Contacts of the strand formed by residues 49 - 58 (chain B) in PDB entry 4G7Z


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 49 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  SER      3.5     8.0    -      -       -      +
     48B  ILE*     1.4    85.7    -      -       +      +
     50B  GLY*     1.3    58.7    +      -       -      +
    146B  ARG*     5.2    12.8    -      -       +      +
    147B  GLY      3.8     0.4    -      -       -      +
    148B  VAL*     3.7    13.7    -      -       +      -
    173B  PRO*     3.3    18.0    -      -       -      +
    205B  VAL*     4.2     8.8    -      -       -      +
    213B  GLN*     3.3    25.4    -      -       +      +
    217B  ILE*     5.7     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  PRO*     1.3    76.9    -      -       -      +
     51B  THR*     1.3    72.6    +      -       -      +
    146B  ARG*     3.2     7.3    -      -       -      +
    147B  GLY      2.7    34.2    +      -       -      +
    171B  PHE      3.8    13.2    -      -       -      -
    173B  PRO*     4.0     6.7    -      -       -      -
    204B  SER*     6.0     0.7    -      -       -      -
    205B  VAL*     5.8     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  GLY*     1.3    81.7    -      -       -      +
     52B  ALA*     1.3    61.8    +      -       -      +
     85B  LEU      4.9     7.3    -      -       -      +
     86B  VAL*     5.6     1.0    -      -       -      +
     87B  VAL*     2.5    35.0    +      -       -      +
     88B  ARG*     5.2     0.2    -      -       -      -
     89B  PHE*     4.3    31.0    -      -       +      +
    144B  VAL*     4.3     9.9    -      -       -      -
    145B  ASP      3.4     9.0    -      -       -      +
    146B  ARG*     4.3     7.4    -      -       +      -
    170B  VAL      3.4    11.3    -      -       -      +
    171B  PHE*     3.7     8.7    +      -       -      +
    202B  ASP*     5.7     1.2    -      -       -      +
    204B  SER*     5.1     5.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 52 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  THR*     1.3    75.6    -      -       -      +
     53B  VAL*     1.3    65.3    +      -       -      +
     54B  THR*     3.4     2.0    +      -       +      +
     85B  LEU      5.7     1.8    -      -       -      -
    144B  VAL*     3.3    10.3    -      -       -      +
    145B  ASP      3.2    28.3    +      -       -      -
    169B  ALA*     3.8     7.4    -      -       +      -
    170B  VAL      3.3    33.4    -      -       -      +
    171B  PHE*     3.4    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  ALA*     1.3    73.0    -      -       -      +
     54B  THR*     1.3    62.0    +      -       -      +
     55B  SER      4.5     1.1    -      -       -      +
     56B  VAL*     3.8    20.9    -      -       +      -
     82B  LEU*     3.4    57.4    -      -       +      +
     83B  LYS*     4.9     5.1    +      -       -      +
     85B  LEU*     4.5    19.7    -      -       +      +
     87B  VAL*     6.0     0.7    -      -       +      -
    142B  VAL*     4.3     4.3    -      -       +      -
    143B  ARG      3.5    10.3    -      -       -      +
    144B  VAL*     4.7     8.5    -      -       +      -
    167B  VAL*     3.5    25.3    -      -       +      +
    168B  ASP      4.2     0.3    -      -       -      +
    169B  ALA*     4.1     6.1    -      -       -      -
    170B  VAL      4.9     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  ALA      3.8    13.2    -      -       -      +
     53B  VAL*     1.3    73.9    -      -       -      +
     55B  SER*     1.3    57.1    +      -       -      +
    143B  ARG*     3.2    13.2    +      -       -      +
    145B  ASP*     3.1    35.2    +      -       +      +
    156B  HIS*     3.0    20.0    +      -       +      +
    158B  ILE*     3.1    27.5    -      -       +      +
    167B  VAL*     2.6    32.2    +      -       -      +
    169B  ALA*     4.6     4.5    -      -       +      -
    171B  PHE*     4.6    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 55 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53B  VAL*     3.8     1.0    -      -       -      +
     54B  THR*     1.3    82.9    +      -       -      +
     56B  VAL*     1.3    68.1    +      -       -      +
    141B  GLU      4.0     0.3    -      -       -      +
    142B  VAL*     3.5     0.3    -      -       -      -
    143B  ARG*     2.8    31.4    +      -       -      +
    158B  ILE*     3.3    38.3    +      -       -      -
    159B  LYS*     4.4     1.5    -      -       -      -
    160B  ASP*     4.8     3.7    +      -       -      -
    164B  ALA*     3.9    15.2    -      -       -      +
    165B  ILE      3.8    15.4    +      -       -      -
    166B  PRO*     4.1     1.3    -      -       -      -
    167B  VAL      4.1     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 56 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53B  VAL*     3.8    13.0    -      -       +      -
     55B  SER*     1.3    83.7    +      -       -      +
     57B  TYR*     1.3    59.6    +      -       -      +
     58B  ILE*     3.7    24.2    +      -       +      +
     79B  ILE*     5.5     4.9    -      -       +      -
     82B  LEU*     3.8    22.7    -      -       +      -
    140B  MET*     4.3     4.7    -      -       -      -
    141B  GLU      3.1    14.6    -      -       -      +
    142B  VAL*     3.6    24.7    -      -       +      -
    164B  ALA*     4.4     2.5    -      -       -      -
    165B  ILE*     3.1    41.6    +      -       +      +
    167B  VAL*     4.1    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 57 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56B  VAL*     1.3    69.6    -      -       -      +
     58B  ILE*     1.3    80.6    +      -       -      +
     59B  GLU*     3.8    29.0    +      -       +      +
    140B  MET*     3.2     7.1    -      -       -      -
    141B  GLU*     2.7    53.2    +      -       +      +
    160B  ASP*     6.4     0.9    -      -       +      -
    161B  ARG*     3.1    54.3    -      -       +      +
    163B  ASN*     3.4    50.0    +      -       +      -
    164B  ALA*     3.7    13.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 58 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56B  VAL*     3.7    16.6    +      -       +      +
     57B  TYR*     1.3    98.4    -      -       -      +
     59B  GLU*     1.3    67.7    +      -       -      +
     60B  ASP      4.7     1.1    -      -       -      +
     61B  VAL*     2.7    64.4    +      -       +      +
     68B  ILE*     5.1     7.0    -      -       +      -
     75B  VAL*     5.7     4.5    -      -       +      -
    138B  LEU*     4.7     9.9    -      -       +      -
    139B  ASN      3.5    12.1    -      -       -      +
    140B  MET*     3.3    33.0    -      -       +      -
    163B  ASN      4.8     1.2    +      -       -      -
    165B  ILE*     5.3     8.0    -      -       +      +
----------------------------------------------------------
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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