Contacts of the strand formed by residues 67 - 80 (chain A) in PDB entry 4SBV


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 THR 67 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  SER*     4.0     7.2    +      -       -      +
     65A  ASP      4.1     2.6    +      -       -      -
     66A  VAL*     1.3    80.2    +      -       -      +
     68A  ILE*     1.3    76.0    -      -       -      +
     69A  LEU*     4.7    10.1    -      -       +      -
    107A  TRP*     3.5    45.2    +      -       +      -
    248A  ILE      4.0     0.2    -      -       -      +
    249A  ARG*     3.5     2.3    -      -       -      -
    250A  LEU*     2.9    33.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  SER*     3.9    31.6    -      -       -      +
     63A  SER*     4.0     8.0    +      -       -      -
     66A  VAL*     4.1    10.8    -      -       +      -
     67A  THR*     1.3    87.3    -      -       -      +
     69A  LEU*     1.3    69.5    +      -       -      +
     70A  SER*     4.9     1.6    -      -       -      +
    113A  VAL*     4.9    10.5    -      -       +      -
    247A  THR*     4.1    16.6    -      -       +      -
    248A  ILE      3.6     6.5    -      -       -      +
    249A  ARG*     4.3    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  THR*     4.7     7.9    -      -       +      -
     68A  ILE*     1.3    78.2    -      -       -      +
     70A  SER*     1.3    73.7    -      -       -      +
     71A  HIS*     4.4     1.8    -      -       +      -
     99A  TRP*     3.7    33.7    -      -       +      -
    100A  LEU*     5.1     1.8    -      -       +      -
    103A  VAL*     3.8    16.6    -      -       +      -
    107A  TRP*     5.1     1.8    -      -       +      -
    246A  TYR*     4.4     4.4    -      -       +      +
    247A  THR*     3.5     0.7    -      -       -      +
    248A  ILE*     2.9    48.5    +      -       +      +
    250A  LEU*     3.3    31.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  ILE*     4.9     2.3    -      -       -      +
     69A  LEU*     1.3    78.8    -      -       -      +
     71A  HIS*     1.3    64.3    +      -       -      +
     99A  TRP*     5.7     0.3    -      -       -      -
    246A  TYR      3.3     5.2    -      -       -      -
    247A  THR*     2.4    35.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  LEU*     4.4     0.2    -      -       +      -
     70A  SER*     1.3    74.9    +      -       -      +
     72A  CYS*     1.3    98.3    +      -       +      +
     73A  GLU*     4.6     3.9    -      -       +      +
     99A  TRP*     3.1    59.6    +      +       +      -
    245A  SER*     3.5     1.6    +      -       -      -
    246A  TYR*     2.9    61.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  HIS*     1.3   104.8    +      -       +      +
     73A  GLU*     1.3    66.5    -      -       -      +
    170A  PHE      4.7     0.2    -      -       -      +
    171A  VAL*     3.6    45.5    -      -       -      +
    243A  TYR*     5.0     2.9    -      -       -      -
    244A  ALA      3.2    11.0    -      -       -      -
    245A  SER*     2.7    26.7    -      -       -      +
    246A  TYR*     4.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  HIS*     4.6     4.9    -      -       +      +
     72A  CYS*     1.3    77.3    -      -       -      +
     74A  LEU*     1.3    61.1    +      -       -      +
     96A  VAL      5.5     0.4    -      -       -      +
     97A  GLY*     3.7    16.3    +      -       -      -
     98A  THR*     3.6     5.7    +      -       -      -
     99A  TRP*     2.9    33.2    +      -       +      +
    100A  LEU*     2.8    24.1    +      -       -      +
    243A  TYR*     3.1    15.2    -      -       -      +
    244A  ALA*     2.7    43.4    +      -       +      +
    246A  TYR*     2.7    35.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  GLU*     1.3    78.9    -      -       -      +
     75A  SER*     1.3    62.8    +      -       -      +
     76A  THR*     3.8    14.8    -      -       -      +
     77A  GLU*     3.9    16.4    -      -       -      +
