Contacts of the strand formed by residues 97 - 104 (chain A) in PDB entry 2N0K


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 VAL 97 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  VAL*     3.0    12.0    -      -       -      +
     94A  LEU*     2.8    52.7    +      -       +      +
     95A  GLY      3.2     3.5    +      -       -      +
     96A  ASP*     1.3    90.5    -      -       -      +
     98A  ILE*     1.3    66.8    +      -       -      +
     99A  GLU*     4.2     4.3    -      -       +      +
    121A  LYS*     3.1    39.7    -      -       +      -
    122A  TYR      4.0     2.7    -      -       -      +
    123A  ARG*     3.6    26.7    -      -       +      +
    124A  ILE*     4.4     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  PHE*     3.9    17.9    -      -       +      -
     91A  VAL*     5.5     2.0    -      -       +      -
     92A  LYS      3.7     6.1    -      -       -      +
     93A  VAL*     4.1    13.0    -      -       +      -
     97A  VAL*     1.3    77.1    -      -       -      +
     99A  GLU*     1.3    51.2    +      -       -      +
    100A  VAL*     3.8    12.8    -      -       +      -
    120A  ARG      2.6    24.4    -      -       -      +
    121A  LYS*     4.1     0.4    -      -       -      -
    122A  TYR*     2.7    68.5    +      -       +      +
    124A  ILE*     3.6    29.8    -      -       +      -
    133A  ILE*     4.2     5.8    -      -       +      -
    145A  VAL*     4.2    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  LYS*     2.6    47.6    +      -       +      +
     93A  VAL*     4.2     0.2    -      -       -      +
     94A  LEU*     3.7    18.3    -      -       +      +
     97A  VAL*     3.9     4.1    -      -       +      -
     98A  ILE*     1.3    69.5    -      -       -      +
    100A  VAL*     1.3    57.4    +      -       -      +
    101A  HIS*     2.9    17.9    +      -       +      +
    119A  HIS*     3.7    35.7    -      -       -      +
    120A  ARG      3.3     4.0    -      -       -      -
    121A  LYS*     3.6    42.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  LEU*     3.7    22.7    -      -       +      -
     89A  LEU*     3.6    28.5    -      -       +      -
     90A  LYS      3.8     3.8    -      -       -      -
     91A  VAL*     4.1    18.2    -      -       +      +
     98A  ILE*     3.8    13.5    -      -       +      -
     99A  GLU*     1.3    66.8    -      -       -      +
    101A  HIS*     1.3    52.2    +      -       -      +
    102A  GLY      2.5    18.0    +      -       -      -
    120A  ARG*     3.0    43.2    +      -       +      +
    122A  TYR*     3.8    15.3    -      -       +      +
    143A  LEU*     3.7    14.6    -      -       +      -
    145A  VAL*     4.6     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  GLU      3.7     0.7    +      -       -      +
     90A  LYS*     2.9    59.5    +      -       +      +
     92A  LYS*     5.1     7.2    -      -       +      -
     99A  GLU*     2.9    22.6    +      -       +      +
    100A  VAL*     1.3    65.6    -      -       -      +
    102A  GLY*     1.3    70.4    +      -       -      +
    103A  LYS*     4.2    11.9    -      -       +      -
    117A  GLU*     3.1    33.0    +      -       +      +
    118A  PHE      3.2    20.9    -      -       -      +
    119A  HIS*     3.5    23.2    +      +       -      +
    120A  ARG      4.2     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  PHE*     3.9     2.5    -      -       -      -
     88A  GLU      3.5     1.3    -      -       -      -
     89A  LEU*     3.8    21.8    -      -       -      -
    100A  VAL*     2.5    15.7    +      -       -      -
    101A  HIS*     1.3    79.2    +      -       -      +
    103A  LYS*     1.3    61.2    +      -       -      +
    118A  PHE*     2.7    45.3    +      -       -      +
    120A  ARG*     5.4     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  PHE*     3.0    19.4    -      -       -      -
     88A  GLU*     2.7    59.9    +      -       -      +
     90A  LYS*     4.9    13.6    -      -       -      +
    101A  HIS*     4.2     9.5    -      -       +      -
    102A  GLY*     1.3    76.1    -      -       -      +
    104A  HIS*     1.3    57.8    +      -       -      +
    105A  GLU*     2.9    45.2    +      -       +      +
    115A  SER*     4.3     0.9    -      -       -      +
    116A  ARG      3.2     8.4    +      -       -      -
    117A  GLU*     3.9    34.3    -      -       +      +
    119B  HIS*     5.9     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 104 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  HIS*     3.1    37.6    +      +       +      +
     84A  PHE*     3.5    21.0    -      -       +      -
     88A  GLU*     3.4     2.2    -      -       -      -
    103A  LYS*     1.3    70.7    -      -       -      +
    105A  GLU*     1.3    82.7    +      -       -      +
    106A  GLU      4.0     6.0    +      -       -      -
    107A  ARG*     3.1    46.6    +      -       +      +
    115A  SER*     2.6    26.1    +      -       -      -
    116A  ARG*     2.8    36.2    +      -       +      +
----------------------------------------------------------
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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