Contacts of the strand formed by residues 128 - 138 (chain A) in PDB entry 6H25


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 LYS 128 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  LEU*     4.6    27.8    +      -       +      +
     64A  VAL      4.5     4.0    -      -       -      +
     65A  SER      5.9     0.2    -      -       -      +
     66A  PRO*     5.1     0.4    -      -       -      -
    123A  VAL*     3.3    18.5    +      -       +      +
    124A  VAL*     2.9    39.1    +      -       +      +
    127A  GLU*     1.3   106.6    +      -       +      +
    129A  VAL*     1.3    61.4    +      -       -      +
    172A  VAL*     4.6    20.2    -      -       +      -
     71C  THR*     4.9    14.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 129 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  LEU*     3.6     7.6    -      -       -      +
     64A  VAL*     3.2    40.8    +      -       +      +
     66A  PRO*     3.7    30.7    -      -       +      -
     71A  ALA      5.5     3.4    -      -       -      +
     72A  THR      5.4     0.2    -      -       -      -
     73A  GLU      3.5    29.2    -      -       -      +
     74A  GLY*     3.7     7.9    -      -       -      -
     75A  ILE*     5.5     5.2    -      -       +      +
    121A  LEU      4.1     0.9    -      -       -      +
    122A  CYS*     3.7    24.7    -      -       +      -
    123A  VAL*     4.3     5.8    -      -       -      +
    124A  VAL      5.2     1.1    -      -       -      +
    128A  LYS*     1.3    76.0    -      -       -      +
    130A  TRP*     1.3    69.0    +      -       -      +
    131A  GLN*     5.8     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 130 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  CYS*     3.4    27.8    -      -       -      -
     62A  GLU      3.3    22.9    -      -       -      -
     63A  LEU*     3.6    28.5    -      -       +      +
     74A  GLY*     3.4    24.3    -      -       -      -
     75A  ILE      3.7     1.2    +      -       -      -
    121A  LEU*     3.1    47.4    +      -       +      +
    123A  VAL*     3.6    18.0    -      -       +      +
    129A  VAL*     1.3    82.0    -      -       -      +
    131A  GLN*     1.3    60.1    +      -       -      +
    162A  ARG*     3.2    32.8    -      -       +      +
    163A  PRO*     3.2    49.6    -      -       +      -
    165A  VAL*     3.6    23.3    -      -       +      +
    174A  LEU*     5.9     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  CYS*     3.3     3.9    -      -       -      -
     62A  GLU*     2.9    43.1    +      -       -      +
     64A  VAL*     3.7    39.7    -      -       +      +
     75A  ILE*     3.7    27.6    +      -       +      +
     77A  PHE*     3.7    31.7    -      -       -      +
    129A  VAL*     4.7     1.1    -      -       +      +
    130A  TRP*     1.3    76.4    -      -       -      +
    132A  ILE*     1.3    65.8    +      -       -      +
    133A  ARG*     3.9    11.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  VAL*     3.9    24.7    -      -       +      -
     60A  SER      3.7     3.1    -      -       -      +
     61A  CYS*     3.6    20.6    -      -       +      -
     75A  ILE      3.0    11.1    +      -       -      +
     76A  LEU*     3.5    12.6    -      -       +      +
     77A  PHE*     2.9    26.0    +      -       -      +
     78A  PHE*     5.5     0.2    -      -       -      -
    116A  ILE*     4.5    16.4    -      -       +      -
    121A  LEU*     3.7    27.6    -      -       +      -
    131A  GLN*     1.3    73.9    -      -       -      +
    133A  ARG*     1.3    61.1    +      -       -      +
    134A  VAL*     4.1    13.1    +      -       +      +
    157A  LEU*     4.9     7.2    -      -       +      -
    160A  PHE*     5.3     0.9    -      -       +      -
    162A  ARG*     6.2     1.3    -      -       -      -
    185A  LEU*     3.7    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  GLN      4.1     0.7    -      -       -      +
     59A  VAL*     3.7     0.7    -      -       -      -
     60A  SER*     2.9    48.2    +      -       -      +
     77A  PHE*     3.2    38.0    -      -       +      +
     79A  ASN*     3.4    27.9    -      -       +      +
    131A  GLN*     3.9    16.0    +      -       -      +
    132A  ILE*     1.3    71.7    -      -       -      +
    134A  VAL*     1.3    63.6    +      -       -      +
    135A  ASP*     3.5    21.4    +      -       -      +
     85D  GLY*     3.7    23.5    -      -       -      +
