Contacts of the strand formed by residues 54 - 68 (chain D) 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 PRO 54 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37D  ARG*     4.4     3.4    -      -       -      -
     38D  VAL      3.3    13.5    -      -       -      +
     39D  ASN*     4.0     1.8    -      -       -      -
     40D  LEU*     4.8     0.7    -      -       -      -
     52D  VAL*     3.4     8.5    -      -       +      -
     53D  LEU*     1.3    92.4    -      -       -      +
     55D  MET*     1.3    59.3    +      -       -      +
    185D  MET*     3.0    30.5    -      -       +      -
    189D  ILE*     3.9    20.4    -      -       +      -
    198D  ALA*     3.6     2.2    -      -       -      -
    199D  LEU*     2.8    45.8    +      -       -      +
    201D  ILE*     3.8    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 55 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37D  ARG*     3.5     2.1    -      -       -      +
     38D  VAL*     3.0    43.7    +      -       +      +
     40D  LEU*     4.5    19.2    -      -       +      +
     54D  PRO*     1.3    74.9    -      -       -      +
     56D  ALA*     1.3    69.2    +      -       -      +
     57D  LEU*     4.0    21.3    -      -       +      -
    189D  ILE*     3.9     8.1    -      -       -      -
    197D  HIS      3.9    19.7    -      -       -      +
    198D  ALA*     4.2     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 56 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35D  PRO*     3.7    26.5    -      -       +      -
     36D  GLY      3.5     5.8    -      -       -      +
     55D  MET*     1.3    84.9    -      -       -      +
     57D  LEU*     1.3    62.2    -      -       -      +
    189D  ILE*     3.7    22.1    -      -       +      +
    193D  GLY*     4.3    15.2    -      -       -      -
    194D  GLN      6.1     1.1    -      -       -      +
    197D  HIS      5.0     2.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 57 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35D  PRO*     3.3    21.7    -      -       -      +
     36D  GLY      2.8    15.5    +      -       -      +
     37D  ARG      3.8    31.6    -      -       -      +
     38D  VAL*     3.7    23.8    -      -       +      +
     55D  MET*     4.0    16.8    -      -       +      -
     56D  ALA*     1.3    74.9    -      -       -      +
     58D  GLU*     1.3    64.0    +      -       -      +
     59D  LEU*     3.2    19.9    -      -       +      +
     60D  MET*     5.6     0.2    -      -       -      +
    139D  LEU*     3.9    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 58 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6D  GLN*     4.8    17.9    -      -       +      +
      7D  PRO      4.3    10.5    -      -       -      +
      8D  GLN*     5.8     1.7    +      -       -      -
     57D  LEU*     1.3    73.1    -      -       -      +
     59D  LEU*     1.3    64.9    +      -       -      +
     60D  MET*     3.6    18.8    +      -       -      +
    132D  SER*     4.4     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 59 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5D  ARG      5.3     2.2    -      -       -      +
      6D  GLN*     4.4    22.7    -      -       +      -
      7D  PRO*     5.1     1.1    -      -       +      +
     35D  PRO*     3.5     0.9    -      -       -      +
     36D  GLY*     2.9    24.0    +      -       -      +
     57D  LEU*     3.2    20.0    -      -       +      +
     58D  GLU*     1.3    79.2    -      -       -      +
     60D  MET*     1.3    58.5    +      -       -      +
    132D  SER*     3.5    27.1    -      -       -      +
    133D  VAL*     3.5    12.3    -      -       +      -
    134D  PRO*     3.7    26.7    -      -       +      -
    139D  LEU*     3.7    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 60 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7D  PRO      4.7     1.3    -      -       -      +
      8D  GLN*     4.6     1.3    -      -       -      -
      9D  VAL*     4.0    33.2    -      -       +      +
     12D  LEU*     3.6    26.0    -      -       +      +
     33D  SER*     3.5    26.0    -      -       -      -
     34D  ALA      3.5    16.8    -      -       -      +
     35D  PRO*     4.3     4.5    -      -       +      -
     58D  GLU      3.8    12.8    -      -       -      +
     59D  LEU*     1.3    75.2    -      -       -      +
     61D  THR*     1.3    73.1    +      -       -      +
     62D  VAL*     4.1     2.5    -      -       -      -
    131D  SER*     3.2     3.6    +      -       -      -
    132D  SER*     2.9    31.5    +      -       -      -
    133D  VAL*     3.3     6.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 61 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33D  SER*     3.1     6.1    -      -       -      -
     34D  ALA      2.8    33.8    +      -       -      -
     60D  MET*     1.3    71.2    -      -       -      +
     62D  VAL*     1.3    65.9    +      -       -      +
     63D  LEU*     4.2     0.4    +      -       +      -
    129D  VAL*     3.6    29.6    -      -       +      -
    130D  VAL      3.5     4.0    -      -       -      +
    131D  SER*     3.2    16.8    +      -       -      -
    133D  VAL*     4.3     0.2    -      -       -      +
    141D  SER*     4.5     1.9    +      -       -      -
    144D  SER*     2.7    35.8    +      -       -      +
    145D  LEU*     4.0     9.8    +      -       +      +
