Contacts of the strand formed by residues 696 - 702 (chain H) 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 696 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    684H  GLY      3.9     1.1    -      -       -      -
    685H  TYR*     3.1     4.3    -      -       -      +
    686H  PHE*     2.7    71.6    +      -       +      +
    694H  PRO*     4.0     2.1    -      -       -      +
    695H  THR*     1.3    85.3    -      -       +      +
    697H  SER*     1.3    67.1    +      -       -      +
    699H  ILE*     4.3    12.8    -      -       +      -
    718H  GLY*     4.3    14.1    -      -       -      +
    721H  SER      4.2     5.2    -      -       -      +
    722H  LEU*     3.4    42.0    -      -       +      +
    725H  ALA*     4.4     0.2    -      -       +      -
    730H  MET*     4.5     1.3    -      -       -      -
    902H  MET*     5.6     2.2    -      -       -      -
    905H  GLY*     3.4    28.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 697 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    684H  GLY      3.3     0.4    +      -       -      -
    685H  TYR*     3.4    17.7    -      -       -      -
    694H  PRO*     3.7    26.3    +      -       -      +
    695H  THR      4.2     0.8    +      -       -      -
    696H  LEU*     1.3    79.5    +      -       -      +
    698H  ASN*     1.3    74.1    +      -       -      +
    699H  ILE*     3.5     1.5    -      -       -      +
    905H  GLY      3.9     5.9    +      -       -      -
    906H  THR*     4.0    20.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 698 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    683H  GLY*     3.8    21.4    -      -       -      -
    684H  GLY      2.6    11.3    +      -       -      -
    685H  TYR*     3.4    24.5    +      -       +      +
    697H  SER*     1.3    75.9    -      -       -      +
    699H  ILE*     1.3    57.0    +      -       -      +
    700H  THR*     4.3     7.1    +      -       -      -
    906H  THR*     4.4     6.3    -      -       +      +
    907H  ILE*     4.2    10.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 699 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    681H  ILE*     3.6    20.9    -      -       +      +
    683H  GLY      3.2     5.2    +      -       -      -
    684H  GLY*     2.5    41.0    +      -       -      +
    686H  PHE*     3.5    27.8    -      -       +      -
    696H  LEU*     4.3    14.4    -      -       +      -
    697H  SER      4.2     6.5    -      -       -      +
    698H  ASN*     1.3    80.6    -      -       -      +
    700H  THR*     1.3    59.4    +      -       -      +
    701H  ILE*     3.8     6.3    -      -       +      -
    722H  LEU*     3.6    23.3    -      -       +      -
    902H  MET*     6.3     0.9    -      -       +      -
    905H  GLY      4.3    12.3    -      -       -      +
    906H  THR*     4.4     0.4    -      -       -      -
    907H  ILE*     4.1    33.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 700 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    681H  ILE      3.2    11.4    -      -       -      +
    682H  MET*     4.9     5.2    -      -       +      -
    683H  GLY*     3.5    13.0    +      -       -      -
    698H  ASN*     4.3     6.8    +      -       -      -
    699H  ILE*     1.3    76.1    +      -       -      +
    701H  ILE*     1.3    74.2    +      -       -      +
    702H  ARG*     6.3     0.4    -      -       +      +
    907H  ILE*     4.1    19.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 701 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    679H  VAL*     4.4     2.9    -      -       +      +
    680H  GLN*     2.9    21.1    -      -       -      +
    681H  ILE*     3.0    43.0    +      -       +      +
    699H  ILE*     3.8    13.2    -      -       +      -
    700H  THR*     1.3    90.1    -      -       -      +
    702H  ARG*     1.3    70.4    +      -       -      +
    703H  ILE*     3.6    24.7    -      -       +      -
    722H  LEU*     3.5    29.2    -      -       +      -
    900H  ILE*     4.8    15.3    -      -       +      -
    907H  ILE*     3.9    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 702 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    677H  CYS*     3.3    34.9    -      -       -      +
    678H  CYS      4.2     2.7    -      -       -      -
    679H  VAL      4.0     4.3    -      -       -      -
    680H  GLN*     2.5    30.3    +      -       -      +
    682H  MET*     5.8     4.6    -      -       -      +
    700H  THR*     6.3     0.6    -      -       +      +
    701H  ILE*     1.3    79.0    +      -       -      +
    703H  ILE*     1.3    70.4    +      -       -      +
    704H  PRO*     4.2     5.8    -      -       +      +
    898H  TRP*     3.2    37.3    +      -       +      +
    900H  ILE*     4.9     1.7    -      -       -      +
----------------------------------------------------------
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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