Contacts of the strand formed by residues 97 - 100 (chain R) 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 PHE 97 (chain R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86R  ASN*     3.5    25.6    -      -       -      +
     87R  VAL      3.7     1.1    -      -       -      -
     88R  ALA*     4.0    21.1    -      -       +      -
     95R  PRO*     4.5     6.5    -      -       +      -
     96R  LEU*     1.3    77.1    -      -       -      +
     98R  VAL*     1.3    71.8    +      -       -      +
     99R  ARG      4.2     0.4    -      -       -      +
    133R  VAL      4.3     0.7    -      -       -      -
    134R  ILE*     3.2    21.3    -      -       -      +
    135R  LEU*     2.7    42.1    +      -       +      -
    137R  GLY*     3.2    32.1    -      -       -      -
    145R  VAL*     4.1     9.2    -      -       +      -
    146R  PRO*     3.5    27.1    -      -       +      -
    148R  ALA*     5.4     0.9    -      -       +      -
    156R  TYR*     3.5    28.9    -      +       -      +
    180R  LEU*     4.9     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 98 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76R  ILE*     3.7    30.7    -      -       +      -
     78R  LEU*     4.8     7.0    -      -       +      -
     81R  ILE*     3.3    38.0    -      -       +      +
     86R  ASN*     3.9     0.9    +      -       -      -
     87R  VAL      3.3    25.5    +      -       -      +
     89R  PHE*     4.3     8.1    -      -       +      -
     96R  LEU*     4.5     7.4    -      -       +      -
     97R  PHE*     1.3    80.3    -      -       -      +
     99R  ARG*     1.3    60.3    +      -       -      +
    132R  TRP*     4.6    11.7    -      -       +      -
    133R  VAL      3.6     4.5    -      -       -      -
    134R  ILE*     4.0    25.6    -      -       +      -
    193R  VAL*     4.9     2.0    -      -       +      -
    195R  VAL*     5.1     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 99 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84R  GLY      5.9     1.8    -      -       -      -
     85R  LYS      3.4    12.7    -      -       -      +
     86R  ASN*     3.7    22.1    -      -       +      +
     98R  VAL*     1.3    75.0    -      -       -      +
    100R  HIS*     1.3    70.2    +      -       -      +
    101R  ARG*     3.4     6.3    +      -       +      +
    105R  GLU*     3.2    27.0    +      -       -      -
    132R  TRP*     3.2     8.4    -      -       -      -
    133R  VAL*     2.9    54.9    +      -       +      +
    149R  ASN*     3.7    23.1    +      -       -      +
    154R  GLY      2.6    25.3    +      -       -      -
    155R  GLY*     3.1    33.1    +      -       -      -
    156R  TYR*     3.7    24.8    -      -       -      +
    167R  ALA*     4.2     8.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 100 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78R  LEU      5.3     0.7    -      -       -      -
     81R  ILE*     3.1    12.2    +      -       +      +
     82R  PRO*     3.2    16.1    -      -       +      +
     83R  GLU*     2.8    44.3    +      -       +      +
     84R  GLY*     2.8    29.3    +      -       -      -
     85R  LYS      2.8    12.3    +      -       -      +
     99R  ARG*     1.3    71.7    +      -       -      +
    101R  ARG*     1.3    62.9    +      -       -      +
    105R  GLU*     4.5     0.3    -      -       -      +
    131R  GLU*     3.0    35.2    -      -       +      +
    132R  TRP*     3.2    36.0    -      +       +      -
----------------------------------------------------------
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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