Contacts of the strand formed by residues 161 - 168 (chain A) in PDB entry 1SID


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 GLN 161 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  GLY      3.3    15.5    +      -       -      +
    160A  SER*     1.3    75.9    -      -       -      +
    162A  TYR*     1.3    65.4    +      -       -      +
    163A  HIS*     4.2     8.4    +      -       +      +
    243A  TYR*     3.8     3.9    -      -       -      -
    244A  THR*     2.8    54.8    +      -       -      +
    249A  THR*     3.6     4.2    +      -       -      +
    250A  PRO      2.8    29.3    +      -       -      -
    251A  PRO*     3.0    29.0    -      -       -      +
    252A  VAL*     3.2    17.1    +      -       -      +
    285A  ILE*     3.2    18.6    -      -       -      +
    286A  MET*     3.6    15.5    +      -       -      +
    136E  LEU*     5.4     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  TRP*     4.4     8.3    -      -       -      -
    161A  GLN*     1.3    76.3    -      -       -      +
    163A  HIS*     1.3    65.1    +      -       -      +
    164A  VAL*     3.2    24.0    -      -       +      +
    224A  VAL*     3.6    22.3    +      -       +      +
    227A  TRP      4.6     3.1    +      -       -      -
    228A  HIS*     4.3     6.1    +      -       -      -
    229A  PRO*     4.9     2.4    -      -       -      +
    242A  ASN      3.3    17.5    -      -       -      -
    243A  TYR*     4.1    14.4    -      +       +      -
    283A  VAL*     3.0    19.4    -      -       +      +
    285A  ILE*     2.7    53.6    +      -       +      +
    133E  GLY*     3.6    24.3    -      -       -      -
    136E  LEU*     3.9    21.5    -      -       +      -
    255E  PHE*     3.2    32.0    -      +       -      -
----------------------------------------------------------
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Residues in contact with HIS 163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  VAL*     5.1     2.8    -      -       +      +
    161A  GLN*     4.2     9.5    +      -       +      +
    162A  TYR*     1.3    82.6    +      -       -      +
    164A  VAL*     1.3    60.0    +      -       -      +
    241A  GLY*     2.9     3.8    -      -       -      -
    242A  ASN*     2.8    45.6    +      -       -      +
    244A  THR*     5.7     1.6    -      -       -      -
    252A  VAL      5.0     2.2    +      -       -      -
    253A  LEU*     4.0    16.1    -      -       +      +
    283A  VAL      2.9     7.9    -      -       -      -
    284A  ASP*     3.0    37.4    +      -       +      +
    285A  ILE      3.1    23.6    +      -       -      -
    286A  MET*     3.3    31.0    -      -       +      +
    304A  ARG*     4.7     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  TRP*     4.0    15.0    -      -       +      -
    162A  TYR*     3.2    42.8    -      -       +      +
    163A  HIS*     1.3    82.7    -      -       -      +
    165A  PHE*     1.3    79.0    +      -       -      +
    229A  PRO*     5.2     3.8    -      -       +      -
    239A  TYR*     5.0     6.5    -      -       +      -
    240A  PHE*     3.0    27.8    -      -       -      +
    241A  GLY*     3.5     1.1    -      -       -      +
    282A  CYS*     3.0     2.2    -      -       -      +
    283A  VAL*     2.8    33.2    +      -       +      -
    284A  ASP*     4.0     0.6    +      -       -      -
    304A  ARG*     3.9     3.3    +      -       -      +
    255E  PHE*     4.1    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  TRP*     4.8     4.0    -      -       -      -
    125A  VAL*     5.0     6.5    -      -       +      -
    127A  THR*     3.9    24.2    -      -       +      -
    164A  VAL*     1.3    81.8    -      -       -      +
    166A  ALA*     1.3    82.5    +      -       -      +
    167A  VAL*     4.3    11.7    -      -       +      -
    239A  TYR*     2.9     3.1    -      -       -      +
    240A  PHE*     2.6    85.8    +      +       +      +
    241A  GLY*     5.6     0.2    -      -       -      -
    261A  THR*     5.9     3.6    -      -       +      -
    281A  SER      2.9    18.2    -      -       -      +
    282A  CYS*     3.3    11.0    -      -       +      +
    304A  ARG*     3.6    30.1    -      -       -      +
    306A  PHE*     4.3    11.9    -      +       +      -
----------------------------------------------------------
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Residues in contact with ALA 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  TRP*     6.4     0.4    -      -       +      -
    165A  PHE*     1.3    87.1    -      -       -      +
    167A  VAL*     1.3    67.1    +      -       -      +
    172A  LEU*     5.1     7.6    -      -       +      -
    237A  THR*     3.5    13.2    -      -       +      -
    238A  ARG      2.7    21.8    -      -       -      +
    239A  TYR*     3.2    14.6    -      -       +      -
    280A  LEU*     3.5     2.9    -      -       -      +
    281A  SER*     2.9    35.1    +      -       -      +
    306A  PHE*     4.5     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  ALA*     5.0     4.7    -      -       +      -
    125A  VAL*     4.6     7.9    -      -       +      -
    165A  PHE*     4.3    16.2    -      -       +      -
    166A  ALA*     1.3    86.8    -      -       -      +
    168A  GLY*     1.3    59.9    +      -       -      +
    237A  THR*     3.1    12.6    -      -       -      +
    238A  ARG*     2.9    17.0    +      -       +      +
    240A  PHE*     5.5     0.9    -      -       +      -
    263A  LEU*     4.4    31.6    -      -       +      -
    271A  PRO*     3.6     8.6    -      -       +      +
    278A  LEU*     3.7    10.5    -      -       +      -
    279A  TYR      3.3     3.4    -      -       -      -
    280A  LEU*     3.6    23.6    -      -       +      -
    306A  PHE*     5.0     7.0    -      -       +      -
    308A  ILE*     4.4    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  VAL*     1.3    77.9    -      -       -      +
    169A  GLY*     1.3    56.7    +      -       -      -
    170A  GLU      3.2     9.9    -      -       -      -
    236A  ASN      3.3    10.3    -      -       -      -
    237A  THR*     3.4    12.7    -      -       -      +
    271A  PRO*     4.2     6.1    -      -       -      -
    273A  CYS*     5.4     0.7    -      -       -      -
    278A  LEU*     3.7     8.0    -      -       -      +
    279A  TYR*     2.8    44.5    +      -       -      -
----------------------------------------------------------
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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