Contacts of the strand formed by residues 708 - 713 (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 LEU 708 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    707G  GLN*     1.3    70.7    -      -       -      +
    709G  THR*     1.3    63.3    +      -       -      +
    710G  MET*     4.9     3.1    -      -       +      -
    868G  MET*     4.4    11.9    -      -       +      -
    872G  ILE*     3.5    25.4    -      -       +      -
    876G  LEU*     3.6    30.7    -      -       +      +
    883G  VAL*     3.5    30.5    -      -       +      +
    885G  LEU*     3.8    25.4    -      -       +      -
    895G  HIS      3.8    19.1    -      -       -      +
    896G  ALA*     3.8     4.6    -      -       -      -
    897G  ASP*     2.7    47.9    +      -       -      +
    898G  TRP      4.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 709 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    703G  ILE*     4.0    20.9    -      -       +      -
    707G  GLN      3.7     1.7    +      -       -      -
    708G  LEU*     1.3    76.6    -      -       -      +
    710G  MET*     1.3    69.7    +      -       -      +
    711G  ILE*     4.5     0.2    -      -       +      -
    883G  VAL      3.6     4.0    +      -       -      -
    884G  VAL*     3.6    36.7    -      -       +      -
    885G  LEU*     3.3    22.2    +      -       -      +
    898G  TRP*     2.8    38.0    +      -       -      -
    900G  ILE*     3.1    20.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 710 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    708G  LEU*     4.9     6.1    -      -       +      -
    709G  THR*     1.3    81.3    +      -       -      +
    711G  ILE*     1.3    63.7    +      -       -      +
    712G  VAL*     4.2     6.7    -      -       +      -
    856G  PHE*     6.3     0.9    -      -       +      -
    868G  MET*     3.9    16.2    -      -       +      -
    885G  LEU*     3.5    26.5    -      -       +      +
    887G  THR*     4.2    12.1    -      -       +      -
    892G  TYR*     3.2    37.9    -      -       +      +
    893G  LEU*     3.6    32.3    -      -       +      -
    896G  ALA*     3.6    24.0    -      -       +      +
    898G  TRP      3.0     5.0    +      -       -      +
    899G  ILE*     3.4     3.9    -      -       +      +
    900G  ILE      2.7    32.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 711 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    703G  ILE*     6.2     0.7    -      -       +      -
    709G  THR*     4.5     0.4    -      -       +      -
    710G  MET*     1.3    81.3    -      -       -      +
    712G  VAL*     1.3    67.6    +      -       -      +
    719G  LYS*     3.9    24.4    -      -       +      +
    722G  LEU*     6.0     1.8    -      -       +      -
    723G  LEU*     4.4    14.6    -      -       +      -
    884G  VAL*     3.7    23.8    -      -       +      -
    885G  LEU      3.2    17.7    +      -       -      +
    886G  VAL*     3.2    34.5    -      -       +      +
    887G  THR      3.8     1.6    +      -       -      -
    900G  ILE*     3.2    31.9    -      -       +      +
    902G  MET*     3.6    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 712 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    710G  MET*     4.8     4.0    -      -       +      -
    711G  ILE*     1.3    81.5    -      -       -      +
    713G  GLY*     1.3    61.6    +      -       -      +
    719G  LYS*     3.6    11.0    -      -       -      +
    887G  THR*     3.6    24.7    -      -       +      +
    890G  LEU*     3.6    32.8    -      -       +      -
    893G  LEU*     4.5     7.2    -      -       +      -
    899G  ILE*     4.8    10.1    -      -       +      -
    900G  ILE      3.1    10.7    +      -       -      +
    901G  ALA*     3.8    11.3    -      -       +      -
    902G  MET*     3.3    27.4    +      -       -      +
    926G  HIS*     4.8    14.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 713 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    712G  VAL*     1.3    80.8    -      -       -      +
    714G  GLN*     1.3    71.0    +      -       -      +
    717G  CYS*     3.9     3.4    -      -       -      -
    719G  LYS*     3.0    13.3    +      -       -      +
    901G  ALA*     6.3     0.2    -      -       -      -
    902G  MET      3.2    15.5    -      -       -      -
    903G  LYS*     5.6     0.2    -      -       -      -
   1512G  ASP*     3.4    14.2    -      -       -      +
----------------------------------------------------------
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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