Contacts of the strand formed by residues 30 - 39 (chain A) in PDB entry 6GR2


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 30 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  PRO*     3.6     0.4    -      -       -      +
     29A  GLU*     1.3    92.2    -      -       +      +
     31A  ALA*     1.3    61.2    +      -       -      +
     64A  VAL*     3.2     6.2    -      -       -      +
     65A  GLY      2.8    29.5    +      -       -      +
     67A  PRO*     4.4    12.1    -      -       +      -
    152A  PHE*     3.6    21.8    -      -       +      -
    155A  GLN*     3.8    35.7    -      -       +      +
    156A  LEU*     3.8    29.6    -      -       +      -
    389A  VAL*     6.4     0.9    -      -       +      -
    390A  LEU      5.2     0.2    -      -       -      -
    392A  LEU*     3.7     4.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  LEU*     3.7    19.1    -      -       +      -
     30A  LEU*     1.3    78.2    -      -       -      +
     32A  VAL*     1.3    68.1    +      -       -      +
     63A  LEU      3.3     6.3    -      -       -      -
     64A  VAL*     4.2     2.7    -      -       +      -
    152A  PHE*     5.5     0.7    -      -       -      -
    155A  GLN*     5.2     1.0    -      -       -      +
    389A  VAL*     3.7     6.5    -      -       -      +
    390A  LEU*     2.9    51.1    +      -       +      +
    392A  LEU*     3.6    18.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  ALA*     1.3    79.6    -      -       -      +
     33A  SER*     1.3    64.0    +      -       -      +
     62A  VAL*     3.3     7.1    -      -       -      +
     63A  LEU*     2.8    45.1    +      -       +      +
    148A  ALA*     3.2    34.5    -      -       +      +
    151A  THR*     3.2    44.2    -      -       +      +
    152A  PHE*     3.9     9.0    -      -       +      +
    155A  GLN*     4.6     4.0    -      -       +      -
    388A  LYS      3.7     9.6    -      -       -      +
    389A  VAL*     4.1     6.3    -      -       +      -
    390A  LEU*     4.0     5.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  VAL*     5.1     1.1    -      -       -      +
     32A  VAL*     1.3    80.8    -      -       -      +
     34A  ALA*     1.3    62.7    +      -       -      +
     35A  PRO*     4.9     0.2    -      -       -      -
     60A  MET*     3.9    22.7    -      -       -      -
     61A  THR      3.3    10.8    -      -       -      -
     62A  VAL*     4.2     2.7    -      -       -      -
    151A  THR*     4.9     0.7    +      -       -      -
    386A  GLY      5.2     1.0    +      -       -      -
    387A  ALA*     3.2     4.0    -      -       -      +
    388A  LYS*     3.0    53.8    +      -       -      +
    390A  LEU*     3.8    17.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  SER*     1.3    77.0    -      -       -      +
     35A  PRO*     1.3    68.2    -      -       +      +
     60A  MET*     4.2     3.4    -      -       -      -
     61A  THR      2.9    20.4    +      -       -      +
    144A  SER*     2.8    27.0    +      -       -      +
    147A  VAL*     4.0     9.0    -      -       +      -
    148A  ALA*     3.4    31.6    -      -       +      +
    190A  SER*     3.8    12.8    -      -       -      +
    387A  ALA*     4.1     1.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  ALA*     1.3    86.6    -      -       -      +
     36A  GLY*     1.3    66.0    +      -       -      +
     56A  ALA*     3.8    11.7    -      -       +      -
     57A  LEU      3.4    21.8    -      -       -      +
     59A  LEU      3.5     6.7    -      -       -      +
     60A  MET*     4.3     5.4    -      -       +      -
    140A  SER      4.8     0.2    -      -       -      +
    144A  SER*     3.6    10.0    +      -       -      -
    190A  SER*     2.9    45.8    +      -       -      +
    385A  ASP      3.1    22.2    -      -       -      +
    386A  GLY*     3.6    16.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  PRO*     1.3    78.1    -      -       -      +
     37A  ARG*     1.3    63.0    +      -       -      +
     56A  ALA*     3.6     5.7    -      -       -      -
     57A  LEU*     3.0    27.2    +      -       -      -
     59A  LEU*     2.9    17.2    +      -       -      -
    133A  VAL*     4.0    15.2    -      -       -      +
    139A  LEU      3.4    11.2    -      -       -      -
    140A  SER*     4.1     6.5    -      -       -      -
    144A  SER*     4.4     0.2    -      -       -      -
    190A  SER*     5.5     1.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  GLY*     1.3    75.9    -      -       -      +
     38A  VAL*     1.3    77.0    +      -       -      +
     39A  ASN*     3.9     6.3    -      -       -      +
     43A  GLU*     5.7     0.8    +      -       -      -
     54A  PRO*     3.9     8.1    -      -       +      -
     55A  MET      3.7     7.6    -      -       -      +
     57A  LEU*     3.7     7.2    -      -       -      +
    138A  GLY      2.1    35.8    +      -       -      -
    139A  LEU*     2.8    31.2    +      -       -      +
    140A  SER*     3.3    14.6    -      -       -      +
    185A  MET*     4.3    14.9    -      -       -      -
    186A  ASP*     2.3    50.9    +      -       -      +
    189A  ILE*     3.4    31.9    -      -       +      -
    190A  SER*     6.0     0.9    -      -       -      -
    344A  THR*     4.7     0.6    -      -       -      -
    345A  GLY*     3.6    25.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  ARG*     1.3    82.0    -      -       -      +
     39A  ASN*     1.3    62.7    +      -       -      +
     40A  LEU*     3.6     8.8    +      -       +      -
     54A  PRO*     3.4     0.5    -      -       -      +
     55A  MET*     3.0    46.2    +      -       +      +
     57A  LEU*     3.6    21.3    -      -       +      +
    139A  LEU*     4.5     5.6    -      -       +      -
    220A  VAL*     4.9     0.2    -      -       +      -
    222A  ILE*     3.9    23.1    -      -       +      -
    344A  THR*     3.8    14.8    -      -       +      +
    353A  VAL*     3.8    31.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  ARG*     3.9     7.4    -      -       -      +
     38A  VAL*     1.3    73.8    -      -       -      +
     40A  LEU*     1.3    67.1    +      -       -      +
     41A  ILE      2.8    20.9    +      -       -      +
     42A  GLY      3.1    27.5    +      -       -      -
     43A  GLU*     2.8    33.7    +      -       -      +
     52A  VAL*     4.6     0.2    -      -       -      +
     53A  LEU      3.3     7.6    +      -       -      -
     54A  PRO*     4.0     3.4    -      -       -      -
    185A  MET*     2.9    33.3    -      -       +      +
    342A  ARG*     3.2     2.1    +      -       -      -
    344A  THR*     2.7    35.1    -      -       +      +
    345A  GLY      5.0     1.3    -      -       -      +
    353A  VAL*     3.9     0.2    -      -       -      +
----------------------------------------------------------
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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