Contacts of the strand formed by residues 161 - 168 (chain F) 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 F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159F  GLY      3.2    16.6    +      -       -      +
    160F  SER*     1.3    74.5    -      -       -      +
    162F  TYR*     1.3    64.4    +      -       -      +
    163F  HIS*     4.4     9.6    +      -       +      +
    242F  ASN      4.4     0.2    -      -       -      -
    243F  TYR*     3.7     4.0    -      -       -      -
    244F  THR*     2.8    52.9    +      -       -      +
    249F  THR*     3.4     5.7    +      -       +      +
    250F  PRO      3.1    13.1    +      -       -      +
    251F  PRO*     3.0    41.6    -      -       -      +
    252F  VAL*     3.2    17.3    +      -       -      +
    285F  ILE*     3.2    15.7    -      -       -      +
    286F  MET*     3.4    18.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 162 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98F  TRP*     4.5     7.3    -      +       -      -
    161F  GLN*     1.3    75.7    -      -       -      +
    163F  HIS*     1.3    66.1    +      -       -      +
    164F  VAL*     3.4    24.5    -      -       +      +
    224F  VAL*     3.4    33.7    -      -       +      +
    227F  TRP      4.3     4.5    +      -       -      -
    228F  HIS*     4.1    19.2    +      +       -      +
    229F  PRO*     4.8     6.1    -      -       -      +
    242F  ASN*     3.5     8.5    -      -       -      -
    243F  TYR*     4.0    35.0    -      +       +      -
    283F  VAL*     3.2    22.3    -      -       +      +
    284F  ASP*     3.2     1.7    -      -       -      -
    285F  ILE*     2.6    51.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 163 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129F  VAL*     4.9     5.5    -      -       +      +
    161F  GLN*     4.4     9.4    +      -       +      +
    162F  TYR*     1.3    73.3    -      -       -      +
    164F  VAL*     1.3    71.2    +      -       -      +
    241F  GLY*     2.9    15.3    -      -       -      -
    242F  ASN*     3.0    20.3    +      -       -      +
    244F  THR*     6.1     0.7    -      -       -      -
    252F  VAL      4.9     2.4    +      -       -      -
    253F  LEU*     4.0    19.5    -      -       +      +
    283F  VAL*     2.7     9.0    -      -       -      -
    284F  ASP*     2.9    37.6    +      -       +      +
    285F  ILE      3.3    24.8    +      -       -      -
    286F  MET*     3.6    24.5    -      -       -      +
    304F  ARG*     4.3     9.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 164 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98F  TRP*     3.5    19.1    -      -       +      -
    162F  TYR*     3.4    30.3    -      -       +      +
    163F  HIS*     1.3    86.3    -      -       -      +
    165F  PHE*     1.3    74.8    +      -       -      +
    229F  PRO*     5.0     7.4    -      -       +      -
    239F  TYR*     4.7    10.8    -      -       +      -
    240F  PHE      2.9    21.5    -      -       -      +
    241F  GLY*     3.6     9.4    -      -       -      -
    242F  ASN*     3.9     4.7    -      -       -      +
    282F  CYS*     3.0     2.9    -      -       -      +
    283F  VAL*     2.7    37.4    +      -       +      +
    284F  ASP*     4.2     0.2    +      -       -      -
    304F  ARG*     3.9     1.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 165 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98F  TRP*     4.8     2.0    -      -       -      -
    125F  VAL*     5.2    10.5    -      -       +      -
    127F  THR*     4.3    22.9    -      -       +      -
    164F  VAL*     1.3    83.6    -      -       -      +
    166F  ALA*     1.3    82.0    +      -       -      +
    167F  VAL*     4.7     9.4    -      -       +      -
    239F  TYR*     3.0     4.1    -      -       -      +
    240F  PHE*     2.7    79.6    +      +       +      +
    241F  GLY*     5.6     0.4    -      -       -      -
    261F  THR*     6.0     4.7    -      -       +      -
    281F  SER      2.9    15.7    -      -       -      +
    282F  CYS*     3.4    11.4    -      -       +      +
    304F  ARG*     4.1    25.4    -      -       -      +
    306F  PHE*     4.2    14.1    -      +       +      -
----------------------------------------------------------
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Residues in contact with ALA 166 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98F  TRP*     6.1     1.1    -      -       +      -
    165F  PHE*     1.3    85.6    -      -       -      +
    167F  VAL*     1.3    64.2    +      -       -      +
    168F  GLY      3.9     0.2    -      -       -      -
    172F  LEU*     4.9     6.1    -      -       +      -
    237F  THR*     3.6    14.8    -      -       +      -
    238F  ARG      2.7    20.6    -      -       -      +
    239F  TYR*     3.2    12.8    -      -       +      +
    279F  TYR      3.3     3.8    -      -       -      +
    280F  LEU*     3.6     2.4    -      -       -      -
    281F  SER*     2.7    35.9    +      -       -      +
    306F  PHE*     4.4     1.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 167 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122F  ALA*     4.2    10.8    -      -       +      -
    125F  VAL*     4.0    30.5    -      -       +      -
    165F  PHE*     4.7     6.4    -      -       +      -
    166F  ALA*     1.3    76.8    -      -       -      +
    168F  GLY*     1.3    60.7    +      -       -      +
    237F  THR*     3.3     4.1    -      -       -      -
    238F  ARG*     2.9    24.4    +      -       -      +
    263F  LEU*     4.0    29.4    -      -       +      -
    271F  PRO*     3.7     8.8    -      -       +      +
    278F  LEU*     3.7    24.0    -      -       +      -
    279F  TYR      3.5     2.2    -      -       -      -
    280F  LEU*     4.1    11.0    -      -       +      -
    306F  PHE*     4.5     8.3    -      -       +      -
    308F  ILE*     4.7     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 168 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167F  VAL*     1.3    74.6    -      -       -      +
    169F  GLY*     1.3    55.5    +      -       -      -
    170F  GLU      3.4     8.5    -      -       -      -
    236F  ASN      3.5     6.3    -      -       -      -
    237F  THR*     3.0    22.6    -      -       -      +
    271F  PRO*     4.4     4.9    -      -       -      -
    273F  CYS*     5.3     0.5    -      -       -      -
    278F  LEU*     3.6     9.0    -      -       -      +
    279F  TYR      2.7    43.7    +      -       -      -
----------------------------------------------------------
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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