Contacts of the strand formed by residues 237 - 250 (chain C) in PDB entry 4SBV


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 237 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79C  ALA*     3.0     2.1    -      -       -      -
     80C  VAL*     2.6    46.5    +      -       +      +
    127C  THR*     4.1    23.6    -      -       +      -
    231C  GLY      5.0     3.8    -      -       -      +
    232C  SER*     6.2     0.7    -      -       -      -
    233C  SER*     3.8    32.1    -      -       -      +
    235C  THR      3.8     0.7    -      -       -      +
    236C  ALA*     1.3    75.1    -      -       -      +
    238C  ASN*     1.3    72.6    -      -       -      +
    239C  THR*     3.5     3.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 238 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78C  LEU      4.2     3.3    -      -       -      +
     79C  ALA*     3.4    16.7    -      -       +      +
    122C  SER*     5.6     1.3    -      -       -      -
    123C  CYS*     4.4     9.9    +      -       -      +
    236C  ALA*     5.1     5.6    +      -       -      +
    237C  VAL*     1.3    83.3    -      -       -      +
    239C  THR*     1.3    62.2    -      -       -      +
    240C  GLY      6.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 239 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78C  LEU*     3.0    18.3    +      -       +      -
     79C  ALA*     4.6     1.6    -      -       -      -
     80C  VAL*     4.3     6.5    -      -       -      +
    119C  TYR*     2.3    34.5    -      -       +      +
    122C  SER*     2.8    34.3    +      -       -      -
    123C  CYS*     3.4    10.2    +      -       -      -
    127C  THR*     4.8     4.0    -      -       -      +
    161C  VAL*     2.8    51.9    -      -       +      +
    228C  MET*     5.5     1.1    -      -       -      -
    237C  VAL*     3.5     7.7    +      -       -      +
    238C  ASN*     1.3    74.3    +      -       -      +
    240C  GLY*     1.3    57.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 240 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77C  GLU*     4.1     3.6    -      -       -      +
     78C  LEU*     3.2    22.4    +      -       -      +
    119C  TYR*     3.2    14.1    -      -       -      -
    120C  LEU      2.9    18.4    -      -       -      -
    121C  PRO      4.3     0.2    -      -       -      -
    122C  SER*     4.1     4.7    -      -       -      -
    238C  ASN*     6.0     0.2    -      -       -      +
    239C  THR*     1.3    83.8    +      -       -      +
    241C  ARG*     1.3    66.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 241 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51C  THR*     5.1     8.9    +      -       -      -
     53C  VAL*     4.5    13.5    -      -       -      +
     74C  LEU*     4.3    12.4    -      -       +      +
     76C  THR      3.5    14.6    -      -       -      +
     77C  GLU*     4.1    18.4    -      -       +      +
     78C  LEU*     4.3     3.8    -      -       -      +
    119C  TYR*     3.6     3.9    -      -       -      -
    120C  LEU*     2.9    45.2    +      -       -      +
    121C  PRO      4.2     4.6    +      -       -      -
    122C  SER*     3.6    23.0    +      -       -      -
    240C  GLY*     1.3    75.6    -      -       -      +
    242C  LEU*     1.3    65.6    -      -       -      +
    243C  TYR*     3.2    37.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 242 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74C  LEU*     3.4     2.9    -      -       -      +
     75C  SER*     2.8    42.6    +      -       -      +
     76C  THR*     3.0    39.7    +      -       +      +
     78C  LEU*     4.5    13.4    -      -       +      +
    117C  TYR*     4.3    22.0    -      -       +      -
    118C  THR      3.2    13.9    -      -       -      +
    119C  TYR*     3.8     9.6    -      -       +      -
    131C  ILE*     5.1     0.9    -      -       +      -
    133C  MET*     3.4    40.6    -      -       +      -
    224C  LEU*     5.1     5.2    -      -       +      -
    226C  THR*     5.5     2.5    -      -       -      +
    241C  ARG*     1.3    78.2    -      -       -      +
    243C  TYR*     1.3    59.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 243 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53C  VAL*     4.0    20.3    -      -       +      +
     55C  LEU*     4.9     7.6    -      -       +      -
     72C  CYS*     4.3     7.4    -      -       -      -
     73C  GLU      3.5     8.1    -      -       -      +
     74C  LEU*     3.5    36.4    -      -       +      +
     75C  SER*     4.1     2.9    -      -       -      +
    116C  ARG      3.1     4.2    -      -       -      +
    117C  TYR*     3.3     4.0    -      -       -      -
    118C  THR*     2.7    34.0    +      -       -      +
    120C  LEU*     3.8    30.3    -      -       +      -
    171C  VAL*     3.6    35.2    -      -       +      -
    241C  ARG*     3.2    46.0    +      -       +      -
    242C  LEU*     1.3    79.9    -      -       -      +
