.0    -      -       -      +
    509A  MET*     1.3    85.6    +      -       -      +
      6T    G      4.5     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 509 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    419A  GLU*     3.5     1.0    -      -       -      -
    420A  ARG      3.3    16.0    +      -       -      +
    422A  PHE*     4.2    11.4    -      -       +      -
    431A  GLN*     4.0    19.5    -      -       +      +
    434A  LEU*     4.9     7.2    -      -       +      -
    435A  CYS*     4.0    29.6    -      -       -      -
    438A  LEU*     3.8    21.5    -      -       +      +
    458A  ILE*     5.1     3.6    -      -       +      -
    459A  LYS      3.0     7.2    -      -       -      -
    460A  LEU*     3.6    16.8    -      -       +      -
    492A  LEU*     3.8    20.6    -      -       +      -
    506A  LEU*     3.6    24.7    -      -       +      -
    508A  LEU*     1.3    93.6    -      -       -      +
    510A  GLY*     1.3    65.4    +      -       -      +
    511A  VAL*     5.4     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 510 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    418A  VAL      3.7    10.5    -      -       -      -
    419A  GLU*     3.8     8.5    -      -       -      -
    438A  LEU*     4.2     3.1    -      -       -      -
    457A  THR      4.4     0.2    -      -       -      -
    458A  ILE*     3.1     8.3    -      -       -      +
    459A  LYS*     2.6    45.6    +      -       -      -
    509A  MET*     1.3    80.0    -      -       -      +
    511A  VAL*     1.3    67.3    +      -       -      +
    512A  ARG      4.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 511 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    417A  SER*     4.2     2.0    -      -       -      -
    418A  VAL      3.3    26.4    +      -       -      +
    435A  CYS*     4.9     7.6    -      -       -      -
    438A  LEU*     4.0    27.1    -      -       +      -
    439A  CYS*     4.2    15.0    -      -       -      +
    442A  LEU*     3.4    31.9    -      -       +      +
    456A  VAL*     4.3    18.2    -      -       +      -
    457A  THR      3.2     7.9    -      -       -      +
    458A  ILE*     5.0     4.7    -      -       +      -
    484A  ILE*     4.4    12.1    -      -       +      -
    488A  ALA*     4.6     6.1    -      -       +      -
    509A  MET*     5.4     1.6    -      -       +      -
    510A  GLY*     1.3    80.8    -      -       -      +
    512A  ARG*     1.3    62.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 512 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    415A  SER*     3.6    24.2    +      -       -      -
    416A  MET      3.6     8.5    -      -       -      +
    417A  SER*     3.1    36.3    +      -       -      +
    442A  LEU*     4.5     1.3    -      -       -      -
    456A  VAL*     3.7     1.1    -      -       -      -
    457A  THR*     2.6    63.7    +      -       -      +
    459A  LYS*     5.9     7.7    -      -       -      +
    469A  THR*     5.9     4.9    -      -       -      +
    510A  GLY      4.3     0.2    -      -       -      -
    511A  VAL*     1.3    74.7    -      -       -      +
    513A  ILE*     1.3    60.1    +      -       -      +
    514A  SER*     4.5     9.6    +      -       -      -
      8T    A      4.7     4.9    +      -       -      -
      9T    T      3.4    31.5    +      -       -      +
     10T    C      5.8     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 513 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    416A  MET*     2.8    41.7    +      -       +      +
    442A  LEU*     4.1    15.7    -      -       +      +
    446A  LEU*     3.3    33.0    -      -       +      -
    453A  GLY      4.6    17.5    -      -       -      +
    455A  THR      3.3    17.9    -      -       -      +
    456A  VAL*     3.2    31.0    -      -       +      -
    478A  VAL*     5.3     7.9    -      -       +      +
    484A  ILE*     4.8     9.2    -      -       +      -
    512A  ARG*     1.3    72.3    -      -       -      +
    514A  SER*     1.3    68.3    +      -       -      +
    516A  PHE*     3.3    14.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 514 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    414A  LYS      4.1     3.4    -      -       -      -
    415A  SER*     4.1    17.9    -      -       -      -
    453A  GLY*     3.3     5.4    -      -       -      -
    454A  ARG      3.2     9.9    +      -       -      -
    455A  THR*     3.1    24.9    +      -       -      +
    457A  THR*     4.0    11.6    +      -       -      -
    512A  ARG*     4.5     5.6    +      -       -      -
    513A  ILE*     1.3    76.1    -      -       -      +
    515A  SER*     1.3    79.0    +      -       -      +
    516A  PHE*     3.2    12.3    -      -       -      -
----------------------------------------------------------
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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