Contacts of the strand formed by residues 30 - 35 (chain B) in PDB entry 1H1B


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 MET 30 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  TRP*     2.9    18.6    +      -       +      +
     28B  PRO      3.3     2.8    -      -       -      +
     29B  PHE*     1.3    83.0    -      -       +      +
     31B  VAL*     1.3    82.7    +      -       -      +
     43B  GLY*     4.2     4.7    -      -       -      -
     44B  ALA      3.9     1.8    -      -       -      +
     45B  THR*     5.2     0.2    -      -       -      +
     67B  VAL      4.6     0.5    -      -       -      +
     69B  GLY      4.4    13.5    +      -       -      -
     70B  ALA      5.1     3.2    +      -       -      +
    139B  MET*     3.9    18.2    -      -       -      +
    140B  GLY*     4.1    11.9    -      -       -      -
    141B  TRP*     3.7    30.5    -      -       +      +
    155B  LEU*     3.9    23.1    -      -       +      -
    197B  SER*     3.8    25.1    -      -       -      +
    198B  PRO*     3.5    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 31 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  PHE      3.5    13.0    -      -       -      +
     30B  MET*     1.3    87.7    -      -       -      +
     32B  SER*     1.3    66.9    +      -       -      +
     33B  LEU*     4.2     0.4    -      -       +      -
     43B  GLY*     3.2     6.8    -      -       -      -
     44B  ALA*     2.8    51.3    +      -       +      +
     45B  THR      4.2     0.4    -      -       -      -
     46B  LEU*     3.7    18.8    -      -       +      +
     52B  VAL*     4.3     2.9    -      -       +      -
     66B  VAL*     3.5    30.3    -      -       +      -
     67B  VAL      3.4    13.2    -      -       -      +
     68B  LEU*     3.7    20.9    -      -       +      -
    141B  TRP*     3.9     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 32 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  VAL*     1.3    71.5    -      -       -      +
     33B  LEU*     1.3    62.0    +      -       -      +
     34B  GLN*     3.0    25.6    +      -       -      +
     40B  HIS*     3.0    20.1    +      -       -      -
     42B  CYS      3.9     2.9    -      -       -      -
     65B  ARG      3.6     1.2    -      -       -      +
     67B  VAL*     2.9    45.1    +      -       -      +
     70B  ALA*     5.1     0.2    -      -       -      -
     73B  LEU*     3.8    10.3    -      -       -      +
    141B  TRP*     3.6    22.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 33 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  VAL*     4.2     0.4    -      -       +      -
     32B  SER*     1.3    73.0    -      -       -      +
     34B  GLN*     1.3    57.3    +      -       -      +
     40B  HIS*     3.6     3.1    -      -       -      -
     41B  PHE*     3.0    48.6    +      -       +      -
     42B  CYS*     2.8    27.3    +      -       +      +
     43B  GLY      3.7     4.9    -      -       -      +
     44B  ALA*     4.0    20.6    -      -       +      -
     52B  VAL*     5.1     0.7    -      -       +      -
     54B  SER*     3.7    27.6    -      -       -      +
     58B  CYS*     5.0     4.0    -      -       +      -
     59B  VAL*     5.1     4.7    -      -       +      -
     65B  ARG*     3.5     9.2    -      -       +      +
     66B  VAL*     3.9    37.9    -      -       +      -
    106B  LEU*     4.6    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 34 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  SER*     3.0    21.0    +      -       -      +
     33B  LEU*     1.3    77.6    -      -       -      +
     35B  LEU*     1.3    62.5    +      -       -      +
     36B  ARG      4.6     4.9    +      -       -      +
     38B  GLY*     3.8    22.8    +      -       -      -
     39B  GLY      3.3    14.4    -      -       -      +
     40B  HIS*     4.2     7.2    -      -       -      -
     41B  PHE*     3.5     5.6    -      -       -      -
     64B  ALA      4.0     0.5    -      -       -      +
     65B  ARG*     2.9    47.9    +      -       -      +
     67B  VAL*     3.7    29.6    -      -       +      +
     73B  LEU*     3.7    18.4    -      -       -      +
     80B  ARG*     5.2     7.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 35 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  GLN*     1.3    74.9    -      -       -      +
     36B  ARG*     1.3    98.6    +      -       -      +
     39B  GLY*     3.1    15.2    +      -       -      +
     41B  PHE*     3.7    15.2    -      -       +      -
     62B  ASN*     3.9    38.6    -      -       +      +
     64B  ALA*     3.5    43.5    -      -       +      +
     65B  VAL*     3.5    20.4    -      -       +      +
----------------------------------------------------------
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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