Contacts of the strand formed by residues 95 - 101 (chain B) in PDB entry 3H1J


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 SER 95 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46B  ARG*     5.4     0.9    +      -       -      -
     89B  ILE*     3.4     7.2    -      -       -      +
     94B  GLY*     1.3    74.1    -      -       -      -
     96B  LEU*     1.3    63.2    +      -       -      +
     97B  SER*     5.0     4.8    +      -       -      -
    108B  CYS      4.8     0.6    +      -       -      -
    109B  VAL*     3.2    27.8    -      -       -      +
    110B  GLU*     3.1    33.3    +      -       -      +
    119B  VAL*     5.7     0.6    -      -       -      +
     71I  ASN*     3.0    22.9    -      -       -      -
     72I  ALA*     6.2     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 96 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73B  SER*     4.4    15.0    -      -       -      +
     85B  ILE*     4.3     9.6    -      -       +      -
     89B  ILE*     3.6    27.1    -      -       +      -
     95B  SER*     1.3    76.7    -      -       -      +
     97B  SER*     1.3    81.2    +      -       -      +
     98B  VAL*     5.1     4.5    -      -       +      -
    107B  TYR*     5.3     4.9    -      -       +      -
    108B  CYS      3.9     9.2    -      -       -      +
    109B  VAL*     3.9    19.5    -      -       +      -
    122B  TYR*     5.2     2.9    -      -       +      +
    123B  LEU*     4.5     8.3    -      -       +      -
    126B  VAL*     4.1    25.4    -      -       +      -
     69I  SER*     3.5     0.2    -      -       -      -
     70I  LEU*     2.8    44.2    +      -       +      +
     71I  ASN*     3.7     5.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 97 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46B  ARG*     6.0     0.4    +      -       -      -
     95B  SER*     5.0     4.9    +      -       -      -
     96B  LEU*     1.3    82.2    +      -       -      +
     98B  VAL*     1.3    69.9    +      -       -      +
     99B  TYR*     3.6    33.3    +      -       -      -
    106B  THR      3.8     0.7    -      -       -      +
    107B  TYR*     3.7     0.2    -      -       -      -
    108B  CYS*     3.2    34.2    +      -       -      +
     68I  ILE      3.2    12.8    -      -       -      -
     69I  SER*     3.3    16.3    +      -       -      +
     71I  ASN*     4.9     1.4    +      -       -      -
     72I  ALA*     5.2     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70B  ARG*     3.9    31.0    -      -       +      +
     73B  SER*     3.8    26.2    -      -       -      +
     96B  LEU*     5.1     2.2    -      -       +      -
     97B  SER*     1.3    81.9    -      -       -      +
     99B  TYR*     1.3    68.5    +      -       -      +
    105B  MET*     5.0     5.2    -      -       +      -
    106B  THR      3.5     4.0    -      -       -      +
    107B  TYR*     3.7    49.1    -      -       +      -
     66I  ALA      3.8     1.0    -      -       -      +
     67I  GLY*     3.3     1.0    -      -       -      -
     68I  ILE*     2.6    39.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46B  ARG*     3.4    18.2    +      -       -      -
     97B  SER*     3.6    27.6    +      -       -      -
     98B  VAL*     1.3    75.0    -      -       -      +
    100B  SER*     1.3    61.1    +      -       -      +
    105B  MET*     3.6     0.2    -      -       -      -
    106B  THR*     2.7    51.9    +      -       +      +
    108B  CYS*     3.6    24.5    -      -       -      -
    376B  GLN*     3.6    30.9    +      -       +      -
     65I  VAL*     4.1    15.7    -      -       +      -
     66I  ALA      3.2     8.3    -      -       -      +
     67I  GLY*     4.0    14.8    -      -       -      -
     69I  SER*     5.8     1.1    -      -       -      -
     75I  SER*     4.4    10.5    -      -       -      -
     77I  ARG*     5.6     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 100 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  GLY*     6.0     0.2    -      -       -      -
     70B  ARG*     3.0    40.2    +      -       -      -
     98B  VAL*     5.2     0.4    -      -       -      -
     99B  TYR*     1.3    76.7    -      -       -      +
    101B  THR*     1.3    67.2    +      -       -      +
    104B  LYS      2.9    14.4    -      -       -      -
    105B  MET*     3.7    26.3    -      -       -      +
    176B  LEU*     3.8     8.9    -      -       -      +
     65I  VAL*     4.1     1.6    -      -       -      +
     66I  ALA*     2.8    32.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  GLY*     4.3     6.1    -      -       -      -
     55B  SER      4.4     0.2    +      -       -      -
    100B  SER*     1.3    80.0    -      -       -      +
    102B  ARG*     1.3    66.8    +      -       -      +
    103B  GLU*     2.9     8.8    +      -       -      +
    104B  LYS*     2.8    46.1    +      -       +      +
    176B  LEU*     3.6     9.7    -      -       -      +
    316B  TYR*     5.3     8.2    -      -       -      -
     63I  ASP*     4.0    11.7    -      -       -      +
     64I  LEU      4.1    10.3    -      -       -      -
     65I  VAL*     3.8    30.3    -      -       +      -
----------------------------------------------------------
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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