    148D  ALA*     3.8    19.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 62 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9D  VAL*     4.7     7.0    -      -       +      -
     12D  LEU*     3.7    31.2    -      -       +      -
     13D  LEU*     4.2    34.5    -      -       +      +
     16D  ALA*     4.2     5.0    -      -       +      +
     32D  VAL      3.3     9.6    -      -       -      +
     33D  SER*     4.2    13.5    -      -       -      -
     60D  MET*     4.3     6.1    -      -       -      -
     61D  THR*     1.3    78.4    -      -       -      +
     63D  LEU*     1.3    62.9    +      -       -      +
     64D  VAL*     4.2     9.2    -      -       +      -
    128D  VAL      3.8     1.2    -      -       -      +
    129D  VAL*     3.6     3.3    -      -       -      +
    130D  VAL*     2.8    45.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 63 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30D  LEU      4.0     0.2    -      -       -      +
     31D  ALA*     3.4     2.1    -      -       -      -
     32D  VAL*     2.8    47.0    +      -       +      +
     61D  THR      4.2     0.6    +      -       -      -
     62D  VAL*     1.3    73.9    -      -       -      +
     64D  VAL*     1.3    65.8    +      -       -      +
     75D  LEU*     6.4     0.9    -      -       +      -
    125D  PHE*     6.1     2.0    -      -       +      -
    127D  ALA*     3.5    24.5    -      -       +      -
    128D  VAL      3.5     8.3    -      -       -      +
    129D  VAL*     4.1    21.5    -      -       +      -
    145D  LEU*     5.5     0.9    -      -       +      -
    148D  ALA*     4.6     6.7    -      -       +      -
    149D  THR*     4.0    37.0    -      -       +      +
    152D  PHE*     3.2    35.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 64 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13D  LEU*     3.7    31.0    -      -       +      -
     16D  ALA*     3.6    23.6    -      -       +      +
     17D  ARG*     4.7     4.7    -      -       +      -
     20D  PHE*     4.0     3.9    -      -       +      -
     28D  PRO*     3.8    21.1    -      -       +      -
     30D  LEU      3.1     8.5    -      -       -      +
     31D  ALA*     4.0     7.2    -      -       +      -
     62D  VAL*     4.2     2.0    -      -       +      -
     63D  LEU*     1.3    82.6    -      -       -      +
     65D  GLY*     1.3    59.4    +      -       -      +
    127D  ALA*     3.0     2.9    -      -       -      +
    128D  VAL*     2.8    54.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 65 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20D  PHE*     3.6     9.4    -      -       -      -
     28D  PRO*     4.0     1.4    -      -       -      +
     29D  GLU      3.2     2.3    +      -       -      -
     30D  LEU*     2.9    33.5    +      -       -      +
     64D  VAL*     1.3    77.2    -      -       -      +
     66D  SER*     1.3    65.6    +      -       -      -
    126D  SER      2.8    15.3    -      -       -      -
    127D  ALA*     3.8     1.1    -      -       -      -
    152D  PHE*     3.6    15.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 66 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20D  PHE*     3.8    11.4    -      -       -      -
     27D  GLU      3.9     1.9    +      -       -      -
     28D  PRO*     3.6     6.4    -      -       -      +
     29D  GLU*     3.1    37.6    +      -       -      +
     30D  LEU*     4.9     0.4    -      -       -      -
     65D  GLY*     1.3    71.2    +      -       -      -
     67D  PRO*     1.3    78.1    -      -       -      +
     68D  ARG*     4.3     0.5    -      -       -      +
    125D  PHE*     3.1     6.7    -      -       -      +
    126D  SER*     2.8    31.8    +      -       -      -
    152D  PHE*     4.0     1.2    -      -       -      -
    156D  LEU*     4.8     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 67 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29D  GLU*     4.0    16.6    -      -       -      +
     30D  LEU*     4.2    18.2    -      -       +      -
     66D  SER*     1.3    94.6    -      -       -      +
     68D  ARG*     1.3    64.3    +      -       -      +
    123D  PRO*     4.5    10.3    -      -       +      -
    124D  GLY      3.4     9.0    -      -       -      +
    125D  PHE*     4.1     2.9    -      -       +      -
    156D  LEU*     4.1    13.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 68 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88C  LEU*     5.5     4.2    -      -       -      +
     89C  GLN*     2.9    36.6    +      -       -      +
     24D  PHE*     4.5     6.1    -      -       -      -
     66D  SER      4.3     0.2    -      -       -      +
     67D  PRO*     1.3    79.6    -      -       -      +
     69D  LYS*     1.3    61.3    +      -       -      +
     70D  ASP*     3.0    35.2    +      -       +      +
     71D  GLY      4.6     0.3    +      -       -      -
     72D  LEU*     3.6    17.1    +      -       -      +
     74D  SER*     4.1    14.5    -      -       -      +
    123D  PRO*     4.1     8.1    -      -       -      +
    124D  GLY*     2.7    29.7    +      -       -      +
    125D  PHE*     3.3    22.2    -      -       -      -
    126D  SER*     2.8    32.2    +      -       -      +
----------------------------------------------------------
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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