Contacts of the strand formed by residues 125 - 131 (chain B) in PDB entry 6MOL


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 VAL 125 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  ALA*     4.0     8.1    -      -       +      +
    124B  PRO*     1.3    81.0    -      -       -      +
    126B  GLY*     1.3    64.3    +      -       -      +
    127B  LEU*     3.4     3.9    +      -       -      +
    142B  TRP*     3.9     2.2    -      -       -      +
    143B  LEU*     2.9    34.8    +      -       +      +
    144B  PRO      3.9    16.8    -      -       -      +
    146B  PRO*     3.9    25.6    -      -       +      -
    213B  SER*     5.3     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 126 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125B  VAL*     1.3    79.8    -      -       -      +
    127B  LEU*     1.3    62.9    +      -       -      +
    128B  VAL*     3.4    10.6    +      -       -      +
    141B  ARG      3.1    14.1    -      -       -      +
    142B  TRP*     3.6     5.5    -      -       -      -
    143B  LEU*     3.9    18.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 127 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125B  VAL*     3.4     2.1    -      -       -      -
    126B  GLY*     1.3    74.9    -      -       -      +
    128B  VAL*     1.3    64.9    +      -       -      +
    140B  LEU*     3.8    25.1    -      -       +      -
    141B  ARG      3.5     2.5    -      -       -      +
    142B  TRP*     3.7    29.2    -      -       +      -
    194B  PHE*     3.5    32.8    -      -       +      +
    195B  ALA*     4.0     2.2    -      -       -      -
    196B  VAL*     4.1    12.1    -      -       +      -
    213B  SER*     3.5    24.7    -      -       -      +
    214B  GLU      3.6    13.7    -      -       -      +
    216B  VAL*     3.3    29.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 128 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126B  GLY*     3.8    11.7    -      -       -      +
    127B  LEU*     1.3    78.7    -      -       -      +
    129B  ALA*     1.3    61.4    +      -       -      +
    130B  ARG*     3.6    42.1    -      -       +      +
    139B  VAL      3.6     2.1    -      -       -      +
    140B  LEU*     3.5     6.0    -      -       -      -
    141B  ARG*     2.9    41.7    +      -       +      +
    216B  VAL*     5.0     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 129 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  VAL*     1.3    72.3    -      -       -      +
    130B  ARG*     1.3    84.2    +      -       -      +
    138B  VAL*     4.2     2.5    -      -       +      -
    139B  VAL      3.6     4.0    -      -       -      -
    140B  LEU*     3.7    17.5    -      -       +      -
    194B  PHE*     4.0    15.9    -      -       +      -
    216B  VAL*     4.0    16.3    -      -       +      +
    218B  LEU*     3.3    34.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 130 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  VAL*     3.6    26.8    -      -       +      +
    129B  ALA*     1.3    93.2    +      -       -      +
    131B  LEU*     1.3    64.7    -      -       -      +
    138B  VAL*     3.3     4.9    -      -       -      +
    139B  VAL*     2.8    46.3    +      -       +      +
    218B  LEU*     3.8    10.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 131 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130B  ARG*     1.3    76.6    -      -       -      +
    132B  ALA*     1.3    63.7    +      -       -      +
    133B  ASP*     3.9     7.6    +      -       -      +
    136B  GLY*     5.2     3.8    -      -       -      +
    137B  HIS      3.7     5.4    -      -       -      +
    138B  VAL*     4.0    22.4    -      -       +      -
    218B  LEU*     4.0    16.7    -      -       +      +
    219B  LEU      3.6    23.3    -      -       -      +
    220B  THR*     4.4     7.6    -      -       +      -
    221B  PRO*     3.9    31.9    -      -       +      -
----------------------------------------------------------
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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