Contacts of the strand formed by residues 67 - 70 (chain A) in PDB entry 4H3I


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 67 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  ASP      4.5     1.4    -      -       -      +
     66A  ASN*     1.3    94.5    -      -       -      +
     68A  ARG*     1.3    64.7    +      -       -      +
     75A  TYR*     4.6     7.2    -      -       +      -
     76A  TYR*     3.4    16.2    -      -       -      +
     77A  VAL*     3.7    21.5    -      -       +      -
     92A  VAL*     4.0     9.0    -      -       +      -
    213A  LEU*     4.4     4.7    -      -       +      -
    214A  GLN      4.3     0.2    -      -       -      +
    215A  LEU*     3.8    26.2    -      -       +      -
    231A  VAL*     3.8     4.0    -      -       -      +
    232A  GLY*     2.7    28.6    +      -       -      -
    233A  GLY*     3.0    18.0    +      -       -      +
    234A  SER      3.6    25.8    -      -       -      +
    235A  MET*     3.9    13.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  ASN      5.6     1.1    -      -       -      +
     67A  LEU*     1.3    79.2    -      -       -      +
     69A  GLY*     1.3    60.2    +      -       -      +
     75A  TYR*     3.2     8.9    -      -       -      -
     76A  TYR*     2.9    66.0    +      -       +      +
     78A  GLU*     5.4     3.6    +      -       -      +
     89A  ASN*     3.8    14.3    +      -       -      +
    175A  ASN*     4.1     0.2    -      -       -      +
    227A  VAL      4.4     2.0    -      -       -      +
    228A  LEU*     2.8    45.2    +      -       -      +
    229A  ALA      5.4     0.4    -      -       -      -
    230A  SER      3.4    17.9    -      -       -      +
    231A  VAL*     5.0     0.9    -      -       -      -
    232A  GLY      3.9     4.9    -      -       -      +
    501A  TLA      2.7    43.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  ARG*     1.3    77.9    -      -       -      +
     70A  LYS*     1.3    66.9    +      -       -      +
     73A  GLN*     4.9     2.9    -      -       -      -
     74A  GLY      3.4     9.0    -      -       -      -
     75A  TYR*     3.7    11.7    -      -       -      -
     76A  TYR*     4.3     8.9    -      -       -      -
    216A  CYS      5.0     1.6    -      -       -      +
    222A  LEU*     4.5     7.3    -      -       -      +
    227A  VAL*     4.1    24.1    +      -       -      +
    230A  SER      5.3     0.6    +      -       -      -
    232A  GLY*     4.4     7.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  GLY*     1.3    76.5    -      -       -      +
     71A  SER*     1.3    58.1    +      -       -      +
     72A  GLY*     4.5     4.5    -      -       -      +
     73A  GLN*     2.9    46.4    +      -       +      +
     74A  GLY      2.6    37.3    +      -       -      -
     75A  TYR*     3.6    16.3    -      -       -      +
    217A  GLY*     6.3     1.3    -      -       -      -
    218A  ALA      6.3     0.9    -      -       -      +
    221A  PRO*     5.8     0.6    -      -       -      +
    222A  LEU*     3.2    43.5    +      -       +      +
    227A  VAL*     4.4    10.9    -      -       +      +
----------------------------------------------------------
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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