Contacts of the strand formed by residues 653 - 658 (chain C) in PDB entry 6CIM


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 LYS 653 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    566C  ALA*     3.9    21.0    +      -       +      +
    569C  ASP*     3.6    19.4    +      -       -      -
    570C  MET*     5.6     5.1    -      -       -      +
    623C  SER*     3.3     1.1    -      -       -      -
    624C  PHE*     2.7    58.1    +      -       +      +
    625C  THR*     5.7     0.4    -      -       -      -
    626C  VAL*     5.9     2.2    -      -       +      +
    651C  CYS*     3.1    11.8    +      -       -      +
    652C  CYS*     1.3    70.0    -      -       -      +
    654C  PRO*     1.3    68.8    -      -       -      +
    655C  LEU      3.6     0.3    +      -       -      -
    992C  TRP*     3.3    43.1    -      -       +      +
    995C  THR*     3.2    40.9    +      -       -      +
    996C  SER*     4.2     4.9    -      -       -      +
    997C  LYS*     4.4     4.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 654 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    557C  PHE*     3.5     9.9    -      -       -      -
    621C  ARG*     5.1     1.3    -      -       +      -
    622C  PHE      4.2     0.7    -      -       -      +
    623C  SER*     4.0    10.1    -      -       -      -
    624C  PHE*     5.6     0.2    -      -       -      -
    652C  CYS      3.3     7.4    -      -       -      +
    653C  LYS*     1.3    82.6    -      -       -      +
    655C  LEU*     1.3    60.0    +      -       -      +
    657C  LEU*     4.9     9.9    -      -       +      -
    988C  LEU*     4.1    15.0    -      -       +      -
    991C  HIS*     3.8    25.1    -      -       +      +
    992C  TRP*     3.3    48.2    -      -       +      +
    995C  THR*     3.8    19.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 655 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    556C  ARG*     3.4     1.6    -      -       -      +
    557C  PHE*     2.9    44.9    +      -       +      +
    559C  TYR*     3.5    51.6    -      -       +      +
    562C  ALA*     3.8    28.7    -      -       +      -
    622C  PHE*     2.8    34.6    +      -       +      +
    623C  SER*     4.2     3.6    -      -       -      -
    624C  PHE*     3.7    15.0    -      -       +      -
    653C  LYS      3.6     0.6    +      -       -      -
    654C  PRO*     1.3    73.9    -      -       -      +
    656C  CYS*     1.3    58.5    +      -       -      +
    675C  LEU*     4.0    11.4    -      -       +      -
    988C  LEU*     4.6     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 656 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    537C  GLY*     5.3     0.4    -      -       -      -
    554C  ALA*     4.8     2.0    -      -       -      -
    555C  LYS      3.5    12.8    -      -       -      -
    556C  ARG*     3.6    11.4    -      -       +      -
    620C  VAL      4.0     0.7    -      -       -      +
    621C  ARG*     3.6     0.9    -      -       -      -
    622C  PHE*     2.9    33.3    +      -       +      +
    654C  PRO      3.9     0.4    -      -       -      -
    655C  LEU*     1.3    80.1    -      -       -      +
    657C  LEU*     1.3    73.3    +      -       -      +
    658C  MET*     3.8    28.0    -      -       -      -
    671C  ILE*     4.0    14.8    -      -       -      -
    672C  LEU*     4.7     0.2    -      -       -      -
    675C  LEU*     3.6    25.6    -      -       +      -
    988C  LEU*     4.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 657 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    554C  ALA*     3.2     2.6    -      -       -      +
    555C  LYS*     2.9    35.0    +      -       +      +
    602C  MET*     4.4     9.6    -      -       +      -
    620C  VAL      3.7     2.0    -      -       -      +
    621C  ARG*     3.3    40.4    -      -       +      -
    654C  PRO*     4.9     5.2    -      -       +      -
    656C  CYS*     1.3    77.7    -      -       -      +
    658C  MET*     1.3    60.4    +      -       -      +
    968C  PHE*     3.9     9.6    -      -       +      -
    984C  MET*     3.4    17.6    -      -       +      +
    987C  VAL*     3.7    29.2    -      -       +      -
    988C  LEU*     4.1    29.8    -      -       +      +
    991C  HIS*     4.5    14.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 658 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    552C  THR*     4.6     0.4    -      -       -      +
    553C  ILE      3.8     1.3    -      -       -      -
    554C  ALA*     3.4    20.4    -      -       +      -
    619C  ALA*     3.0     9.0    -      -       -      +
    620C  VAL*     2.9    68.2    +      -       +      +
    622C  PHE*     5.5     1.3    -      -       +      -
    656C  CYS*     3.8    15.3    -      -       -      +
    657C  LEU*     1.3    74.9    -      -       -      +
    659C  LEU*     1.3    62.8    +      -       -      +
    660C  ALA*     4.1    11.2    -      -       +      -
    668C  LEU*     4.4    11.2    -      -       +      -
    671C  ILE*     3.5    43.1    -      -       +      -
    672C  LEU*     4.0    20.9    -      -       +      -
    968C  PHE*     5.5     0.2    -      -       -      -
    984C  MET*     4.2     2.2    -      -       -      +
----------------------------------------------------------
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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