Contacts of the strand formed by residues 7002 - 7009 (chain C) in PDB entry 6W75


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 ALA7002 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   6968C  LYS*     3.4     4.5    -      -       -      +
   6969C  ILE*     2.8    39.8    +      -       +      +
   6990C  ALA*     4.4     4.5    -      -       +      -
   6991C  PHE      3.3    19.5    -      -       -      +
   6992C  VAL*     4.0     6.1    -      -       +      +
   7000C  SER      3.6     0.6    +      -       -      -
   7001C  GLU*     1.3    73.2    -      -       -      +
   7003C  PHE*     1.3    65.0    +      -       -      +
   7004C  LEU      4.0     0.4    -      -       -      -
   7026C  TYR*     3.2    36.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE7003 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   6844C  LYS*     4.1    26.9    -      -       +      -
   6845C  TYR*     5.4     6.7    -      +       -      -
   6848C  LEU*     3.9    46.9    -      -       +      -
   6926C  ILE*     5.5     2.7    -      -       +      -
   6927C  SER      4.1     8.3    -      -       -      -
   6928C  ASP*     4.2     9.4    -      -       +      -
   6966C  ALA*     4.4     9.0    -      -       +      -
   6967C  ILE      3.5     3.1    -      -       -      +
   6968C  LYS*     3.6    36.3    -      -       +      -
   6990C  ALA*     3.5     1.7    -      -       -      -
   6991C  PHE*     2.7    41.1    +      +       -      +
   6993C  THR*     4.2    12.6    -      -       +      -
   7001C  GLU*     4.1    18.2    -      -       -      -
   7002C  ALA*     1.3    75.8    -      -       -      +
   7004C  LEU*     1.3    62.2    -      -       -      +
   7005C  ILE*     3.3    12.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU7004 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   6965C  VAL*     3.8     3.3    -      -       -      +
   6966C  ALA*     3.4     2.3    +      -       -      -
   6967C  ILE*     2.8    46.2    +      -       +      +
   6969C  ILE*     3.6    43.1    -      -       +      -
   6975C  ASN      5.6     0.4    -      -       -      +
   6978C  LEU*     3.9    21.1    -      -       +      -
   6979C  TYR*     3.6    40.6    -      -       +      +
   6982C  MET*     4.2    15.7    -      -       +      -
   6988C  TRP*     4.2     6.5    -      -       +      -
   6989C  THR      3.5     3.4    -      -       -      +
   6990C  ALA*     3.9    21.8    -      -       +      -
   7002C  ALA      4.0     0.8    -      -       -      -
   7003C  PHE*     1.3    68.4    -      -       -      +
   7005C  ILE*     1.3    60.5    +      -       -      +
   7006C  GLY      4.0     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE7005 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   6848C  LEU*     4.0     9.9    -      -       +      -
   6851C  TYR*     3.7    21.8    -      -       +      -
   6852C  LEU*     3.9    17.5    -      -       +      -
   6855C  LEU*     3.8    23.8    -      -       +      -
   6857C  LEU*     6.1     0.4    -      -       +      -
   6964C  SER*     5.9     2.0    -      -       -      -
   6965C  VAL      3.2     9.4    -      -       -      +
   6966C  ALA*     4.1    14.6    -      -       +      -
   6982C  MET*     3.8     2.8    -      -       -      +
   6987C  TRP*     5.3     1.1    -      -       +      -
   6988C  TRP*     3.0     9.4    -      -       -      +
   6989C  THR*     2.8    42.3    +      -       +      +
   6991C  PHE*     3.7    28.3    -      -       +      -
   7003C  PHE*     3.6     9.4    -      -       +      +
   7004C  LEU*     1.3    74.3    -      -       -      +
   7006C  GLY*     1.3    66.6    +      -       -      +
   7007C  CYS*     4.7     3.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY7006 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   6964C  SER*     3.2     7.3    -      -       -      -
   6965C  VAL*     2.9    37.9    +      -       -      +
   6982C  MET*     3.8     8.2    -      -       -      -
   6985C  PHE*     3.2    32.4    -      -       -      -
   6987C  TRP      3.8     2.5    -      -       -      -
   6988C  TRP*     4.4     0.4    -      -       -      -
   7005C  ILE*     1.3    73.9    -      -       -      +
   7007C  CYS*     1.3    58.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS7007 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   6855C  LEU*     4.0    17.7    -      -       +      -
   6856C  THR*     3.7    30.3    -      -       -      -
   6857C  LEU*     4.2     4.0    -      -       -      -
   6964C  SER*     3.4     9.6    -      -       -      -
   6985C  PHE*     3.6     0.8    -      -       -      -
   6986C  ALA*     3.2    14.0    +      -       -      +
   6987C  TRP*     2.8    41.2    +      -       +      +
   7005C  ILE*     4.0     2.8    -      -       +      -
   7006C  GLY*     1.3    71.5    -      -       -      -
   7008C  ASN*     1.3    92.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN7008 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   6856C  THR*     2.8    42.7    +      -       -      -
   6858C  ALA      4.2     3.0    -      -       -      +
   6962C  GLY      3.1    19.1    +      -       -      +
   6963C  GLY      3.3     6.0    +      -       -      -
   6964C  SER*     3.1    14.8    +      -       -      -
   6985C  PHE*     3.7     1.5    -      -       -      -
   6986C  ALA*     2.9    31.7    +      -       +      +
   7007C  CYS*     1.3    76.1    -      -       -      +
   7009C  TYR*     1.3    65.6    +      -       -      +
   7010C  LEU*     3.6     4.8    +      -       -      +
   7073C  LEU      3.2    24.6    +      -       -      +
   7074C  SER      3.5     9.9    -      -       -      +
   7076C  GLY*     3.6    10.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR7009 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   6955C  ILE*     3.6    27.7    +      -       +      -
   6956C  GLN*     3.6    11.0    -      -       +      +
   6959C  LEU*     3.6    42.0    -      -       +      -
   6960C  ALA      3.7     9.6    -      -       -      +
   6961C  LEU*     3.4    17.5    -      -       +      +
   6962C  GLY*     2.8    26.4    +      -       -      +
   6963C  GLY      2.7    18.1    +      -       -      +
   6981C  LEU*     5.9     0.4    -      -       +      -
   6984C  HIS*     3.6    28.2    +      -       +      -
   6985C  PHE*     3.5    23.1    -      +       +      -
   7008C  ASN*     1.3    71.0    -      -       -      +
   7010C  LEU*     1.3    61.4    +      -       -      +
   7011C  GLY*     3.4    26.3    -      -       -      -
   7073C  LEU*     4.4     1.0    -      -       -      +
   7103C   NA      2.6    26.5    -      -       -      -
----------------------------------------------------------
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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