Contacts of the strand formed by residues 118 - 123 (chain A) in PDB entry 2NNA


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 ASN 118 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  VAL*     1.3    79.1    -      -       -      +
    119A  ILE*     1.3    63.4    +      -       -      +
    120A  THR*     4.1     9.0    -      -       +      -
    164A  LYS      3.4     1.6    -      -       -      +
    165A  VAL*     3.3     5.7    -      -       -      -
    166A  GLU*     2.9    68.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  CYS*     4.2     3.6    -      -       -      -
    109A  VAL*     3.5    29.4    -      -       +      -
    117A  VAL*     4.1    14.9    +      -       +      -
    118A  ASN*     1.3    77.7    -      -       -      +
    120A  THR*     1.3    66.0    +      -       -      +
    121A  TRP*     5.1     0.4    -      -       -      +
    132A  VAL*     5.4     3.5    -      -       -      +
    134A  GLU*     4.2    17.5    +      -       -      +
    147A  LYS*     3.5    39.7    -      -       +      +
    149A  SER*     3.5    30.3    +      -       -      +
    163A  CYS*     3.7    24.7    -      -       -      -
    164A  LYS      3.4     2.7    -      -       -      +
    165A  VAL*     4.4     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  ASN*     4.9     8.1    -      -       +      -
    119A  ILE*     1.3    83.5    -      -       -      +
    121A  TRP*     1.3    69.7    +      -       -      +
    122A  LEU*     5.1     3.1    -      -       -      +
    127A  SER*     6.1     1.6    -      -       -      -
    128A  VAL      5.9     0.2    -      -       -      -
    132A  VAL*     5.9     1.1    -      -       -      -
    163A  CYS*     3.6     5.2    -      -       -      -
    164A  LYS*     2.7    56.2    +      -       -      +
    166A  GLU*     6.1     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  VAL*     4.3     8.3    -      -       +      -
    105A  LEU*     3.7    43.5    -      -       +      -
    106A  ILE      3.9     2.5    -      -       -      -
    107A  CYS*     3.3    38.6    -      -       +      -
    120A  THR*     1.3    82.9    -      -       -      +
    122A  LEU*     1.3    70.5    +      -       -      +
    127A  SER*     3.6     1.4    -      -       -      -
    128A  VAL*     3.1    36.7    +      -       +      +
    132A  VAL*     3.6    24.9    -      -       +      +
    149A  SER*     2.8    38.6    +      -       -      -
    150A  TYR      3.7     5.7    +      -       -      -
    151A  LEU*     3.7    33.4    -      -       +      -
    161A  TYR*     4.8     3.6    -      -       +      -
    162A  ASP      3.5    17.7    -      -       -      -
    163A  CYS*     4.1    13.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  THR*     5.1     6.7    -      -       -      +
    121A  TRP*     1.3    86.9    -      -       -      +
    123A  SER*     1.3    60.3    +      -       -      +
    124A  ASN      4.1     0.2    -      -       -      -
    125A  GLY*     4.1    21.3    -      -       -      +
    126A  HIS      3.1     4.0    -      -       -      +
    127A  SER*     3.7    28.0    -      -       -      +
    128A  VAL*     4.5     1.1    -      -       -      -
    161A  TYR*     3.2    11.5    -      -       -      +
    162A  ASP*     2.8    49.1    +      -       +      +
    164A  LYS*     4.6    16.2    -      -       +      +
    175A  LEU*     3.7    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  LEU*     1.3    72.3    -      -       -      +
    124A  ASN*     1.3    70.0    +      -       -      +
    125A  GLY      3.0     0.2    -      -       -      -
    126A  HIS*     2.7    43.0    +      -       -      -
    128A  VAL*     3.4    24.1    -      -       -      +
    159A  GLU*     2.8    31.0    +      -       -      +
    160A  ILE      3.5     4.5    +      -       -      -
    161A  TYR*     3.7    15.1    -      -       -      -
----------------------------------------------------------
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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