Contacts of the strand formed by residues 210 - 220 (chain C) in PDB entry 6A3V


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 GLN 210 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133C  LEU      3.9     0.5    -      -       -      +
    134C  VAL*     3.3     5.0    -      -       -      +
    135C  VAL*     2.9    31.5    +      -       +      -
    167C  LEU*     4.2    21.2    -      -       +      +
    169C  PRO*     3.2    44.8    +      -       -      +
    205C  HIS      4.2     3.6    -      -       -      +
    206C  LEU*     3.5    23.6    -      -       +      -
    207C  SER*     2.6    54.0    +      -       -      +
    208C  ALA      3.3     0.4    -      -       -      -
    209C  GLY*     1.3    78.5    -      -       -      +
    211C  ARG*     1.3    68.0    +      -       -      +
    212C  LEU*     3.9     8.4    -      -       +      +
     60F  ARG*     4.5     6.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 211 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132C  GLU*     3.2    33.9    +      -       +      +
    133C  LEU      3.7     4.5    -      -       -      +
    134C  VAL*     3.9    20.9    -      -       +      -
    166C  HIS      3.6     0.5    -      -       -      +
    167C  LEU*     3.5     5.7    -      -       -      -
    168C  GLN*     3.1    52.8    +      -       +      +
    169C  PRO*     3.9    14.3    -      -       -      +
    209C  GLY      3.2    17.5    -      -       -      -
    210C  GLN*     1.3    77.8    -      -       -      +
    212C  LEU*     1.3    62.5    +      -       -      +
    213C  GLY      4.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 212 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109C  TRP*     5.8     1.0    +      -       -      -
    131C  LYS      4.4     0.3    -      -       -      +
    132C  GLU*     3.2    20.4    -      -       -      +
    133C  LEU*     3.1    39.0    +      -       +      +
    135C  VAL*     3.7    26.9    -      -       +      -
    143C  VAL*     4.8     6.1    -      -       +      -
    165C  LEU*     4.1    26.9    -      -       +      -
    166C  HIS      3.4     4.9    -      -       -      +
    167C  LEU*     3.6    18.6    -      -       +      -
    204C  LEU*     5.9     0.4    -      -       +      -
    206C  LEU*     4.0    22.9    -      -       +      -
    210C  GLN*     3.9    12.1    -      -       +      +
    211C  ARG*     1.3    78.1    -      -       -      +
    213C  GLY*     1.3    59.7    +      -       -      +
    214C  VAL*     5.4     0.4    -      -       -      +
    235C  LEU*     5.3     1.0    -      -       +      +
    237C  LEU*     4.3    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 213 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109C  TRP*     6.0     0.2    -      -       -      -
    131C  LYS      4.2     7.0    -      -       -      -
    132C  GLU*     4.0    12.1    -      -       -      +
    164C  ALA      4.3     0.2    -      -       -      -
    165C  LEU*     3.2     8.1    -      -       -      +
    166C  HIS*     3.0    34.4    +      -       -      -
    168C  GLN*     4.7     9.6    -      -       -      +
    211C  ARG      4.1     0.4    -      -       -      -
    212C  LEU*     1.3    75.1    -      -       -      +
    214C  VAL*     1.3    67.0    +      -       -      +
    215C  HIS*     4.7     7.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 214 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106C  PRO*     3.3     6.0    -      -       -      +
    107C  LEU*     3.0    50.3    +      -       +      -
    109C  TRP*     3.5    31.2    -      -       +      +
    131C  LYS      4.8     3.4    +      -       -      -
    145C  PHE*     3.8    31.4    -      -       +      -
    163C  LEU*     4.2     9.6    -      -       +      -
    164C  ALA      3.2     6.3    -      -       -      +
    165C  LEU*     4.6     1.3    -      -       +      -
    212C  LEU      5.4     0.2    -      -       -      +
    213C  GLY*     1.3    79.7    -      -       -      +
    215C  HIS*     1.3    65.8    +      -       -      +
    235C  LEU*     3.8    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 215 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105C  GLY*     3.7     7.4    -      -       -      -
    106C  PRO*     3.6    36.8    -      -       +      +
    162C  SER      3.6     1.4    -      -       -      +
    163C  LEU*     3.4     4.2    -      -       -      -
    164C  ALA*     2.8    40.7    +      -       +      +
    166C  HIS*     3.7    33.2    +      +       +      -
    168C  GLN*     5.1    12.3    -      -       -      -
    213C  GLY*     4.7     2.4    -      -       -      -
    214C  VAL*     1.3    83.0    +      -       -      +
    216C  LEU*     1.3    60.7    +      -       -      +
    217C  HIS*     3.8     3.9    +      -       +      +
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Residues in contact with LEU 216 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101C  LEU      5.4     3.1    -      -       -      +
    102C  LEU*     3.8    27.6    -      -       +      +
    103C  ILE      4.3     5.8    -      -       -      +
    104C  ASP*     3.2    13.2    -      -       -      +
    105C  GLY      3.0    26.7    +      -       -      +
    107C  LEU*     3.8    20.1    -      -       +      +
    161C  VAL*     3.8    23.3    -      -       +      -
    162C  SER      3.3     3.6    -      -       -      -
    163C  LEU*     3.7    23.6    -      -       +      -
    214C  VAL      4.2     0.4    +      -       -      -
    215C  HIS*     1.3    69.9    -      -       -      +
    217C  HIS*     1.3    60.8    +      -       -      +
    218C  THR*     3.9     7.6    -      -       +      -
    228C  LEU*     3.7    41.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 217 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104C  ASP*     3.3    17.9    +      -       +      -
    160C  SER      4.6     0.2    -      -       -      +
    162C  SER*     2.9    41.4    +      -       -      +
    215C  HIS*     3.8     4.1    +      -       +      +
    216C  LEU*     1.3    73.3    -      -       -      +
    218C  THR*     1.3    61.0    +      -       -      +
    219C  GLU*     3.8    34.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 218 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102C  LEU*     3.2    40.5    -      -       +      +
    104C  ASP*     2.9    17.8    +      -       -      +
    160C  SER      3.4     6.2    +      -       -      -
    161C  VAL*     3.3    35.4    -      -       -      +
    216C  LEU*     3.9     2.5    -      -       +      -
    217C  HIS*     1.3    75.8    -      -       -      +
    219C  GLU*     1.3    65.2    +      -       -      +
    220C  ALA*     4.0     9.2    -      -       -      +
    223C  ARG*     2.9    36.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 219 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159C  GLY*     3.5     2.1    -      -       -      -
    160C  SER*     3.0    37.6    +      -       -      +
    217C  HIS*     3.8    27.1    +      -       +      -
    218C  THR*     1.3    71.7    -      -       -      +
    220C  ALA*     1.3    60.7    +      -       -      +
    223C  ARG*     4.8     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 220 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102C  LEU*     5.0     0.7    -      -       +      -
    158C  SER      3.2    17.9    -      -       -      +
    159C  GLY*     3.9     5.4    -      -       -      -
    185C  LEU*     4.3    11.4    -      -       +      -
    218C  THR*     4.0    14.3    +      -       -      +
    219C  GLU*     1.3    74.6    -      -       -      +
    221C  ARG*     1.3    67.4    +      -       -      +
    223C  ARG*     4.3    26.8    +      -       +      +
    226C  TRP*     6.2     0.2    -      -       +      -
----------------------------------------------------------
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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