     86D  LEU*     3.9    25.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  GLN      3.4     7.4    -      -       -      +
     59A  VAL*     3.7    22.4    -      -       +      -
     76A  LEU*     6.4     0.2    -      -       +      -
     77A  PHE      3.0     9.0    +      -       -      +
     78A  PHE*     3.5    30.2    -      -       +      -
     79A  ASN      3.0    21.1    +      -       -      -
    106A  MET*     3.8    19.5    -      -       +      -
    132A  ILE*     4.1    14.6    -      -       +      -
    133A  ARG*     1.3    77.2    -      -       -      +
    135A  ASP*     1.3    70.3    +      -       -      +
    136A  LEU*     5.1     6.7    -      -       +      -
    153A  ALA*     5.3     3.8    -      -       +      -
    156A  ALA*     6.1     0.7    -      -       +      -
    157A  LEU*     3.7    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 135 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  LEU      3.8     0.7    -      -       -      +
     57A  GLY*     3.5     3.1    -      -       -      -
     58A  GLN*     2.9    37.9    +      -       +      +
     60A  SER*     5.3     1.9    +      -       -      -
     79A  ASN*     3.3    24.3    -      -       -      +
    133A  ARG*     3.5    18.8    +      -       -      +
    134A  VAL*     1.3    82.7    -      -       -      +
    136A  LEU*     1.3    63.2    +      -       -      +
    137A  HIS*     4.2    13.9    -      -       +      +
     83D  LYS      2.9    28.7    -      -       -      +
     84D  ILE*     3.6     4.5    -      -       -      +
     85D  GLY      3.4    20.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  VAL*     4.6     4.5    -      -       +      -
     56A  LEU      3.3     3.4    -      -       -      +
     57A  GLY*     3.7    19.1    -      -       -      -
     58A  GLN      4.8     0.4    -      -       -      +
     79A  ASN      2.9     8.2    +      -       -      +
     80A  LEU*     3.4    16.1    -      -       +      +
     81A  GLU*     3.2    25.6    +      -       -      +
    106A  MET*     3.7    37.7    -      -       +      -
    134A  VAL*     5.1     4.5    -      -       +      -
    135A  ASP*     1.3    83.0    -      -       -      +
    137A  HIS*     1.3    65.4    +      -       -      +
    149A  ALA*     3.4    36.8    -      -       +      +
    152A  ALA*     4.1    14.4    -      -       +      -
    153A  ALA*     4.1    12.1    -      -       +      +
    156A  ALA*     5.6     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 137 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  VAL*     3.5     6.7    -      -       -      +
     56A  LEU*     2.9    45.4    +      -       +      -
     58A  GLN*     5.9     0.9    -      -       +      -
     80A  LEU*     5.2     0.2    -      -       -      -
     81A  GLU*     3.7    19.7    +      -       +      +
     83A  SER*     5.3     5.1    -      -       -      -
    135A  ASP*     4.2    14.9    -      -       +      +
    136A  LEU*     1.3    79.4    +      -       -      +
    138A  LEU*     1.3    60.8    +      -       -      +
    139A  LEU*     3.3    19.7    -      -       +      +
     81D  ARG*     4.5    17.4    +      -       -      -
     82D  PRO      4.2     6.7    -      -       -      -
     83D  LYS*     3.5    28.6    +      -       +      -
     85D  GLY      5.7     2.2    -      -       -      -
    121D  GLN*     3.3    37.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 138 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  THR*     4.7     3.8    -      -       +      -
     54A  ARG      4.1     0.4    -      -       -      +
     55A  VAL*     3.8    20.6    -      -       +      -
     80A  LEU*     4.9     4.7    -      -       +      +
     81A  GLU      3.6     7.5    +      -       -      +
     82A  LEU*     3.7    35.2    -      -       +      -
     83A  SER*     3.3    23.2    +      -       -      +
     86A  ALA*     3.5    23.8    -      -       +      +
     90A  PHE*     4.2    10.3    -      -       +      -
    136A  LEU      4.1     0.6    +      -       -      -
    137A  HIS*     1.3    70.7    -      -       -      +
    139A  LEU*     1.3    59.8    +      -       -      +
    140A  ASN      3.8    18.4    -      -       -      +
    141A  HIS*     4.2     8.1    -      -       +      -
    145A  ILE*     3.7    42.0    -      -       +      -
----------------------------------------------------------
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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