Contacts of the strand formed by residues 137 - 142 (chain A) in PDB entry 3H44


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 137 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  LEU*     3.8    10.4    -      -       -      +
    136A  GLY*     1.3    76.1    -      -       -      -
    138A  SER*     1.3    62.1    +      -       -      +
    151A  PHE*     3.2     4.9    -      -       -      +
    152A  ASP*     2.9    43.1    +      -       -      +
    431A  ARG*     3.1    20.3    +      -       -      -
    892A  ARG*     5.0     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 138 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  PHE*     3.7    10.4    -      -       -      -
    127A  TYR*     2.7    31.9    +      -       -      -
    128A  SER*     6.4     0.9    -      -       -      -
    131A  LEU*     3.6    15.5    -      -       -      -
    137A  SER*     1.3    80.9    +      -       -      +
    139A  ASN*     1.3    69.0    +      -       -      +
    150A  TYR      2.7    17.9    +      -       -      -
    151A  PHE*     4.0     0.9    -      -       -      +
    431A  ARG*     4.0    10.3    +      -       -      +
     20C  GLN*     5.7     1.0    +      -       -      -
     21C  VAL*     5.4     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 139 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  PHE*     4.1    10.2    -      -       -      -
    138A  SER*     1.3    76.9    +      -       -      +
    140A  ALA*     1.3    68.3    +      -       -      +
    149A  TYR*     3.7     0.3    -      -       -      -
    150A  TYR*     3.0    60.4    +      -       +      +
    431A  ARG*     4.1     7.9    -      -       -      +
     19C  ARG*     4.3     6.9    -      -       -      +
     20C  GLN*     2.6    65.5    +      -       -      +
     21C  VAL*     3.8    13.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 140 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  GLN*     3.5    31.9    -      -       +      +
    115A  PHE*     3.8     8.5    -      -       +      -
    139A  ASN*     1.3    85.1    +      -       -      +
    141A  PHE*     1.3    66.3    +      -       -      +
    148A  ASN      3.0    16.2    -      -       -      +
    149A  TYR*     3.7    16.4    -      -       +      -
    150A  TYR*     4.1     3.4    -      -       -      -
     19C  ARG*     3.4    23.5    -      -       -      +
     20C  GLN*     4.4     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 141 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  ASP*     5.3     0.7    -      -       -      -
    111A  GLN*     3.5     3.1    -      -       -      +
    140A  ALA*     1.3    76.0    -      -       -      +
    142A  THR*     1.3    65.6    +      -       -      +
    143A  SER*     4.1    23.1    -      -       -      -
    146A  HIS*     5.1     4.9    -      -       +      -
    147A  THR*     3.5     3.8    -      -       -      +
    148A  ASN*     3.0    70.4    +      -       +      -
    150A  TYR*     4.1    13.5    -      +       -      -
    435A  SER*     4.1     7.9    -      -       -      -
     17C  ARG*     3.7    49.4    -      -       +      +
     18C  SER      3.2    16.6    -      -       -      +
     19C  ARG*     4.3    15.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 142 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  SER*     4.1     8.0    +      -       -      +
    107A  SER*     3.6    23.8    -      -       -      +
    108A  HIS*     3.5    25.4    -      -       +      +
    111A  GLN*     2.7    32.8    +      -       -      +
    141A  PHE*     1.3    74.7    -      -       -      +
    143A  SER*     1.3    69.6    +      -       -      +
    146A  HIS      3.3     2.9    -      -       -      +
    147A  THR*     3.5    17.7    -      -       -      +
     16C  LYS      4.9     0.2    -      -       -      +
     17C  ARG*     3.8     2.3    -      -       -      -
     18C  SER*     3.0    29.9    +      -       -      -
----------------------------------------------------------
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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