Contacts of the strand formed by residues 169 - 177 (chain C) in PDB entry 6NMY


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 LEU 169 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133C  PRO*     3.7    37.7    -      -       +      -
    134C  PRO*     4.4     8.7    -      -       +      -
    154C  VAL*     5.7     3.4    -      -       +      -
    156C  LEU*     6.4     1.1    -      -       +      -
    164C  LEU*     3.7    34.5    -      -       +      -
    165C  SER      5.9     0.4    -      -       -      +
    167C  GLY*     3.3    10.5    +      -       -      +
    168C  ASP*     1.3    90.0    -      -       +      +
    170C  GLU*     1.3    63.4    +      -       -      +
    171C  PHE*     4.8    13.8    -      -       +      -
    191C  ASN*     5.5     4.7    -      -       -      +
    214C  THR*     4.9     9.0    -      -       +      -
    215C  ARG      3.4     7.9    -      -       -      +
    216C  LEU*     3.9    11.7    -      -       +      -
    217C  ALA*     4.0     3.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 170 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169C  LEU*     1.3    74.9    -      -       -      +
    171C  PHE*     1.3    67.8    +      -       -      +
    189C  LEU*     3.4    34.7    -      -       +      +
    190C  SER      3.6    13.6    +      -       -      +
    191C  ASN*     4.8    10.8    -      -       -      +
    214C  THR*     3.6     4.9    -      -       -      -
    215C  ARG*     2.9    58.7    +      -       +      +
    216C  LEU      4.4     0.9    -      -       -      +
    217C  ALA*     4.0    12.4    -      -       +      +
    218C  PRO*     3.6    27.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 171 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136C  PRO*     4.5     3.8    -      -       +      -
    152C  TRP*     3.1    48.9    -      +       +      -
    154C  VAL*     5.0    13.7    -      -       +      -
    169C  LEU*     4.8    12.3    -      -       +      -
    170C  GLU*     1.3    84.3    -      -       -      +
    172C  GLU*     1.3    62.3    +      -       -      +
    173C  VAL*     4.0     0.9    -      -       +      -
    188C  LEU      3.6     0.9    -      -       -      +
    189C  LEU*     3.3     9.2    -      -       -      +
    190C  SER*     2.9    41.8    +      -       -      +
    191C  ASN      4.9     1.6    -      -       -      -
    192C  THR*     3.1    28.5    -      -       -      -
    193C  SER*     4.5     7.0    -      -       -      -
    212C  VAL*     5.2     1.8    -      -       +      -
    213C  ARG      3.4     7.2    -      -       -      +
    214C  THR*     3.3    33.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 172 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170C  GLU      4.3     0.2    +      -       -      -
    171C  PHE*     1.3    71.9    -      -       -      +
    173C  VAL*     1.3    61.7    +      -       -      +
    174C  VAL*     4.1    17.8    -      -       +      +
    187C  ILE*     4.2    31.1    -      -       +      +
    188C  LEU      3.7     2.7    -      -       -      -
    189C  LEU*     4.8     4.7    -      -       +      +
    212C  VAL*     3.2     3.2    -      -       -      -
    213C  ARG*     2.9    77.5    +      -       +      +
    215C  ARG*     3.1    33.9    +      -       -      +
    229C  TRP*     3.7     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 173 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150C  LEU*     3.9    21.1    -      -       +      -
    152C  TRP*     4.0    21.1    -      -       +      -
    171C  PHE      4.9     1.8    -      -       -      +
    172C  GLU*     1.3    75.9    -      -       -      +
    174C  VAL*     1.3    68.3    +      -       -      +
    175C  TYR*     4.1     9.6    -      -       +      -
    186C  ALA      3.5     0.7    -      -       -      +
    187C  ILE*     3.4     5.7    -      -       -      +
    188C  LEU*     2.9    49.0    +      -       +      +
    190C  SER*     5.0     2.0    -      -       -      -
    195C  ALA*     4.3    12.8    -      -       +      -
    197C  LEU*     5.7     0.2    -      -       +      -
    210C  ALA*     4.6     8.1    -      -       +      -
    211C  ARG      3.6     4.0    -      -       -      +
    212C  VAL*     3.6    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 174 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172C  GLU*     4.1    13.7    -      -       +      +
    173C  VAL*     1.3    78.2    -      -       -      +
    175C  TYR*     1.3    59.3    +      -       -      +
    182C  TRP*     3.4    25.5    -      -       +      +
    185C  ALA*     3.4    30.3    -      -       +      -
    186C  ALA      3.2     4.0    -      -       -      +
    187C  ILE*     4.2    12.8    -      -       +      -
    210C  ALA*     3.3     2.0    -      -       -      -
    211C  ARG*     2.9    40.9    +      -       +      +
    229C  TRP*     3.4    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 175 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173C  VAL*     4.5     9.2    -      -       +      -
    174C  VAL*     1.3    75.6    -      -       -      +
    176C  LYS*     1.3    63.9    +      -       -      +
    185C  ALA*     3.6     0.4    -      -       -      +
    186C  ALA*     2.9    66.8    +      -       +      +
    187C  ILE      4.4     3.7    +      -       -      -
    188C  LEU*     4.1    20.8    -      -       +      +
    197C  LEU*     3.5    51.1    -      -       +      +
    201C  HIS*     3.6    34.0    +      -       -      +
    202C  LEU*     3.9    14.1    -      -       +      -
    208C  TYR*     4.4     5.8    -      +       +      -
    209C  VAL      3.2    10.3    -      -       -      +
    210C  ALA*     4.2     9.6    -      -       +      -
    235C  TRP*     4.4     4.9    -      -       +      -
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Residues in contact with LYS 176 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175C  TYR*     1.3    77.1    -      -       -      +
    177C  ARG*     1.3    93.0    +      -       -      +
    178C  LEU*     3.8     9.3    +      -       -      +
    180C  ASP*     3.2    34.8    +      -       +      +
    181C  SER      3.3    23.6    -      -       -      +
    182C  TRP*     3.5    40.4    -      -       +      +
    185C  ALA*     3.7    15.3    -      -       +      +
    208C  TYR*     3.5    10.2    -      -       -      -
    209C  VAL*     2.8    48.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 177 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176C  LYS*     1.3   101.9    +      -       -      +
    178C  LEU*     1.3    59.6    +      -       -      +
    179C  GLN*     3.0    38.0    +      -       -      +
    180C  ASP*     2.8    46.8    +      -       -      +
    203C  MET*     3.4    36.8    -      -       +      +
    206C  SER*     4.4    13.4    +      -       -      -
    207C  THR      3.5     7.4    -      -       -      +
    208C  TYR*     3.5    29.2    -      -       +      +
----------------------------------------------------------
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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