Contacts of the strand formed by residues 154 - 159 (chain A) in PDB entry 1SOT


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 154 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  TYR*     3.8    38.4    -      -       +      +
    152A  GLY      3.4     0.2    +      -       -      -
    153A  ASP*     1.3    74.6    -      -       -      +
    155A  VAL*     1.3    68.8    +      -       -      +
    156A  LEU*     4.9     2.7    -      -       +      -
    170A  GLN*     4.1    10.1    -      -       -      +
    171A  GLY      3.5    10.3    -      -       -      +
    172A  ILE*     4.2     4.0    -      -       +      -
    207A  ASN*     3.5    22.3    -      -       -      +
    208A  SER*     3.9     7.0    +      -       -      +
     45C  ALA*     3.1    36.2    +      -       +      +
     46C  SER      4.3     0.7    -      -       -      +
     47C  TYR*     3.8    30.1    -      -       +      -
    170C  GLN*     5.9     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  ASP      4.1     3.8    -      -       -      +
    154A  VAL*     1.3    78.0    -      -       -      +
    156A  LEU*     1.3    61.5    +      -       -      +
    170A  GLN*     3.2     8.1    -      -       -      +
    171A  GLY      2.9    34.6    +      -       -      +
    172A  ILE      4.4     1.3    -      -       -      -
    173A  ILE*     3.8    20.0    -      -       +      -
    192A  THR*     3.5    22.2    -      -       -      +
    194A  ALA*     4.4     3.1    -      -       +      -
    205A  LEU*     3.0    42.8    -      -       +      -
    206A  VAL      3.2    14.4    -      -       -      +
    207A  ASN      5.0     0.2    -      -       -      -
    213A  MSE      3.9    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  TYR*     3.9    27.8    -      -       +      -
     50A  ALA*     3.7    28.5    -      -       +      -
     51A  VAL*     3.8    25.4    -      -       +      +
    154A  VAL*     4.9     3.4    -      -       +      -
    155A  VAL*     1.3    77.7    -      -       -      +
    157A  ALA*     1.3    59.9    +      -       -      +
    158A  ILE*     4.0     2.2    +      -       +      -
    168A  ILE*     3.9    11.2    -      -       +      -
    169A  THR      3.3     5.4    -      -       -      +
    170A  GLN*     3.3    29.4    -      -       +      -
    204A  ALA      3.5     1.6    -      -       -      +
    205A  LEU*     3.2     5.8    -      -       -      -
    206A  VAL*     2.8    46.3    +      -       +      +
    207A  ASN      5.0     2.7    -      -       -      +
    208A  SER*     5.7     0.4    -      -       -      -
    152B  GLY*     5.5     0.2    -      -       -      -
    172B  ILE*     4.3     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  VAL      4.2     0.2    -      -       -      -
    156A  LEU*     1.3    72.3    -      -       -      +
    158A  ILE*     1.3    60.2    +      -       -      +
    159A  GLY      4.0     0.6    +      -       -      -
    167A  THR      3.6     1.0    -      -       -      +
    168A  ILE*     3.2     7.3    -      -       -      +
    169A  THR*     2.9    43.6    +      -       -      +
    194A  ALA*     4.1     5.1    -      -       +      +
    196A  ILE*     3.6    31.0    -      -       +      -
    200A  ASN*     3.8     9.5    -      -       -      +
    204A  ALA      3.3     5.2    -      -       -      -
    205A  LEU*     3.9     8.5    -      -       +      +
    216A  ASN*     4.0     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ALA      5.2     2.0    -      -       -      +
     51A  VAL*     5.2     3.4    -      -       -      -
     54A  ALA*     4.1    20.0    -      -       +      -
     55A  ALA*     4.2    12.6    -      -       +      +
     58A  VAL*     3.6    32.3    -      -       +      +
    156A  LEU*     4.4     5.4    -      -       +      +
    157A  ALA*     1.3    78.5    -      -       -      +
    159A  GLY*     1.3    61.0    +      -       -      +
    166A  GLN*     3.9    15.3    -      -       -      -
    167A  THR      3.4     2.5    -      -       -      -
    168A  ILE*     3.8    30.3    -      -       +      -
    200A  ASN*     3.6     2.6    -      -       -      +
    203A  GLY*     3.4     6.6    -      -       -      -
    204A  ALA*     2.7    34.1    +      -       +      +
    206A  VAL*     4.0    26.2    -      -       +      -
    216A  ASN*     4.1     1.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  SER*     3.7     5.8    -      -       -      -
    158A  ILE*     1.3    75.1    -      -       -      +
    160A  ASN*     1.3    61.0    +      -       -      -
    161A  PRO*     2.9     3.7    -      -       -      +
    167A  THR      2.6    41.9    +      -       -      +
    199A  GLY      3.1    20.2    -      -       -      -
    200A  ASN*     3.1    15.0    +      -       -      -
----------------------------------------------------------
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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