Contacts of the strand formed by residues 35 - 42 (chain C) in PDB entry 1S4Y


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 LEU 35 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4C  THR*     5.2     9.2    -      -       -      -
      5C  ARG*     3.2    53.2    +      -       +      +
     27C  CYS*     3.8    27.6    -      -       +      +
     28C  GLU      3.5    11.2    -      -       -      +
     29C  GLY*     3.4    37.2    -      -       -      +
     33C  LYS      3.9    11.4    -      -       -      +
     34C  ARG*     1.3    79.8    -      -       -      +
     36C  HIS*     1.3    67.5    +      -       -      +
     56C  TRP      4.1     4.0    -      -       -      +
     57C  LEU*     5.2     4.0    -      -       +      -
     82C  CYS      4.5     0.2    -      -       -      +
     83C  GLU*     4.2     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 36 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  ARG*     5.5     0.9    -      -       -      -
      7C  CYS*     3.6     4.1    -      -       -      -
     27C  CYS*     4.2     2.1    -      -       -      -
     34C  ARG*     3.8    14.1    -      -       +      +
     35C  LEU*     1.3    75.3    -      -       -      +
     37C  CYS*     1.3    68.8    +      -       -      +
     55C  CYS*     3.4     6.6    -      -       -      +
     56C  TRP*     2.9    35.1    +      -       +      +
     57C  LEU      3.3    24.7    -      -       -      -
     58C  ASP*     3.5     9.3    -      -       -      -
     59C  ASP      3.1    22.6    +      -       -      -
     62C  CYS*     3.1    39.1    -      -       +      +
     63C  TYR*     3.9    10.0    -      +       -      -
     82C  CYS      3.1    10.9    +      -       -      +
     83C  GLU*     3.4    27.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 37 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  ARG*     4.8     2.7    -      -       -      -
      6C  GLU      3.9     3.4    -      -       -      -
      7C  CYS*     2.1    48.0    -      -       -      -
     36C  HIS*     1.3    74.4    -      -       -      +
     38C  TYR*     1.3    60.9    +      -       -      +
     54C  GLY      3.3     6.3    -      -       -      -
     56C  TRP*     4.4     1.6    -      -       -      -
     81C  CYS*     3.2     8.5    -      -       -      +
     82C  CYS*     3.0    30.0    +      -       -      -
     84C  GLY      3.7    11.7    -      -       -      -
     87C  CYS*     3.4    30.1    -      -       -      -
     88C  ASN*     3.6    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 38 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37C  CYS*     1.3    75.0    -      -       -      +
     39C  ALA*     1.3    65.4    +      -       -      +
     40C  SER*     3.9    10.8    -      -       -      -
     52C  LYS*     3.2    42.8    -      -       +      +
     53C  LYS*     3.2     2.9    +      -       -      -
     54C  GLY*     2.9    53.5    +      -       -      -
     55C  CYS      3.5    20.4    -      -       -      -
     56C  TRP*     3.7    14.8    -      +       +      -
     68C  CYS*     4.5     0.7    -      -       -      -
     79C  PHE*     3.7    27.4    -      +       +      -
     80C  CYS      3.2    14.8    -      -       -      +
     81C  CYS*     4.2     0.4    -      -       -      +
     88C  ASN*     2.6    29.8    +      -       -      -
     92D  LEU*     4.7     6.3    -      -       +      -
    102D  LYS*     3.3    32.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 39 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  TYR*     1.3    78.6    -      -       -      +
     40C  SER*     1.3    63.0    +      -       -      +
     41C  TRP*     4.0     3.8    -      -       +      -
     52C  LYS      3.4     7.4    -      -       -      -
     53C  LYS*     4.2    13.7    -      -       +      -
     68C  CYS*     4.0     3.8    -      -       -      -
     79C  PHE*     3.3     5.5    -      -       -      -
     80C  CYS*     3.0    47.6    +      -       -      +
     88C  ASN*     4.5     4.0    -      -       +      -
     91C  PHE*     4.2    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 40 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  TYR*     3.9     2.5    -      -       -      -
     39C  ALA*     1.3    77.6    -      -       -      +
     41C  TRP*     1.3    67.7    +      -       -      +
     50C  LEU*     3.9     4.9    -      -       -      +
     51C  VAL*     2.9    26.0    +      -       -      +
     52C  LYS*     2.8    35.4    +      -       -      +
     77C  VAL*     4.3     6.1    -      -       -      -
     78C  TYR      3.1    14.1    -      -       -      -
     79C  PHE*     4.5     0.2    -      -       -      -
     92D  LEU*     3.6    29.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 41 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39C  ALA*     4.0     6.3    -      -       +      -
     40C  SER*     1.3    89.7    -      -       -      +
     42C  ARG*     1.3    85.7    +      -       -      +
     43C  ASN*     4.3     3.4    -      -       +      +
     48C  ILE*     4.1    19.7    -      -       +      +
     49C  GLU      3.3    12.8    -      -       -      +
     50C  LEU*     4.1     7.2    -      -       +      -
     51C  VAL*     3.9     7.3    -      -       -      +
     70C  ALA*     3.7    12.1    -      -       +      -
     77C  VAL*     3.7     3.7    -      -       -      +
     78C  TYR*     2.9    67.1    +      +       +      -
     80C  CYS*     3.7    23.1    -      -       +      -
     91C  PHE*     3.3    47.3    -      +       +      -
     92C  THR*     3.5    29.6    -      -       -      -
     93C  HIS*     4.6     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 42 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41C  TRP*     1.3    86.4    -      -       -      +
     43C  ASN*     1.3    64.5    +      -       -      +
     44C  SER*     5.1     2.7    -      -       -      +
     47C  THR      4.6     0.2    -      -       -      -
     48C  ILE*     3.5     0.5    -      -       -      -
     49C  GLU*     2.7    66.7    +      -       +      +
     51C  VAL*     3.6     8.6    -      -       +      +
     76C  GLN*     3.8    19.1    +      -       -      +
     77C  VAL*     4.3     6.7    -      -       +      +
     78C  TYR*     4.4     0.9    -      -       -      -
     94D  TYR*     3.7    27.9    +      -       -      -
     98D  GLN      5.4     2.6    +      -       -      -
    100D  ILE*     3.3    29.0    -      -       -      +
----------------------------------------------------------
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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