Contacts of the strand formed by residues 774 - 784 (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 GLY 774 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    770C  TRP*     3.7     1.7    -      -       -      -
    771C  THR*     2.8    36.5    +      -       -      +
    772C  ALA      3.6     0.8    -      -       -      -
    773C  MET*     1.3    81.4    -      -       -      +
    775C  GLY*     1.3    59.1    +      -       -      -
    897C  GLU*     3.8    25.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 775 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    769C  ALA      3.7     7.0    -      -       -      -
    771C  THR*     4.2     4.0    +      -       -      -
    774C  GLY*     1.3    76.0    -      -       -      -
    776C  SER*     1.3    57.3    +      -       -      -
    897C  GLU*     3.5    29.4    +      -       -      +
    901C  ALA*     3.3     7.0    -      -       -      -
    904C  ARG*     2.6    28.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 776 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    768C  LEU*     3.4     2.9    -      -       -      +
    769C  ALA*     2.7    39.8    +      -       -      +
    771C  THR*     3.6    19.2    -      -       -      +
    775C  GLY*     1.3    75.7    -      -       -      -
    777C  THR*     1.3    66.5    +      -       -      +
    778C  LEU*     3.2    23.1    +      -       -      +
    901C  ALA*     3.4     9.0    -      -       -      +
    904C  ARG*     3.7     5.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 777 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    755C  ARG*     6.2     0.2    -      -       -      -
    766C  MET*     3.8    33.9    -      -       +      -
    767C  GLY      3.4    12.3    -      -       -      +
    768C  LEU*     3.8    11.1    -      -       +      +
    776C  SER*     1.3    75.7    +      -       -      +
    778C  LEU*     1.3    64.8    +      -       -      +
    779C  PHE*     4.3    13.0    -      -       +      -
    901C  ALA*     3.0    30.7    +      -       -      +
    902C  ALA      3.7     2.1    +      -       -      -
    904C  ARG*     4.7     1.9    +      -       -      +
    905C  ALA*     3.8    16.3    -      -       +      +
    907C  VAL*     4.7     3.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 778 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    766C  MET*     3.2     5.2    -      -       -      +
    767C  GLY*     2.8    38.0    +      -       -      +
    769C  ALA*     3.6    25.8    -      -       +      -
    776C  SER*     3.2    34.0    +      -       -      +
    777C  THR*     1.3    76.2    -      -       -      +
    779C  PHE*     1.3    63.3    +      -       -      +
    780C  VAL*     5.1     2.4    -      -       +      +
    845C  PRO*     3.8    32.8    -      -       +      +
    846C  GLU      3.4    27.4    -      -       -      +
    847C  GLY*     4.1     5.2    -      -       -      -
    848C  ALA*     4.6     2.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 779 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    755C  ARG*     3.3    38.4    -      -       +      -
    756C  MET*     3.7    41.3    -      -       +      -
    757C  TYR*     3.7    28.9    -      +       +      -
    760C  THR*     4.3    10.5    -      -       +      -
    764C  VAL*     3.9    23.3    -      -       +      -
    765C  VAL      3.7     2.0    -      -       -      -
    766C  MET*     3.7    26.5    -      -       +      -
    777C  THR*     4.3    13.9    -      -       +      -
    778C  LEU*     1.3    76.0    -      -       -      +
    780C  VAL*     1.3    60.6    +      -       -      +
    781C  GLU*     3.6     7.4    +      -       -      +
    843C  HIS*     5.2     0.2    +      -       -      -
    845C  PRO*     2.7    31.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 780 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    764C  VAL*     3.2     8.3    -      -       -      +
    765C  VAL      2.9    37.0    +      -       -      +
    767C  GLY*     5.1     3.4    -      -       -      +
    778C  LEU*     3.8     2.9    +      -       +      +
    779C  PHE*     1.3    75.3    -      -       -      +
    781C  GLU*     1.3    62.2    +      -       -      +
    842C  LEU*     3.7    20.6    -      -       +      -
    843C  HIS      3.6     7.4    -      -       -      +
    844C  VAL*     5.1     4.7    -      -       +      -
    845C  PRO*     4.0     9.4    -      -       +      -
    856C  ALA*     5.2     5.4    -      -       +      +
    859C  THR*     3.5    32.3    -      -       +      +
    860C  ILE*     4.6    10.8    -      -       +      -
    863C  ALA*     3.7    25.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 781 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    756C  MET*     3.4    24.9    -      -       +      +
    763C  GLY      3.4     7.4    -      -       -      -
    764C  VAL*     3.9    15.7    -      -       +      -
    779C  PHE      3.6     8.0    +      -       -      +
    780C  VAL*     1.3    82.3    -      -       -      +
    782C  THR*     1.3    63.7    +      -       -      +
    842C  LEU*     3.5     1.7    -      -       -      +
    843C  HIS*     2.7    49.2    +      -       +      +
    845C  PRO*     5.6     0.5    -      -       -      +
    884D  SER*     2.8    19.9    +      -       -      -
    885D  LEU*     3.7    21.2    +      -       +      +
    886D  THR*     2.5    34.8    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 782 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    762C  PRO      5.0     0.7    -      -       -      +
    763C  GLY*     2.9    32.2    +      -       -      +
    781C  GLU*     1.3    69.5    -      -       -      +
    783C  SER*     1.3    65.1    +      -       -      +
    840C  ILE*     4.4     2.0    -      -       +      -
    841C  HIS      3.1    12.3    -      -       -      +
    842C  LEU*     3.4    30.7    -      -       +      -
    863C  ALA*     3.5    16.0    +      -       +      -
    864C  LEU*     3.8    23.8    -      -       +      -
    867C  LEU*     3.7    17.1    -      -       -      +
    885D  LEU*     3.6     3.1    -      -       -      -
    886D  THR*     4.0    13.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 783 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    782C  THR*     1.3    77.2    -      -       -      +
    784C  LEU*     1.3    88.7    +      -       -      +
    840C  ILE*     3.3     4.9    -      -       -      +
    841C  HIS*     2.8    34.4    +      -       -      -
    867C  LEU*     3.9    13.5    -      -       -      -
    819D  THR*     4.1     9.9    -      -       -      +
    823D  ALA*     3.4    17.8    -      -       -      +
    885D  LEU*     4.0    21.1    -      -       -      -
    886D  THR*     5.4     2.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 784 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    783C  SER*     1.3    96.9    +      -       -      +
    785C  ARG*     1.3    56.7    +      -       -      +
    786C  ARG      3.0    26.5    -      -       -      +
    787C  PRO*     4.8    10.3    -      -       +      +
    834C  TYR*     3.5    27.1    +      -       +      +
    838C  SER*     3.7    25.1    -      -       -      -
    839C  HIS      3.1    23.1    -      -       -      +
    840C  ILE*     4.6     1.6    -      -       +      +
    867C  LEU*     4.1     6.9    -      -       -      +
    819D  THR*     3.8     1.6    -      -       -      +
    823D  ALA*     3.7    11.9    -      -       +      +
    826D  MET*     4.0    20.0    -      -       +      -
----------------------------------------------------------
 Back to top of page


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