Contacts of the strand formed by residues 1373 - 1378 (chain G) in PDB entry 6C3P


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 LYS1373 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1371G  GLY      2.6     6.0    +      -       -      -
   1372G  GLN*     1.3    79.1    -      -       +      +
   1374G  ILE*     1.3    55.3    +      -       -      +
   1524G  MET*     3.4    43.3    -      -       +      -
   1532G  VAL*     3.7     8.3    -      -       +      +
   1534G  THR*     5.4     1.3    -      -       +      -
   1544G  SER      5.5     0.4    -      -       -      +
   1545G  ALA*     3.2     7.1    -      -       +      -
   1546G  ASP*     2.3    41.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1374 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1368G  ILE*     4.3    27.1    -      -       +      -
   1369G  ALA      6.2     0.2    -      -       -      +
   1371G  GLY*     3.6    18.1    +      -       -      +
   1373G  LYS*     1.3    80.0    -      -       -      +
   1375G  GLY*     1.3    63.3    +      -       -      +
   1531G  THR*     5.8     0.9    -      -       +      -
   1532G  VAL      3.4    11.3    +      -       -      +
   1533G  VAL*     3.7    33.9    -      -       +      -
   1534G  THR*     2.8    26.7    +      -       -      +
   1545G  ALA*     3.5     4.0    -      -       -      -
   1546G  ASP*     4.2     4.5    -      -       +      -
   1547G  LEU*     3.4    39.0    -      -       +      +
   1549G  ILE*     3.8    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY1375 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1374G  ILE*     1.3    71.4    -      -       -      +
   1376G  ILE*     1.3    58.9    +      -       -      -
   1534G  THR*     3.2    11.0    -      -       -      -
   1542G  ILE*     3.5    20.4    -      -       -      -
   1545G  ALA*     3.5     1.7    -      -       -      +
   1547G  LEU      2.3    23.8    +      -       -      +
   1548G  VAL      3.2     0.9    -      -       -      -
   1549G  ILE*     2.4    37.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1376 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1368G  ILE*     6.2     0.7    -      -       +      -
   1375G  GLY*     1.3    75.2    -      -       -      -
   1377G  CYS*     1.3    68.7    +      -       -      +
   1384G  LYS*     4.5     1.3    -      -       +      -
   1387G  PHE*     3.8    31.0    -      -       +      -
   1503G  ILE*     5.5     0.7    -      -       +      -
   1533G  VAL*     3.7    26.5    -      -       +      -
   1534G  THR      2.8    18.9    +      -       -      +
   1535G  ILE*     3.4    36.1    -      -       +      +
   1536G  ALA      3.5     2.8    +      -       -      -
   1542G  ILE*     3.8     1.7    -      -       -      +
   1549G  ILE*     3.2    46.0    -      -       +      +
   1551G  LEU*     4.1    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS1377 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1376G  ILE*     1.3    79.2    -      -       -      +
   1378G  GLY*     1.3    61.7    +      -       -      +
   1384G  LYS*     3.7    16.3    -      -       -      +
   1536G  ALA      4.1    16.6    -      -       -      +
   1539G  VAL*     4.8     8.7    -      -       +      -
   1542G  ILE*     3.7    20.6    -      -       +      -
   1548G  VAL*     4.2     1.3    -      -       -      -
   1549G  ILE      2.8    15.5    +      -       -      +
   1550G  VAL*     4.1    17.5    -      -       -      -
   1551G  LEU*     3.4    15.8    +      -       -      +
   1573G  PHE*     3.6    31.9    -      -       -      -
   1576G  PHE*     5.0     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY1378 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    860G  ASP*     4.5     6.2    -      -       -      +
   1377G  CYS*     1.3    81.9    -      -       -      +
   1379G  ARG*     1.3    67.2    +      -       -      -
   1384G  LYS*     3.3    11.7    +      -       -      +
   1536G  ALA      5.1     3.0    +      -       -      +
   1539G  VAL*     6.1     0.2    -      -       -      +
   1550G  VAL*     5.2     1.1    -      -       -      -
   1551G  LEU      4.1    12.3    -      -       -      -
   1576G  PHE*     4.3    18.8    -      -       -      -
----------------------------------------------------------
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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