Contacts of the strand formed by residues 191 - 196 (chain A) in PDB entry 6GL7


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 ALA 191 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  LEU*     3.5    24.0    -      -       +      +
    128A  ARG*     2.9    44.2    +      -       -      +
    129A  TYR*     3.8     9.2    -      -       -      -
    130A  CYS      4.1     0.4    -      -       -      +
    167A  PRO*     3.9    24.0    -      -       +      -
    169A  ALA      3.7     5.2    -      -       -      -
    170A  TYR*     3.7     6.3    -      -       -      -
    190A  SER*     1.3    71.3    +      -       -      +
    192A  ARG*     1.3    60.1    +      -       -      +
    193A  GLU      4.3     0.2    -      -       -      +
    141B  TYR*     4.0     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 192 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  LEU*     3.3    16.0    -      -       -      +
    128A  ARG*     5.3     9.3    +      -       -      +
    169A  ALA*     2.7    37.1    +      -       -      +
    170A  TYR      3.3    30.7    +      -       -      +
    171A  GLU*     3.9     6.5    -      -       +      +
    172A  ASP*     3.7    21.2    +      -       -      +
    190A  SER      3.4     1.2    +      -       -      -
    191A  ALA*     1.3    74.4    -      -       -      +
    193A  GLU*     1.3    70.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  LEU*     4.1     7.2    -      -       -      +
    167A  PRO*     3.1    12.1    -      -       -      +
    168A  THR*     2.9    44.2    +      -       -      +
    169A  ALA*     3.2    24.9    +      -       +      +
    192A  ARG*     1.3    93.3    +      -       +      +
    194A  CYS*     1.3    59.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  CYS*     3.3    19.8    -      -       -      +
    104A  GLY*     3.4    24.9    -      -       -      -
    105A  LEU*     3.6    23.6    -      -       +      +
    130A  CYS*     2.0    46.0    -      -       -      -
    166A  ARG      4.0     0.4    -      -       -      -
    168A  THR*     4.6     1.6    -      -       -      -
    193A  GLU*     1.3    76.5    -      -       -      +
    195A  ALA*     1.3    63.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  CYS*     4.1     8.1    -      -       -      -
    164A  CYS      3.6     0.3    -      -       -      +
    166A  ARG      2.5    36.1    +      -       -      +
    168A  THR*     3.8    20.1    -      -       +      +
    194A  CYS*     1.3    77.3    -      -       -      +
    196A  CYS*     1.3    66.5    +      -       -      +
    197A  VAL*     3.8     6.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  CYS*     3.4    25.3    -      -       -      -
    134A  CYS*     2.0    59.9    -      -       +      -
    135A  GLU      4.8     1.1    -      -       -      +
    136A  ALA*     5.3     9.7    -      -       +      +
    163A  PRO*     3.9     7.7    -      -       +      +
    164A  CYS      3.2     4.0    -      -       -      -
    165A  CYS*     3.6     2.7    -      -       -      -
    195A  ALA*     1.3    75.7    -      -       -      +
    197A  VAL*     1.3    62.7    +      -       -      +
----------------------------------------------------------
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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