     96A  VAL      4.6     0.7    -      -       -      -
     97A  GLY*     4.1    13.5    -      -       -      -
     98A  THR      5.1     0.7    +      -       -      -
    241A  ARG*     3.6    40.4    -      -       +      +
    242A  LEU      3.7    12.1    -      -       -      +
    243A  TYR*     3.8    16.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  GLU      3.6     2.2    +      -       -      -
     74A  LEU*     1.3    76.0    -      -       -      +
     76A  THR*     1.3    74.8    -      -       -      +
     89A  GLU*     4.9    10.4    -      -       -      +
     95A  THR      4.5     4.3    +      -       -      +
     96A  VAL*     2.9    27.2    +      -       -      +
     97A  GLY*     5.4     1.0    -      -       -      -
    117A  TYR*     3.6    32.2    -      -       -      -
    242A  LEU*     2.8    14.0    +      -       -      +
    244A  ALA*     4.2     8.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  LEU*     3.5     9.6    -      -       -      -
     75A  SER*     1.3    88.1    -      -       -      +
     77A  GLU*     1.3    73.9    +      -       -      +
     78A  LEU*     5.0     8.7    -      -       +      -
     89A  GLU*     4.8    20.2    +      -       +      -
    226A  THR*     6.0     2.5    -      -       +      -
    241A  ARG*     3.5     2.6    -      -       -      +
    242A  LEU*     2.7    61.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  LEU*     3.9    22.0    -      -       +      +
     76A  THR*     1.3    85.4    +      -       -      +
     78A  LEU*     1.4    70.4    +      -       -      +
    238A  ASN*     5.5     6.3    -      -       -      +
    240A  GLY      3.8     8.5    -      -       -      +
    241A  ARG*     2.9    34.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  THR*     4.7    11.7    -      -       +      +
     77A  GLU*     1.4    81.8    -      -       -      +
     79A  ALA*     1.4    60.4    -      -       -      +
    119A  TYR*     3.6    33.9    -      -       +      -
    131A  ILE*     4.1    10.8    -      -       +      -
    226A  THR*     3.9    24.0    -      -       +      +
    228A  MET*     3.1    28.0    -      -       +      -
    238A  ASN*     3.6     5.3    -      -       -      +
    239A  THR*     2.8    32.6    +      -       -      +
    240A  GLY      2.9    19.3    +      -       -      +
    241A  ARG*     4.0    10.8    -      -       -      -
    242A  LEU*     4.1     7.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  LEU*     1.4    75.9    -      -       -      +
     80A  VAL*     1.3    55.6    +      -       -      +
     81A  THR*     4.5     1.8    +      -       -      +
     85A  VAL*     5.7     2.4    -      -       -      +
    228A  MET*     3.7    20.9    -      -       -      +
    236A  ALA*     4.3     9.9    -      -       +      -
    237A  VAL      2.6    34.5    -      -       -      +
    238A  ASN*     3.6    14.6    -      -       -      +
    239A  THR*     4.2     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  ALA*     1.3    72.1    -      -       -      +
     81A  THR*     1.3    64.9    +      -       -      +
    127A  THR*     4.9     9.0    -      -       +      -
    128A  SER      4.9     4.5    -      -       -      +
    129A  GLY*     3.8    18.4    -      -       -      -
    161A  VAL*     4.1    10.5    -      -       +      -
    228A  MET*     4.3     8.7    -      -       +      -
    229A  GLU      3.6    28.5    -      -       -      +
    230A  GLY*     3.8     7.0    -      -       -      -
    231A  GLY*     4.2     2.5    -      -       -      +
    232A  SER      5.8     0.6    +      -       -      +
    233A  SER      4.5     0.3    -      -       -      +
    235A  THR      3.4     4.2    -      -       -      +
    236A  ALA*     4.7     0.2    -      -       -      -
    237A  VAL*     3.0    49.8    +      -       +      +
    239A  THR*     4.3    14.1    -      -       -      +
----------------------------------------------------------
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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