Contacts of the strand formed by residues 218 - 222 (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 LYS 218 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171A  THR*     6.5     0.2    -      -       -      -
    172A  VAL      3.6     6.5    -      -       -      +
    173A  ASN*     3.9    33.6    -      -       +      +
    213A  ILE*     4.0     0.5    -      -       -      +
    214A  PHE*     3.0    31.5    +      -       -      +
    216A  SER*     3.2    11.1    +      -       -      +
    217A  GLY*     1.3    81.0    -      -       -      +
    219A  MET*     1.3    61.0    +      -       -      +
     15E    A      3.6    34.4    +      -       -      +
     16E    G      3.3    29.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171A  THR*     3.2     9.2    -      -       -      -
    172A  VAL*     3.0    57.9    +      -       +      +
    174A  LEU*     4.1    21.5    -      -       +      -
    211A  ALA*     4.3     2.9    -      -       +      -
    212A  LEU      3.2    13.5    -      -       -      +
    213A  ILE*     4.0    22.4    -      -       +      -
    214A  PHE*     4.9     0.2    -      -       -      -
    217A  GLY      4.7     3.1    -      -       -      +
    218A  LYS*     1.3    78.2    -      -       -      +
    220A  VAL*     1.3    76.6    +      -       -      +
    221A  CYS*     4.8     2.0    -      -       +      +
    234A  ALA*     3.6    27.1    -      -       +      +
    237A  TYR*     3.6    27.4    -      -       +      -
    238A  ALA      4.4     1.3    -      -       -      +
     15E    A      5.4     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 220 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  VAL*     3.7    11.4    -      -       +      -
    170A  SER      3.3    10.3    -      -       -      +
    171A  THR*     4.1     9.0    -      -       +      -
    210A  THR      4.0     0.3    -      -       -      +
    211A  ALA*     3.1     7.8    -      -       -      +
    212A  LEU*     2.8    42.2    +      -       +      +
    214A  PHE*     4.5     4.5    -      -       +      -
    219A  MET*     1.3    79.0    -      -       -      +
    221A  CYS*     1.3    61.5    +      -       -      +
    222A  THR*     4.0    11.7    -      -       +      -
     14E    A      3.5    26.7    -      -       +      +
     15E    A      3.4    43.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 221 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168A  ILE      3.5     1.6    -      -       -      +
    169A  VAL*     3.2     6.1    -      -       -      +
    170A  SER*     2.8    49.1    +      -       -      +
    171A  THR*     4.9     0.4    -      -       -      +
    172A  VAL*     6.4     0.4    -      -       +      -
    209A  THR*     4.3    13.0    -      -       -      -
    210A  THR      3.7     2.7    -      -       -      -
    211A  ALA*     4.5     1.6    -      -       +      +
    219A  MET*     5.4     2.0    -      -       +      -
    220A  VAL*     1.3    72.3    -      -       -      +
    222A  THR*     1.3    66.1    +      -       -      +
    224A  ALA*     5.3     0.9    -      -       -      -
    230A  SER*     3.9    15.7    +      -       -      -
    233A  ALA*     3.8    29.2    -      -       -      -
    234A  ALA*     4.2    16.2    -      -       +      -
    237A  TYR*     4.3     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 222 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168A  ILE      3.5     5.2    -      -       -      -
    169A  VAL*     4.2    13.2    -      -       +      -
    209A  THR*     3.0    26.5    -      -       -      -
    210A  THR*     2.8    28.8    +      -       -      +
    212A  LEU*     5.2     3.6    -      -       +      -
    220A  VAL*     4.0    15.9    -      -       +      +
    221A  CYS*     1.3    80.8    -      -       -      +
    223A  GLY*     1.3    61.7    -      -       -      +
    224A  ALA      3.5     3.1    -      -       -      -
      4F    T      3.6    25.8    -      -       +      +
      5F    T      3.0    34.4    +      -       -      +
----------------------------------------------------------
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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