Contacts of the strand formed by residues 73 - 82 (chain A) in PDB entry 2NSQ


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 LYS 73 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  VAL      3.6     5.4    -      -       -      +
     28A  SER*     3.8    14.6    -      -       -      -
     29A  GLY      5.2     0.6    +      -       -      +
     64A  LYS*     4.9     0.5    +      -       -      -
     66A  ILE*     3.7    19.3    -      -       -      +
     71A  ASN*     2.8    31.2    +      -       -      +
     72A  PRO*     1.3    75.4    -      -       -      +
     74A  TRP*     1.3    62.6    +      -       -      +
     75A  ASN*     4.2    14.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  VAL*     3.6    26.2    -      -       +      +
     27A  VAL      2.8     8.7    +      -       -      -
     28A  SER*     3.5    17.7    -      -       -      -
     29A  GLY*     3.3    22.4    -      -       -      -
     43A  PRO*     3.2    17.1    +      -       +      -
     44A  TYR*     3.8    13.5    -      -       -      -
     45A  VAL*     3.4    26.5    -      -       +      -
     63A  THR*     3.4    14.6    +      -       -      -
     64A  LYS*     2.9    55.2    +      -       +      +
     66A  ILE*     3.7    17.1    -      -       +      +
     72A  PRO*     3.5    28.3    -      -       +      -
     73A  LYS*     1.3    74.0    -      -       -      +
     75A  ASN*     1.3    69.6    +      -       -      +
     76A  GLU*     3.3     9.8    +      -       +      +
     93A  VAL*     4.4    11.9    -      -       +      -
    146A  LEU*     3.7     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  LYS*     3.5    36.8    +      -       -      +
     26A  VAL      3.0     6.3    +      -       -      -
     27A  VAL*     2.9    31.2    +      -       -      +
     73A  LYS*     4.2    15.9    -      -       -      +
     74A  TRP*     1.3    77.5    -      -       -      +
     76A  GLU*     1.3    59.5    +      -       -      +
     77A  GLU      4.3     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  LYS*     3.2     4.9    -      -       -      +
     26A  VAL*     2.7    36.5    +      -       -      +
     62A  GLN      4.4     1.4    -      -       -      +
     63A  THR*     3.3    26.4    -      -       +      -
     64A  LYS*     2.8    61.9    +      -       -      +
     74A  TRP*     3.5     5.2    -      -       +      +
     75A  ASN*     1.3    77.0    -      -       -      +
     77A  GLU*     1.3    60.7    +      -       -      +
     78A  PHE*     3.7    22.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  GLU*     4.2    14.6    -      -       -      +
     10A  TYR*     5.4     0.3    -      -       -      -
     23A  ARG*     2.6    42.0    +      -       +      +
     24A  VAL      3.3     7.2    -      -       -      +
     25A  LYS*     4.2     9.9    -      -       +      +
     75A  ASN      4.3     0.6    +      -       -      +
     76A  GLU*     1.3    72.9    -      -       -      +
     78A  PHE*     1.3    76.9    +      -       -      +
     79A  TYR*     3.5    32.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  TYR*     3.8    26.2    -      +       +      -
     22A  LEU      3.8     0.3    -      -       -      +
     23A  ARG*     3.6     2.9    -      -       -      +
     24A  VAL*     2.7    38.1    +      -       +      +
     26A  VAL*     4.0    16.4    -      -       +      -
     47A  LEU*     3.9    20.2    -      -       +      -
     61A  VAL*     3.8    32.8    -      -       +      -
     62A  GLN      4.4     1.6    -      -       -      -
     63A  THR*     4.0    15.3    -      -       +      -
     76A  GLU*     3.7    46.2    -      -       +      -
     77A  GLU*     1.3    79.8    -      -       -      +
     79A  TYR*     1.3    66.8    +      -       -      +
     80A  PHE*     3.6    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  GLU*     3.7    35.3    -      -       +      +
      8A  PRO*     3.6    17.0    +      -       +      +
      9A  VAL*     3.4    14.7    -      -       +      -
     10A  TYR*     2.8    31.2    +      -       -      -
     21A  ILE*     3.8    21.8    -      -       +      -
     22A  LEU      3.3     3.8    -      -       -      +
     23A  ARG*     3.5    43.9    +      -       +      -
     77A  GLU*     3.5    29.4    +      -       +      -
     78A  PHE*     1.3    76.3    -      -       -      +
     80A  PHE*     1.3    61.8    +      -       -      +
    120A  PRO*     4.5     7.1    -      -       -      +
    153A  MET*     4.0    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  VAL*     4.0     4.9    -      -       -      -
     10A  TYR*     3.3    31.4    -      +       +      -
     20A  ARG      3.5     0.9    -      -       -      +
     21A  ILE*     3.4     4.9    -      -       -      -
     22A  LEU*     2.7    39.9    +      -       +      +
     24A  VAL*     3.9    18.8    -      -       +      -
     47A  LEU*     3.8    31.0    -      -       +      -
     49A  LEU*     4.1    27.1    -      -       +      -
     59A  ALA*     4.4     7.9    -      -       +      -
     61A  VAL*     4.0    18.2    -      -       +      -
     78A  PHE*     3.6    20.9    -      -       +      -
     79A  TYR*     1.3    76.1    -      -       -      +
     81A  ARG*     1.3    58.3    +      -       -      +
     82A  VAL*     3.4    19.5    +      -       +      +
     89A  LEU*     4.1    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  VAL*     3.7    36.7    +      -       +      +
     10A  TYR      2.9     8.9    +      -       -      +
     11A  GLY*     2.8    43.7    +      -       -      +
     12A  LEU*     4.4     9.3    -      -       -      +
     13A  SER*     3.1    41.5    -      -       -      +
     16A  GLU*     6.3     0.2    -      -       -      +
     19A  SER*     4.0    12.3    -      -       -      +
     20A  ARG      3.5     5.8    -      -       -      +
     21A  ILE*     4.4    13.6    -      -       +      +
     49A  LEU*     3.4    18.5    -      -       -      +
     58A  LEU*     5.6     0.2    -      -       -      +
     80A  PHE*     1.3    69.9    -      -       -      +
     82A  VAL*     1.3    61.3    +      -       -      +
     87A  HIS*     4.6     3.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  GLU      3.7     0.2    -      -       -      +
     19A  SER*     3.1     8.4    -      -       -      -
     20A  ARG      2.8    40.6    +      -       -      +
     22A  LEU*     4.2     9.4    -      -       +      -
     49A  LEU*     3.6    16.6    -      -       +      -
     80A  PHE*     3.4    27.6    -      -       +      +
     81A  ARG*     1.3    80.2    -      -       -      +
     83A  ASN*     1.3    61.0    +      -       -      +
     84A  PRO*     3.7     1.6    -      -       -      +
     87A  HIS*     3.7     9.4    -      -       -      +
    112A  LEU*     3.9    19.5    -      -       +      -
    152A  TYR*     3.5    39.7    -      -       +      +
----------------------------------------------------------
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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