Contacts of the strand formed by residues 70 - 79 (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 ILE 70 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  TRP*     3.6    35.7    -      -       +      +
     64A  ARG      3.0     4.7    -      -       -      +
     65A  ASN*     4.6    14.4    -      -       -      +
     68A  GLY      5.8     0.4    -      -       -      -
     69A  THR*     1.3    74.7    -      -       -      +
     71A  GLU*     1.3    63.7    +      -       -      +
     72A  LEU*     4.0     3.0    +      -       +      +
    113A  PHE*     3.9    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  TRP*     3.1     4.7    -      -       -      -
     64A  ARG*     2.8    53.5    +      -       +      +
     69A  THR*     3.8     2.2    +      -       -      +
     70A  ILE*     1.3    73.7    -      -       -      +
     72A  LEU*     1.3    68.8    +      -       -      +
     73A  VAL*     3.7     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  TYR*     3.5    46.4    -      -       +      +
     34A  ALA*     3.7    13.2    -      -       -      +
     62A  SER      3.4    19.5    -      -       -      +
     63A  TRP*     4.1     7.9    -      -       +      -
     64A  ARG*     5.4     1.2    +      -       -      -
     70A  ILE*     4.0     4.1    +      -       +      +
     71A  GLU*     1.3    81.4    -      -       -      +
     73A  VAL*     1.3    61.7    +      -       -      +
     74A  LYS      4.4     1.6    -      -       -      +
     75A  LYS*     3.8    38.6    -      -       +      +
    113A  PHE*     4.5    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  TYR*     3.7     2.8    -      -       -      -
     34A  ALA*     2.9    36.0    +      -       +      +
     62A  SER*     3.1    17.5    +      -       -      +
     63A  TRP*     3.6    26.0    -      -       -      +
     64A  ARG*     4.2    21.8    -      -       +      +
     71A  GLU      3.7     2.9    -      -       -      +
     72A  LEU*     1.3    79.5    -      -       -      +
     74A  LYS*     1.3    80.1    +      -       +      +
     99A  VAL*     4.9     1.6    -      -       +      -
    100B  ILE*     3.7    35.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  TYR*     5.6     3.2    +      -       -      -
     32A  TYR*     3.3    10.5    -      -       -      +
     33A  ASN*     3.1    29.3    +      -       -      +
     35A  ASN*     5.9     1.6    -      -       -      -
     39A  GLU*     3.7    20.3    +      -       -      -
     60A  TYR*     3.3    22.8    -      -       +      +
     61A  ALA*     3.6     0.3    -      -       -      -
     62A  SER*     2.9    35.1    +      -       -      +
     72A  LEU*     4.4     1.3    -      -       -      +
     73A  VAL*     1.3    99.2    -      -       +      +
     75A  LYS*     1.3    65.8    +      -       -      +
     92B  LEU*     4.3     7.9    -      -       +      -
    100B  ILE*     4.4    16.8    +      -       +      +
    101B  ILE*     4.8     1.8    -      -       -      +
    102B  LYS*     4.2    26.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  ILE*     3.5    28.0    -      -       +      +
     31A  TYR*     3.3    11.6    -      -       -      -
     32A  TYR*     2.9    37.5    +      -       +      +
     60A  TYR*     3.6    26.2    +      -       -      +
     61A  ALA*     3.8     6.3    -      -       +      -
     72A  LEU*     3.8    29.7    -      -       +      +
     74A  LYS*     1.3    79.7    -      -       -      +
     76A  GLY*     1.3    59.3    +      -       -      +
    110A  ASN*     3.0    26.9    +      -       -      +
    111A  GLU*     3.5    25.9    +      -       -      +
    113A  PHE*     3.8    18.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  CYS*     4.3     7.6    -      -       -      -
     30A  ILE      3.3    13.6    +      -       -      -
     31A  TYR*     4.3     2.0    -      -       -      -
     47A  GLU*     3.3    12.1    -      -       -      -
     59A  CYS*     3.5     0.7    -      -       -      -
     60A  TYR*     2.8    43.0    +      -       -      -
     75A  LYS*     1.3    76.6    -      -       -      +
     77A  CYS*     1.3    63.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  CYS*     4.2     4.7    -      -       -      +
     47A  GLU*     2.9    35.8    +      -       -      +
     48A  ARG      3.8     4.5    -      -       -      -
     49A  CYS*     2.0    64.4    -      -       +      -
     50A  GLU      5.4     0.4    -      -       -      +
     58A  HIS      3.6     4.5    -      -       -      -
     59A  CYS*     3.9     1.6    -      -       -      -
     60A  TYR*     3.6     4.0    -      -       -      -
     76A  GLY*     1.3    75.5    -      -       -      +
     78A  TRP*     1.3    59.2    +      -       -      +
     79A  LEU*     6.4     1.8    -      -       +      -
    102B  LYS*     3.3    21.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  LEU*     4.0     1.9    -      -       -      +
     58A  HIS*     2.7    46.3    +      +       -      +
     59A  CYS*     4.2    11.4    -      -       -      +
     60A  TYR*     3.8    22.0    -      +       +      -
     77A  CYS*     1.3    74.2    -      -       -      +
     79A  LEU*     1.3    83.0    +      -       -      +
     81A  ASP*     3.1    31.8    +      -       +      +
     84A  CYS*     3.9     0.9    -      -       -      -
    101A  PHE*     3.7    32.1    -      +       -      -
    103A  CYS*     3.6    21.4    -      -       -      -
     31B  ALA*     3.7    20.6    -      -       +      -
     32B  PRO*     4.1     9.0    -      -       +      -
     90B  SER*     3.6    36.5    -      -       -      -
     91B  MET      4.1     3.4    -      -       -      -
     92B  LEU*     3.9     7.0    -      -       +      -
    102B  LYS*     4.0    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  GLU*     4.2    26.9    -      -       +      +
     52A  GLU*     6.0     4.3    -      -       +      +
     56A  ARG      4.9     0.7    -      -       -      -
     57A  LEU*     4.6    10.1    -      -       +      -
     58A  HIS*     3.9     0.4    -      -       -      -
     77A  CYS*     6.3     2.0    -      -       +      -
     78A  TRP*     1.3    88.6    +      -       -      +
     80A  ASP*     1.3    72.0    +      -       +      +
     81A  ASP*     3.0     4.0    +      -       -      +
     88B  PRO*     3.5    44.4    -      -       +      +
     89B  MET*     5.4     0.2    -      -       -      -
     90B  SER*     3.1    27.0    +      -       -      +
    104B  ASP*     3.6    29.4    -      -       +      +
----------------------------------------------------------
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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