Contacts of the strand formed by residues 765 - 771 (chain C) in PDB entry 2X36


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 765 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    760C  THR*     5.2     2.7    -      -       -      -
    764C  VAL*     1.3    83.6    -      -       -      +
    766C  MET*     1.3    70.7    +      -       -      +
    767C  GLY      3.5     1.0    +      -       -      -
    779C  PHE*     3.7     3.3    -      -       -      -
    780C  VAL*     2.9    33.2    +      -       +      +
    859C  THR*     3.8    24.0    -      -       +      +
    862C  THR*     4.1     3.6    -      -       +      -
    863C  ALA*     3.6    31.9    -      -       +      +
    866C  SER*     5.2     0.2    -      -       -      -
    873C  VAL*     3.7    28.0    -      -       +      -
    877C  LEU      5.2     3.1    -      -       -      +
    879C  MET*     4.5    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 766 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    755C  ARG*     3.2    39.3    -      -       -      +
    760C  THR*     5.1     9.2    -      -       +      +
    765C  VAL*     1.3    81.7    -      -       -      +
    767C  GLY*     1.3    59.2    +      -       -      +
    777C  THR*     3.8    22.9    -      -       +      -
    778C  LEU      3.2    12.3    -      -       -      +
    779C  PHE*     3.7    28.8    -      -       +      +
    859C  THR*     3.9     3.5    -      -       -      +
    876C  ASN*     4.0    18.2    -      -       -      +
    877C  LEU      3.4    23.6    +      -       -      +
    878C  ALA*     3.4    29.3    -      -       +      -
    879C  MET      3.4     3.8    +      -       -      -
    905C  ALA*     5.4     0.2    -      -       -      -
    907C  VAL*     4.4     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 767 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    765C  VAL      3.5     2.4    +      -       -      -
    766C  MET*     1.3    75.6    -      -       -      +
    768C  LEU*     1.3    66.3    +      -       -      +
    769C  ALA      4.0     0.2    -      -       -      -
    777C  THR*     3.4     5.7    -      -       -      +
    778C  LEU*     2.8    34.7    +      -       -      -
    780C  VAL*     5.1     2.0    -      -       -      +
    859C  THR*     3.7    17.3    -      -       -      +
    879C  MET      3.4    10.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 768 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    767C  GLY*     1.3    78.1    -      -       -      +
    769C  ALA*     1.3    58.4    +      -       -      +
    776C  SER      3.4     3.6    -      -       -      +
    777C  THR*     3.8    22.7    -      -       +      +
    852C  ASP*     4.1     1.0    -      -       -      +
    855C  SER*     4.2     2.1    +      -       -      -
    878C  ALA*     3.6    19.3    -      -       +      +
    879C  MET*     3.3    36.9    +      -       -      +
    880C  THR*     3.7    12.9    +      -       +      +
    898C  LYS*     3.4    60.8    -      -       +      +
    902C  ALA*     4.1    13.7    -      -       +      +
    910C  ILE*     4.8    11.4    -      -       +      -
    911C  VAL      5.5     0.4    -      -       -      +
    912C  LEU*     5.8     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 769 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    767C  GLY      4.0     0.8    +      -       -      -
    768C  LEU*     1.3    73.7    -      -       -      +
    770C  TRP*     1.3    59.4    +      -       -      +
    771C  THR*     3.4     7.7    +      -       +      -
    775C  GLY*     3.7     4.3    -      -       -      -
    776C  SER      2.7    36.6    +      -       -      +
    778C  LEU*     3.6    32.8    -      -       +      -
    848C  ALA*     4.2    17.7    -      -       +      +
    852C  ASP*     3.4     6.3    -      -       -      +
    898C  LYS*     3.9     6.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 770 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    769C  ALA*     1.3    68.6    -      -       -      +
    771C  THR*     1.3    74.8    +      -       -      +
    774C  GLY      3.9     7.9    -      -       -      -
    775C  GLY*     5.1     0.2    -      -       -      -
    848C  ALA*     3.5     3.4    -      -       -      -
    849C  THR*     3.4    28.9    +      -       +      +
    851C  LYS*     4.5    30.3    -      -       +      -
    852C  ASP*     2.6    39.7    +      -       +      +
    893C  GLY*     3.5    15.3    -      -       -      -
    894C  GLY*     3.4    32.8    -      -       -      -
    897C  GLU*     4.1    25.9    +      -       +      +
    898C  LYS*     3.7     9.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 771 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    769C  ALA*     3.4     3.5    +      -       +      +
    770C  TRP*     1.3    86.9    +      -       -      +
    772C  ALA*     1.3    64.8    +      -       -      +
    773C  MET*     3.4    14.0    +      -       +      +
    774C  GLY      2.8    45.0    +      -       -      +
    775C  GLY      3.8     1.9    +      -       -      -
    776C  SER*     3.6    33.2    -      -       -      +
    847C  GLY*     3.4    28.9    -      -       -      +
    849C  THR*     4.4     1.5    -      -       -      +
----------------------------------------------------------
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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