Contacts of the strand formed by residues 4 - 8 (chain C) in PDB entry 4CQM


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 VAL 4 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3C  LYS*     1.3    75.0    -      -       -      +
      5C  CYS*     1.3    67.0    +      -       -      +
     28C  ARG*     3.3    27.8    -      -       +      +
     29C  LEU*     5.3     1.6    -      -       -      -
     30C  ALA*     6.1     0.7    -      -       +      -
     70C  LEU*     5.8     2.0    -      -       +      -
     74C  LEU*     3.6    44.4    -      -       +      +
     75C  GLY*     4.9     0.2    -      -       -      -
     76C  ARG      3.5    23.8    -      -       -      +
     77C  VAL*     4.8     8.5    -      -       +      -
     78C  ASN*     3.1    29.7    +      -       -      +
     79C  PHE*     3.1     7.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 5 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3C  LYS      3.8     0.2    +      -       -      -
      4C  VAL*     1.3    79.3    -      -       -      +
      6C  ALA*     1.3    73.5    +      -       -      +
      7C  VAL*     4.1     5.2    -      -       -      -
     22C  MET*     3.6    33.2    -      -       +      -
     27C  TYR*     4.5     4.0    -      -       +      -
     28C  ARG      2.5    17.7    +      -       -      +
     29C  LEU*     3.3    20.1    -      -       +      +
     30C  ALA*     3.2    18.2    +      -       -      +
     77C  VAL*     5.4     1.1    -      -       -      -
     79C  PHE*     3.3    29.2    -      -       +      -
     81C  VAL*     4.2     8.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 6 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  CYS*     1.3    74.9    -      -       -      +
      7C  VAL*     1.3    62.6    +      -       -      +
      8C  PHE*     4.0     6.7    -      -       +      -
     30C  ALA*     4.1     4.0    -      -       -      +
     32C  ILE*     4.7     3.8    -      -       +      -
     67C  PHE*     5.7     0.7    -      -       +      -
     70C  LEU*     4.4    27.6    -      -       +      -
     77C  VAL*     4.5    12.1    -      -       +      +
     79C  PHE      3.0     8.9    +      -       -      +
     80C  LEU*     3.5    20.8    -      -       +      +
     81C  VAL*     2.8    27.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 7 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  CYS*     4.1    14.6    -      -       -      -
      6C  ALA*     1.3    75.8    -      -       -      +
      8C  PHE*     1.3    65.0    +      -       -      +
     10C  GLY*     3.6    15.7    +      -       -      +
     15C  GLY*     3.4    32.3    -      -       -      +
     18C  VAL*     4.0    20.9    -      -       +      -
     19C  ALA*     4.7    11.0    -      -       +      +
     29C  LEU*     4.5    13.7    -      -       +      -
     30C  ALA      3.1    13.4    +      -       -      +
     31C  VAL*     4.0     1.1    -      -       -      -
     32C  ILE*     3.1    24.7    +      -       -      -
     81C  VAL*     3.6    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 8 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  ALA*     4.5     3.8    -      -       +      -
      7C  VAL*     1.3    71.6    -      -       -      +
      9C  GLY*     1.3    64.1    +      -       -      +
     32C  ILE*     3.5    43.1    -      -       +      -
     55C  CYS*     4.5    11.0    -      -       -      -
     57C  VAL*     3.6    21.3    -      -       +      -
     63C  VAL*     5.7     0.9    -      -       +      -
     66C  THR*     5.1     2.9    -      -       +      -
     67C  PHE*     3.4    34.1    -      +       -      -
     70C  LEU*     5.2     1.1    -      -       +      -
     80C  LEU*     3.5    32.3    -      -       +      -
     81C  VAL      2.8    13.4    +      -       -      +
     82C  ASN*     4.1    11.4    -      -       -      +
     83C  ALA*     2.9    28.2    +      -       -      +
     84C  ALA*     3.8    12.8    -      -       +      -
    114C  THR*     3.6    18.6    -      -       +      -
----------------------------------------------------------
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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