Contacts of the strand formed by residues 87 - 98 (chain D) 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 LEU 87 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80D  GLU*     4.0     8.1    -      -       +      +
     81D  PHE      4.0     4.3    -      -       -      +
     82D  ARG*     3.3    28.4    -      -       -      +
     86D  GLU*     1.3    76.0    -      -       +      +
     88D  ILE*     1.3    73.0    +      -       -      +
     89D  LYS*     3.2    51.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 88 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358C  MET*     6.0     1.6    -      -       +      -
    360C  LEU*     3.7    30.5    -      -       +      -
    361C  ASN*     3.7    20.9    -      -       -      +
    365C  TYR*     3.4    44.9    -      -       +      +
     79D  VAL      3.9     0.5    -      -       -      +
     80D  GLU*     3.5     2.8    -      -       -      -
     81D  PHE*     2.8    53.6    +      -       +      +
     83D  GLU*     5.2     9.4    -      -       +      +
     86D  GLU      4.4     5.6    -      -       -      +
     87D  LEU*     1.3    81.8    -      -       -      +
     89D  LYS*     1.3    63.6    +      -       -      +
     90D  VAL*     5.8     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 89 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361C  ASN*     3.3    22.2    +      -       -      +
     79D  VAL      3.5     4.0    -      -       -      +
     80D  GLU*     3.3    34.1    +      -       +      +
     87D  LEU*     3.2    47.6    -      -       +      +
     88D  ILE*     1.3    73.2    -      -       -      +
     90D  VAL*     1.3    61.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 90 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333C  ASN*     3.0    28.9    -      -       +      +
    360C  LEU*     5.0     5.2    -      -       +      -
    361C  ASN*     4.4     9.2    -      -       -      +
     78D  ASP*     3.3     2.9    -      -       -      -
     79D  VAL*     2.8    49.8    +      -       +      +
     81D  PHE*     3.6    31.9    -      -       +      -
     88D  ILE*     5.8     0.2    -      -       +      -
     89D  LYS*     1.3    76.2    -      -       -      +
     91D  ASP*     1.3    65.2    +      -       -      +
     92D  LYS      3.0    25.8    -      -       -      +
     93D  VAL*     4.2     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 91 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77D  ASN*     3.1    15.2    +      -       -      +
     78D  ASP*     2.9    33.4    +      -       -      +
     90D  VAL*     1.3    78.7    -      -       -      +
     92D  LYS*     1.3    61.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 92 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332C  GLU*     6.5     0.9    -      -       +      -
    333C  ASN*     2.7    36.3    +      -       -      +
     75D  VAL*     4.5    16.6    -      -       +      -
     76D  LEU      3.3     9.0    -      -       -      +
     77D  ASN*     3.8    11.7    -      -       -      +
     90D  VAL*     3.0     8.2    -      -       -      +
     91D  ASP*     1.3    86.6    -      -       +      +
     93D  VAL*     1.3    65.2    +      -       -      +
     94D  LYS*     6.2     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 93 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333C  ASN*     3.6    17.7    -      -       +      +
    335C  VAL*     4.0    19.5    -      -       +      -
    360C  LEU*     4.3     4.7    -      -       +      -
     75D  VAL*     3.3     3.4    -      -       -      -
     76D  LEU*     2.9    43.6    +      -       +      +
     79D  VAL*     3.4    28.9    -      -       +      -
     81D  PHE*     3.8    27.8    -      -       +      -
     90D  VAL*     4.2     5.2    -      -       +      -
     92D  LYS*     1.3    79.8    -      -       -      +
     94D  LYS*     1.3    66.8    +      -       -      +
     95D  ILE*     4.1     5.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 94 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332C  GLU*     3.7    22.8    +      -       +      +
    333C  ASN      3.1    13.0    +      -       -      +
    334C  VAL*     3.3    11.6    -      -       +      +
    335C  VAL      2.9    25.6    +      -       -      +
     73D  THR*     4.2    22.3    -      -       +      +
     74D  PHE      3.4    12.1    -      -       -      +
     75D  VAL*     4.3    14.7    -      -       +      +
     92D  LYS*     5.3     1.8    -      -       +      +
     93D  VAL*     1.3    72.5    -      -       -      +
     95D  ILE*     1.3    63.2    +      -       -      +
     96D  VAL*     4.3    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 95 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    335C  VAL*     3.4    35.0    -      -       +      +
    337C  CYS*     4.2    15.3    -      -       -      -
    351C  PHE*     5.8     0.7    -      -       +      -
    353C  LEU*     4.2    11.4    -      -       +      -
     58D  PHE*     3.8    34.5    -      -       +      -
     72D  TRP      3.5     1.7    -      -       -      +
     73D  THR*     3.2     4.9    -      -       -      -
     74D  PHE*     2.8    55.8    +      -       +      -
     76D  LEU*     4.2    17.9    -      -       +      -
     81D  PHE*     5.2     2.5    -      -       +      -
     93D  VAL*     4.4     9.4    -      -       +      +
     94D  LYS*     1.3    78.8    -      -       -      +
     96D  VAL*     1.3    65.9    +      -       -      +
     97D  ALA*     4.7     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 96 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334C  VAL*     5.3     2.9    -      -       +      -
    335C  VAL      2.9    11.0    +      -       -      +
    336C  VAL*     3.5    12.1    -      -       +      -
    337C  CYS*     3.0    25.7    +      -       -      +
      5D  LEU*     4.4    12.1    -      -       +      +
     71D  VAL*     4.0    21.3    -      -       +      -
     72D  TRP      3.4     3.6    -      -       -      +
     73D  THR*     4.4    11.2    -      -       +      +
     94D  LYS*     4.3    26.2    -      -       +      +
     95D  ILE*     1.3    75.8    -      -       -      +
     97D  ALA*     1.3    64.1    +      -       -      +
     98D  CYS*     4.4     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 97 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    337C  CYS*     3.1    23.1    -      -       -      +
    339C  TYR*     3.3    30.9    -      -       +      +
    353C  LEU*     4.4     5.6    -      -       +      -
     71D  VAL*     3.5     4.3    -      -       -      -
     72D  TRP*     2.7    45.3    +      -       +      +
     74D  PHE*     5.3     1.6    -      -       +      -
     95D  ILE*     4.7     4.9    -      -       +      -
     96D  VAL*     1.3    77.4    -      -       -      +
     98D  CYS*     1.3    62.9    +      -       -      +
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Residues in contact with CYS 98 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    337C  CYS      3.0     7.9    +      -       -      +
    338C  GLN*     2.8     9.5    -      -       +      -
    339C  TYR*     2.7    30.5    +      -       -      -
      3D  TYR*     3.7    33.2    -      -       +      -
      5D  LEU*     3.4    30.9    -      -       +      +
     70D  ASN      4.4     4.0    -      -       -      -
     71D  VAL*     3.9    23.6    -      -       +      -
     96D  VAL*     5.6     0.4    -      -       -      -
     97D  ALA*     1.3    73.4    -      -       -      +
     99D  ASP*     1.3    56.8    +      -       -      +
----------------------------------------------------------
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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