Contacts of the strand formed by residues 164 - 173 (chain A) in PDB entry 1NVP


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 164 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  VAL*     2.8    39.2    +      -       -      +
    163A  PRO*     1.3    78.4    +      -       -      +
    165A  LEU*     1.3    65.1    +      -       -      +
    166A  GLN*     3.5    20.3    +      -       -      +
    260A  GLY*     3.2     2.0    -      -       -      -
    261A  SER      2.9    31.8    +      -       -      +
    262A  CYS*     6.0     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163A  PRO      3.9     3.3    +      -       -      +
    164A  GLN*     1.3    75.3    -      -       -      +
    166A  GLN*     1.3    62.0    +      -       -      +
    167A  ASN      5.1     0.9    -      -       -      +
    168A  ILE*     4.6     7.2    -      -       +      -
    225A  LYS*     3.4    40.5    -      -       -      +
    227A  GLU*     4.5     1.1    -      -       -      +
    258A  MET*     3.7    30.7    -      -       +      -
    259A  VAL      3.4    14.1    -      -       -      +
    260A  GLY*     4.5     2.0    -      -       -      -
    318A  ARG*     3.5    46.2    -      -       +      +
    321A  ILE*     4.2    28.7    -      -       +      -
    322A  TYR*     5.4     2.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  GLN*     3.5    26.5    +      -       -      +
    165A  LEU*     1.3    77.6    -      -       -      +
    167A  ASN*     1.3    62.8    +      -       +      +
    223A  GLY      4.2     1.0    -      -       -      +
    225A  LYS*     3.0    46.6    +      -       -      +
    259A  VAL*     2.7    18.7    +      -       +      +
    260A  GLY      4.4     0.4    -      -       -      -
    261A  SER*     2.9    33.1    +      -       -      +
      6F    T      3.2    15.6    -      -       -      +
      7F    A      3.6    33.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165A  LEU      3.9     0.4    -      -       -      -
    166A  GLN*     1.3    82.7    -      -       -      +
    168A  ILE*     1.3    73.3    +      -       -      +
    169A  VAL*     4.4     5.7    -      -       -      +
    222A  THR*     4.6     0.2    -      -       -      -
    223A  GLY*     3.0    31.5    +      -       -      -
    224A  ALA      3.4     6.8    +      -       -      -
    225A  LYS*     4.8     0.2    -      -       -      +
    257A  ASN      5.4     0.2    -      -       -      -
    258A  MET*     3.4     0.7    -      -       -      -
    259A  VAL*     2.8    39.0    +      -       +      +
     12E    A      4.9     1.8    -      -       -      -
     13E    A      4.9     0.6    -      -       -      -
      5F    T      2.9    30.2    +      -       -      +
      6F    T      3.0    41.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165A  LEU*     4.6     5.2    -      -       +      -
    167A  ASN*     1.3    82.5    +      -       -      +
    169A  VAL*     1.3    67.4    +      -       -      +
    221A  CYS      3.5     5.4    -      -       -      +
    222A  THR*     3.5     0.5    -      -       -      -
    223A  GLY      3.4    19.9    +      -       -      -
    224A  ALA      3.0    12.9    +      -       -      +
    225A  LYS      3.7     4.0    -      -       -      +
    226A  SER*     3.2    50.5    -      -       -      +
    227A  GLU*     3.6     4.7    -      -       -      +
    230A  SER*     3.7    24.3    +      -       -      +
    255A  ILE*     3.9    22.9    -      -       +      -
    257A  ASN      3.3    10.8    -      -       -      +
    258A  MET*     4.3    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  ASN*     4.4     4.9    -      -       -      +
    168A  ILE*     1.3    78.4    -      -       -      +
    170A  SER*     1.3    59.2    +      -       -      +
    220A  VAL*     3.7    15.3    -      -       +      -
    221A  CYS      3.2     3.4    -      -       -      +
    222A  THR*     4.2     9.4    -      -       +      -
    255A  ILE*     3.7     1.9    -      -       -      -
    256A  GLN*     2.7    39.4    +      -       +      -
    257A  ASN*     2.9    18.1    +      -       +      +
     13E    A      3.6    33.7    -      -       +      +
     14E    A      3.6    29.4    -      -       +      +
      5F    T      3.6    12.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168A  ILE      4.2     0.2    -      -       -      -
    169A  VAL*     1.3    74.9    -      -       -      +
    171A  THR*     1.3    71.2    +      -       -      +
    220A  VAL*     3.3     2.6    -      -       -      +
    221A  CYS*     2.8    45.6    +      -       -      +
    230A  SER*     2.8    26.0    +      -       -      -
    253A  PHE*     3.4    25.6    -      -       -      -
    254A  LYS      3.2    14.4    -      -       -      -
    255A  ILE*     4.1     3.8    -      -       -      -
    256A  GLN      4.2     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 171 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  VAL*     5.3     0.4    -      -       +      -
    170A  SER*     1.3    80.4    -      -       -      +
    172A  VAL*     1.3    67.1    +      -       -      +
    218A  LYS*     6.5     0.2    -      -       -      -
    219A  MET      3.2    12.8    -      -       -      +
    220A  VAL*     4.1     6.7    -      -       +      -
    221A  CYS*     4.9     0.4    -      -       -      +
    234A  ALA*     6.3     0.2    -      -       -      -
    252A  ASP      3.9     2.4    +      -       -      +
    253A  PHE*     3.4     3.8    -      -       -      -
    254A  LYS*     2.9    34.0    +      -       -      +
    256A  GLN*     2.9    35.1    +      -       +      -
     14E    A      3.8    32.8    +      -       +      +
     15E    A      4.9     6.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 172 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171A  THR*     1.3    79.9    -      -       -      +
    173A  ASN*     1.3    64.2    +      -       -      +
    174A  LEU*     3.9     3.9    +      -       +      -
    218A  LYS*     3.6     3.5    -      -       -      +
    219A  MET*     3.0    64.4    +      -       +      +
    221A  CYS*     6.4     0.2    -      -       +      -
    234A  ALA*     4.4     6.5    -      -       +      -
    250A  PHE*     3.8    38.1    -      -       +      -
    251A  LEU      3.3    18.2    -      -       -      +
    252A  ASP      4.2     3.1    -      -       -      -
    253A  PHE*     3.9    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 173 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172A  VAL*     1.3    73.6    -      -       -      +
    174A  LEU*     1.3    64.2    +      -       -      +
    175A  GLY*     2.8    29.1    +      -       -      +
    216A  SER      4.9     2.1    -      -       -      +
    217A  GLY*     3.8     8.1    -      -       -      +
    218A  LYS*     3.9    33.7    -      -       +      +
    251A  LEU*     2.8    58.8    +      -       +      +
    252A  ASP*     4.8     9.1    +      -       +      +
----------------------------------------------------------
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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