Contacts of the strand formed by residues 201 - 205 (chain Z) in PDB entry 1NJI


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 GLU 201 (chain Z).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182Z  PHE*     3.6     5.5    -      -       -      -
    183Z  GLU*     3.3    20.1    -      -       +      +
    185Z  VAL*     3.9    21.7    -      -       +      +
    195Z  GLY      4.3     2.8    -      -       -      +
    196Z  VAL*     3.5    16.9    -      -       +      +
    197Z  ASP*     2.6    44.4    +      -       -      +
    198Z  GLY*     3.7    15.6    -      -       -      +
    200Z  THR*     1.3    93.9    -      -       +      +
    202Z  ALA*     1.3    61.5    +      -       -      +
    226Z  ILE*     4.3     5.9    -      -       -      +
    227Z  ARG      4.9     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 202 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182Z  PHE*     3.6    34.5    -      -       +      -
    183Z  GLU      3.1     7.5    +      -       -      +
    184Z  GLU*     3.6     2.4    -      -       -      -
    185Z  VAL*     3.1    25.3    +      -       -      +
    196Z  VAL*     5.4     0.7    -      -       -      -
    201Z  GLU*     1.3    75.8    -      -       -      +
    203Z  VAL*     1.3    61.3    +      -       -      +
    226Z  ILE*     4.6     1.8    -      -       -      -
    227Z  ARG*     3.7    14.1    -      -       +      +
    229Z  LEU*     3.8    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 203 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185Z  VAL*     3.1    29.4    -      -       +      +
    187Z  VAL*     3.5    36.6    -      -       +      -
    193Z  LEU*     4.1    18.2    -      -       +      -
    196Z  VAL*     5.1     5.8    -      -       +      -
    202Z  ALA*     1.3    73.9    -      -       -      +
    204Z  ARG*     1.3    59.2    +      -       -      +
    205Z  ILE*     4.7     1.6    -      -       +      -
    217Z  ILE*     5.4     0.4    -      -       +      -
    221Z  ALA*     5.0     0.4    -      -       +      -
    226Z  ILE*     4.1    12.3    -      -       +      +
    227Z  ARG      2.9    10.5    +      -       -      +
    228Z  VAL*     3.4    29.7    -      -       +      +
    229Z  LEU*     2.9    27.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 204 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    552A    A      2.9    16.8    +      -       -      -
    553A    G      2.5    29.7    +      -       -      -
   1324A    G      3.1    24.8    -      -       -      +
   1325A    G      5.1     4.4    +      -       -      -
   1333A    U      3.8    15.2    +      -       -      +
   1334A    C      3.3    28.9    +      -       -      -
    178Z  HIS*     4.0     0.6    -      -       -      -
    184Z  GLU*     2.5    49.6    +      -       -      +
    185Z  VAL      2.9    13.6    +      -       -      +
    186Z  ARG*     3.6    12.6    -      -       -      +
    187Z  VAL*     2.9    24.9    +      -       -      -
    202Z  ALA      4.3     0.2    +      -       -      -
    203Z  VAL*     1.3    72.7    -      -       -      +
    205Z  ILE*     1.3    61.7    +      -       -      +
    206Z  ALA*     3.3     1.4    +      -       -      -
    229Z  LEU*     3.5    14.9    -      -       +      +
    230Z  ASN*     3.4    13.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 205 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1334A    C      3.9     4.4    -      -       -      +
    187Z  VAL*     3.3    22.7    -      -       +      +
    203Z  VAL*     4.7     2.0    -      -       +      -
    204Z  ARG*     1.3    70.4    -      -       -      +
    206Z  ALA*     1.3    79.0    +      -       -      +
    207Z  SER      3.3     1.2    +      -       -      -
    209Z  VAL*     3.8    23.6    -      -       +      -
    214Z  ARG*     3.5    35.4    -      -       +      +
    217Z  ILE*     3.7    26.9    -      -       +      -
    218Z  GLU*     4.0    22.0    -      -       +      -
    228Z  VAL*     4.1    16.8    -      -       +      -
    230Z  ASN*     3.0    23.5    +      -       -      +
----------------------------------------------------------
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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