Contacts of the strand formed by residues 95 - 106 (chain A) in PDB entry 1W51


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 VAL 95 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  ASP      3.5     0.5    -      -       -      +
     84A  LEU*     3.1     9.0    -      -       -      -
     85A  VAL*     2.8    43.7    +      -       -      +
     93A  VAL*     4.7     2.5    -      -       +      -
     94A  THR*     1.3    80.7    -      -       -      +
     96A  ARG*     1.3    70.7    +      -       -      +
     97A  ALA*     3.5    10.2    +      -       +      +
    136A  PHE*     4.6    12.1    -      -       +      -
    139A  SER*     4.1    22.7    -      -       -      +
    140A  LEU*     3.6    33.2    -      -       +      -
    143A  GLN*     3.9    13.9    -      -       +      +
    144A  THR*     4.7     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  THR*     3.0    38.6    +      -       -      +
     61A  ARG*     3.5    43.7    -      -       -      +
     82A  THR*     2.8    42.0    +      -       -      +
     83A  ASP*     3.3    17.2    -      -       -      +
     84A  LEU*     3.6    30.7    -      -       +      +
     95A  VAL*     1.3    75.5    -      -       -      +
     97A  ALA*     1.3    57.3    +      -       -      +
    139A  SER*     4.2     1.0    -      -       -      -
    143A  GLN*     3.4    20.3    +      -       -      +
   1505A  IOD      3.6    24.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  PHE*     4.6     0.9    -      -       +      -
     82A  THR*     3.3    21.3    -      -       -      -
     83A  ASP      3.1    10.9    +      -       -      +
     85A  VAL*     3.7    16.8    -      -       +      -
     95A  VAL*     3.5     8.4    +      -       +      -
     96A  ARG*     1.3    74.4    -      -       -      +
     98A  ASN*     1.3    72.6    +      -       -      +
     99A  ILE*     3.9     2.6    -      -       -      +
    136A  PHE*     3.7    35.9    -      -       +      -
    139A  SER*     4.5     5.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  PHE*     3.4    23.2    -      -       -      +
     63A  LEU*     4.5     4.3    -      -       -      +
     80A  LEU*     5.2     1.6    -      -       +      -
     81A  GLY      3.5     7.4    -      -       -      +
     82A  THR*     3.2    20.5    -      -       -      +
     97A  ALA*     1.3    76.6    -      -       -      +
     99A  ILE*     1.3    62.8    +      -       -      +
    132A  SER      5.2     0.2    +      -       -      -
    133A  LEU*     3.6    30.0    -      -       +      +
    134A  GLU*     3.2    49.3    +      -       -      +
    136A  PHE*     5.6     1.4    +      -       -      +
    139A  SER*     4.9     1.2    +      -       -      -
   1505A  IOD      4.1     9.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  VAL*     3.1    35.9    -      -       +      -
     38A  PHE*     3.6    22.7    -      -       +      +
     40A  VAL*     3.7    29.2    -      -       +      -
     52A  TYR*     3.9    16.2    -      -       +      +
     60A  TYR*     5.7     1.8    -      -       +      -
     79A  GLU      3.7     1.2    -      -       -      +
     80A  LEU*     3.8     4.0    -      -       -      -
     81A  GLY*     3.0    35.8    +      -       -      +
     82A  THR*     5.1     0.4    -      -       -      -
     83A  ASP*     3.8    19.3    -      -       +      +
     85A  VAL*     3.9    11.2    -      -       +      -
     97A  ALA      3.9     6.7    -      -       -      +
     98A  ASN*     1.3    81.1    -      -       -      +
    100A  ALA*     1.3    65.0    +      -       -      +
    101A  ALA*     3.8     0.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  ASN*     5.2     2.9    -      -       -      +
     38A  PHE      3.1    14.1    +      -       -      +
     39A  ALA*     3.5     0.6    -      -       -      -
     40A  VAL      3.0    26.2    +      -       -      +
     67A  VAL*     4.4     5.2    -      -       +      -
     76A  TRP*     3.3    39.5    -      -       +      -
