Contacts of the strand formed by residues 708 - 713 (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 708 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    707H  GLN*     1.3    69.4    -      -       -      +
    709H  THR*     1.3    62.9    +      -       -      +
    710H  MET*     4.9     3.6    -      -       +      -
    868H  MET*     4.4    11.9    -      -       +      -
    872H  ILE*     3.5    25.8    -      -       +      -
    876H  LEU*     3.6    30.1    -      -       +      +
    883H  VAL*     3.5    30.1    -      -       +      +
    885H  LEU*     3.8    26.7    -      -       +      -
    895H  HIS*     3.8    19.1    -      -       +      +
    896H  ALA*     3.8     5.7    -      -       -      -
    897H  ASP*     2.7    47.4    +      -       -      +
    898H  TRP      3.2     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 709 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    703H  ILE*     4.0    20.9    -      -       +      -
    707H  GLN*     3.7     1.4    +      -       -      -
    708H  LEU*     1.3    76.4    -      -       -      +
    710H  MET*     1.3    70.5    +      -       -      +
    711H  ILE*     4.5     0.4    -      -       +      -
    883H  VAL      3.6     3.4    +      -       -      -
    884H  VAL*     3.6    37.1    -      -       +      -
    885H  LEU*     3.3    22.3    +      -       -      +
    898H  TRP*     2.8    38.0    +      -       -      -
    900H  ILE*     3.1    20.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 710 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    708H  LEU*     4.9     5.6    -      -       +      -
    709H  THR*     1.3    79.8    +      -       -      +
    711H  ILE*     1.3    63.0    +      -       -      +
    712H  VAL*     4.2     8.3    -      -       +      -
    856H  PHE*     6.3     0.7    -      -       +      -
    868H  MET*     3.9    16.6    -      -       +      -
    885H  LEU*     3.5    27.1    -      -       +      +
    887H  THR*     4.2    11.7    -      -       +      -
    892H  TYR*     3.2    37.7    -      -       +      +
    893H  LEU*     3.6    31.6    -      -       +      -
    896H  ALA*     3.6    24.2    -      -       +      +
    898H  TRP      3.0     5.6    +      -       -      +
    899H  ILE*     3.4     4.4    -      -       +      +
    900H  ILE      2.7    31.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 711 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    703H  ILE*     6.2     0.4    -      -       +      -
    709H  THR*     4.5     0.2    -      -       +      -
    710H  MET*     1.3    81.3    -      -       -      +
    712H  VAL*     1.3    67.3    +      -       -      +
    719H  LYS*     3.9    23.9    -      -       +      +
    722H  LEU*     6.0     1.6    -      -       +      -
    723H  LEU*     4.4    13.2    -      -       +      -
    884H  VAL*     3.7    23.6    -      -       +      -
    885H  LEU      3.2    17.9    +      -       -      +
    886H  VAL*     3.2    35.5    -      -       +      +
    887H  THR      3.8     1.2    +      -       -      -
    900H  ILE*     3.2    33.0    -      -       +      +
    902H  MET*     3.6    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 712 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    710H  MET*     4.8     3.8    -      -       +      -
    711H  ILE*     1.3    81.8    -      -       -      +
    713H  GLY*     1.3    60.3    +      -       -      +
    719H  LYS*     3.6    11.4    -      -       -      +
    887H  THR*     3.6    26.0    -      -       +      +
    890H  LEU*     3.6    32.3    -      -       +      -
    893H  LEU*     4.5     7.0    -      -       +      -
    899H  ILE*     4.8     9.9    -      -       +      -
    900H  ILE      3.1    10.4    +      -       -      +
    901H  ALA*     3.8    10.5    -      -       +      -
    902H  MET*     3.3    27.0    +      -       -      +
    926H  HIS*     4.8    15.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 713 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    712H  VAL*     1.3    81.5    -      -       -      +
    714H  GLN*     1.3    72.0    +      -       -      +
    717H  CYS*     3.9     3.6    -      -       -      -
    719H  LYS*     3.0    11.8    +      -       -      +
    902H  MET      3.2    15.5    -      -       -      -
   1512H  ASP*     3.4    13.9    -      -       -      +
----------------------------------------------------------
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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