    244C  ALA*     1.3    60.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 244 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72C  CYS*     3.0     8.3    -      -       -      +
     73C  GLU*     2.9    35.7    +      -       +      +
     75C  SER*     4.5     5.0    -      -       -      -
     96C  VAL*     3.6    35.7    -      -       +      +
    115C  ILE*     4.9     2.2    -      -       +      -
    116C  ARG      3.1     7.2    -      -       -      +
    117C  TYR*     4.0    16.8    -      -       +      -
    243C  TYR*     1.3    73.8    -      -       -      +
    245C  SER*     1.3    63.5    -      -       -      +
    246C  TYR*     4.2     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 245 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71C  HIS      3.4     6.3    -      -       -      -
     72C  CYS*     3.9    13.9    -      -       -      -
    114C  ALA*     3.7     2.5    -      -       -      +
    115C  ILE*     3.1     4.0    +      -       -      -
    116C  ARG*     2.6    58.9    +      -       -      +
    118C  THR*     3.8    12.1    -      -       -      +
    170C  PHE      4.3    14.3    +      -       -      -
    171C  VAL*     5.5     0.2    -      -       -      +
    244C  ALA*     1.3    79.3    -      -       -      +
    246C  TYR*     1.3    59.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 246 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69C  LEU*     4.2     9.2    -      -       +      -
     70C  SER*     3.2     2.3    +      -       -      -
     71C  HIS*     3.1    64.4    +      -       +      +
     72C  CYS*     4.1     4.9    -      -       -      -
     73C  GLU*     2.5    38.2    +      -       +      -
     96C  VAL*     4.6    14.4    -      -       +      -
     99C  TRP*     4.4     2.4    -      -       -      -
    100C  LEU*     3.5    44.2    +      -       +      +
    112C  TRP*     3.5    20.0    -      +       +      -
    114C  ALA*     2.8    14.8    -      -       -      +
    115C  ILE*     4.2     4.3    -      -       +      -
    244C  ALA      4.4     1.3    -      -       -      -
    245C  SER*     1.3    79.7    -      -       -      +
    247C  THR*     1.3    68.7    +      -       -      +
    248C  ILE*     4.3    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 247 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68C  ILE*     3.6    25.4    -      -       +      -
     69C  LEU      3.2     3.4    -      -       -      +
     70C  SER*     2.4    28.1    +      -       -      +
    112C  TRP*     3.6     0.7    -      -       -      -
    113C  VAL*     2.6    58.4    +      -       +      +
    114C  ALA*     2.8    20.2    +      -       -      +
    246C  TYR*     1.3    74.3    +      -       -      +
    248C  ILE*     1.3    57.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 248 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68C  ILE*     3.6     4.3    -      -       -      +
     69C  LEU*     2.9    51.5    +      -       +      +
     93C  PRO*     4.2    13.2    -      -       +      -
    100C  LEU*     4.1    26.7    -      -       +      -
    104C  ALA*     4.6     1.8    -      -       +      -
    110C  TYR*     3.9    15.7    -      -       +      -
    111C  ALA      3.5    10.1    -      -       -      +
    112C  TRP*     4.0    21.3    -      -       +      -
    113C  VAL*     4.1     4.0    -      -       -      +
    246C  TYR*     4.3     5.8    -      -       +      -
    247C  THR*     1.3    77.8    -      -       -      +
    249C  ARG*     1.3    62.3    +      -       -      +
    250C  LEU*     3.6    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 249 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191B  GLU*     2.6    35.4    +      -       -      -
     66C  VAL*     3.3    28.6    -      -       +      +
     67C  THR      3.7     1.8    -      -       -      -
     68C  ILE*     3.5    21.8    -      -       +      -
    110C  TYR*     3.1    26.6    -      -       -      +
    111C  ALA*     2.7    29.0    +      -       +      +
    113C  VAL*     4.0    10.1    -      -       +      +
    196C  ARG*     2.8    19.8    -      -       -      +
    248C  ILE*     1.3    70.4    -      -       -      +
    250C  LEU*     1.3    63.1    +      -       -      +
    251C  ILE*     3.0    22.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 250 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66C  VAL*     3.6     0.3    -      -       -      -
     67C  THR*     2.6    45.4    +      -       +      +
     69C  LEU*     4.7     9.4    -      -       +      -
    103C  VAL*     4.5     7.6    -      -       +      -
    104C  ALA*     4.0    18.4    -      -       +      +
    107C  TRP*     3.3    57.9    -      -       +      -
    109C  LYS      4.4     1.1    -      -       -      -
    110C  TYR*     4.0     6.1    -      -       +      -
    248C  ILE*     3.6    36.8    -      -       +      +
    249C  ARG*     1.3    80.2    -      -       -      +
    251C  ILE*     1.4    75.1    -      -       -      +
----------------------------------------------------------
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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