     79A  GLU      3.7     5.2    -      -       -      +
     80A  LEU*     4.3    16.3    -      -       +      +
     99A  ILE*     1.3    75.9    -      -       -      +
    101A  ALA*     1.3    60.2    +      -       -      +
    102A  ILE      3.6     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  VAL*     3.7     6.7    -      -       -      -
     42A  ALA*     3.6    17.9    -      -       +      -
     52A  TYR*     4.9     4.5    -      -       +      -
     54A  ARG*     3.6    33.7    -      -       -      +
     60A  TYR*     6.1     0.2    -      -       +      -
     78A  GLY*     3.1     3.6    -      -       -      -
     79A  GLU      2.9    35.2    +      -       -      +
     99A  ILE*     3.8     2.0    +      -       -      +
    100A  ALA*     1.3    71.1    -      -       -      +
    102A  ILE*     1.3    64.9    +      -       -      +
    103A  THR*     3.3     5.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  ALA*     3.7    15.0    -      -       +      +
     40A  VAL      2.8    41.6    +      -       -      +
     41A  GLY*     3.9     3.9    -      -       -      -
     42A  ALA*     3.1    21.5    +      -       -      +
     43A  ALA*     3.9     6.2    +      -       -      +
     76A  TRP*     3.6    29.6    -      -       +      -
     77A  GLU      3.7     3.8    -      -       -      -
     78A  GLY*     4.3     0.2    -      -       -      -
    100A  ALA      4.4     0.2    -      -       -      +
    101A  ALA*     1.3    68.4    -      -       -      +
    103A  THR*     1.3    61.0    +      -       -      +
    104A  GLU      4.0    17.0    -      -       -      +
    105A  SER*     4.3     0.4    -      -       -      -
    108A  PHE*     3.9    25.8    -      -       +      -
    109A  PHE*     3.9    25.6    -      -       +      -
   1502A  IOD      4.1     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ALA*     5.2     1.6    -      -       +      -
     43A  ALA*     4.6    11.6    -      -       +      +
     54A  ARG*     4.4     9.0    -      -       -      +
     77A  GLU*     3.0    18.6    +      -       -      +
     78A  GLY*     4.3     2.6    -      -       -      -
     79A  GLU*     3.8    32.1    +      -       +      +
    101A  ALA      3.3    17.3    -      -       -      +
    102A  ILE*     1.3    75.0    -      -       -      +
    104A  GLU*     1.3    66.5    +      -       -      +
   1502A  IOD      3.7    10.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 104 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  LYS*     3.2    20.2    +      -       -      -
     76A  TRP*     3.4     2.6    -      -       -      +
     77A  GLU*     2.7    69.8    +      -       +      +
    102A  ILE*     4.0     0.6    -      -       -      +
    103A  THR*     1.3    82.9    +      -       -      +
    105A  SER*     1.3    64.3    +      -       -      +
   1502A  IOD      3.5     6.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 105 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  HIS*     3.9    14.4    +      -       -      -
     75A  LYS*     3.4    16.2    -      -       -      +
     76A  TRP*     4.2     5.4    -      -       -      -
    102A  ILE*     4.3     0.7    -      -       -      -
    104A  GLU*     1.3    79.7    -      -       -      +
    106A  ASP*     1.3    61.9    +      -       -      +
    107A  LYS      4.2     0.6    +      -       -      -
    108A  PHE*     4.1    14.9    +      -       -      +
    109A  PHE*     3.4    27.8    +      -       -      -
   1502A  IOD      3.6    14.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  GLY*     3.9     0.9    -      -       -      -
     75A  LYS*     3.0    50.9    +      -       +      +
    105A  SER*     1.3    75.0    -      -       -      +
    107A  LYS*     1.3    98.8    +      -       -      +
    108A  PHE      3.1     2.3    +      -       -      -
   1504A  IOD      4.6     2.0    -      -       -      -
----------------------------------------------------------
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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