Contacts of the strand formed by residues 57 - 65 (chain A) in PDB entry 1NYU


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 57 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  ARG*     4.1    24.8    -      -       +      +
     49A  CYS*     3.9    25.6    -      -       +      +
     50A  GLU      4.0    10.5    -      -       -      +
     51A  GLY*     3.6    27.4    -      -       -      +
     52A  GLU      5.2     2.0    -      -       -      +
     55A  LYS*     3.6    12.3    +      -       +      +
     56A  ARG*     1.3    85.6    -      -       -      +
     58A  HIS*     1.3    70.2    +      -       -      +
     78A  TRP      4.3     0.9    -      -       -      +
     79A  LEU*     4.6    17.3    -      -       +      -
     80A  ASP      4.7     2.0    -      -       -      +
    105A  GLU*     3.6    15.0    +      -       -      +
    106A  GLY      4.8     1.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 58 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  CYS*     4.0     4.0    -      -       -      -
     56A  ARG*     3.5    28.5    -      -       +      -
     57A  LEU*     1.3    84.9    +      -       -      +
     59A  CYS*     1.3    72.3    +      -       -      +
     77A  CYS*     3.5     1.0    -      -       -      -
     78A  TRP*     2.7    37.7    +      +       +      +
     79A  LEU      3.6    11.9    -      -       -      -
     80A  ASP*     3.2     7.3    +      -       -      -
     81A  ASP      2.8    35.7    +      -       -      -
     84A  CYS*     3.4    26.6    -      -       +      +
     85A  TYR*     3.9    14.6    -      +       -      -
    103A  CYS*     4.5     3.4    -      -       -      -
    104A  CYS      2.8    16.4    -      -       -      +
    105A  GLU*     3.7    16.3    -      -       -      +
    106A  GLY      5.4     0.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  ARG*     6.1     0.7    -      -       -      -
     29A  CYS*     2.0    53.8    -      -       +      -
     49A  CYS*     3.8    11.7    -      -       -      -
     57A  LEU      5.7     0.2    -      -       -      -
     58A  HIS*     1.3    88.7    -      -       -      +
     60A  TYR*     1.3    61.7    -      -       -      +
     76A  GLY      3.5     3.6    -      -       -      +
     77A  CYS*     3.9     3.1    -      -       -      -
     78A  TRP*     4.0     4.0    -      -       -      +
    103A  CYS*     3.8     2.6    -      -       -      -
    104A  CYS*     2.9    33.5    +      -       -      +
    106A  GLY      5.4     1.3    -      -       -      -
    109A  CYS*     4.2    10.7    -      -       -      -
    110A  ASN*     3.8    11.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  TYR*     5.8     1.4    -      -       -      -
     59A  CYS*     1.3    75.2    -      -       -      +
     61A  ALA*     1.3    77.0    +      -       -      +
     62A  SER*     3.8    17.7    -      -       -      -
     74A  LYS*     3.3    26.8    -      -       +      +
     75A  LYS*     3.6     9.7    +      -       -      -
     76A  GLY*     2.8    50.1    +      -       -      -
     77A  CYS      3.6    15.9    -      -       -      -
     78A  TRP*     3.8    16.8    -      +       +      -
     90A  CYS*     4.7     0.7    -      -       -      -
    101A  PHE*     3.7    31.4    -      +       +      -
    102A  CYS      3.6     6.3    -      -       -      +
    110A  ASN*     2.7    31.3    +      -       -      +
     92B  LEU*     4.4     5.8    -      -       +      -
    102B  LYS*     3.1    40.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  TYR*     1.3    80.6    -      -       -      +
     62A  SER*     1.3    60.7    +      -       -      +
     63A  TRP*     3.6    11.2    -      -       +      -
     74A  LYS      3.6     8.3    -      -       -      -
     75A  LYS*     3.8    21.3    -      -       +      -
     90A  CYS*     4.2     2.7    -      -       -      -
    101A  PHE*     3.3     5.7    -      -       -      -
    102A  CYS*     3.2    46.1    +      -       -      +
    110A  ASN*     4.3     4.7    -      -       +      +
    113A  PHE*     4.3     6.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  TYR*     3.8     5.4    -      -       -      -
     61A  ALA*     1.3    74.7    -      -       -      +
     63A  TRP*     1.3    65.8    +      -       -      +
     72A  LEU*     3.4     8.0    -      -       -      +
     73A  VAL*     3.1    30.3    +      -       -      +
     74A  LYS*     2.9    33.7    +      -       -      +
     99A  VAL*     4.3     3.8    -      -       -      -
    100A  TYR      3.2    14.1    -      -       -      -
    101A  PHE*     4.7     1.1    -      -       -      -
     92B  LEU*     3.8    24.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  ALA*     3.6    17.7    -      -       +      -
     62A  SER*     1.3    86.7    -      -       -      +
     64A  ARG*     1.3    91.5    +      -       -      +
     65A  ASN*     4.2     4.6    -      -       -      +
     70A  ILE*     3.6    27.4    -      -       +      +
     71A  GLU      3.1    18.6    -      -       -      +
     72A  LEU*     4.1     6.7    -      -       +      -
     73A  VAL*     3.6     4.4    -      -       -      +
     92A  ALA*     3.8    12.1    -      -       +      -
     99A  VAL*     3.4     4.9    -      -       -      +
    100A  TYR*     2.9    62.6    +      +       +      +
    102A  CYS*     3.7    17.0    -      -       -      -
    113A  PHE*     3.4    42.5    -      +       +      -
    114A  THR      3.6    26.7    -      -       -      -
    115A  HIS*     5.0     1.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  TRP*     1.3    90.0    -      -       -      +
     65A  ASN*     1.3    59.0    +      -       -      +
     66A  SER*     3.5    14.1    -      -       -      +
     69A  THR      3.0     2.1    -      -       -      +
     70A  ILE*     3.0     9.0    -      -       -      -
     71A  GLU*     2.8    47.5    +      -       +      +
     72A  LEU      5.4     1.0    +      -       -      -
     73A  VAL*     4.2    15.4    -      -       +      +
     98A  GLN*     3.7    18.2    +      -       -      +
     99A  VAL*     4.2    11.3    -      -       +      +
    100A  TYR*     4.4     1.3    -      -       -      -
     94B  TYR*     5.2     4.6    +      -       -      -
     98B  GLN      5.9     0.4    +      -       -      -
    100B  ILE*     3.8    27.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  TRP*     4.9     5.0    -      -       +      +
     64A  ARG*     1.3    70.3    -      -       -      +
     66A  SER*     1.3    60.4    +      -       -      +
     67A  SER      5.0     0.9    -      -       -      -
     68A  GLY*     3.9    20.8    -      -       -      -
     69A  THR      3.5     7.5    +      -       -      +
     70A  ILE*     4.6    11.9    -      -       -      +
     98A  GLN      5.0     0.8    +      -       -      -
    100A  TYR*     3.5    44.2    +      -       +      +
    115A  HIS*     5.2     7.9    -      -       -      +
----------------------------------------------------------
 Back to top of page


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