Contacts of the strand formed by residues 81 - 95 (chain B) 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 CYS 81 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  CYS*     2.0    56.5    -      -       +      -
     12B  CYS      3.7    14.4    -      -       -      -
     40B  CYS*     3.8    23.8    -      -       +      +
     41B  GLU      4.0     4.3    -      -       -      -
     42B  GLY      3.6    23.2    +      -       -      +
     44B  CYS*     3.5     4.6    -      -       -      -
     80B  CYS*     1.3    73.0    -      -       -      +
     82B  VAL*     1.3    66.0    +      -       -      +
     83B  PRO*     4.9     0.2    -      -       -      +
    113B  CYS*     4.1     2.5    -      -       -      -
    114B  GLY      3.2     4.9    -      -       -      -
    116D  SER*     5.9     1.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 82 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  CYS*     3.5     6.3    -      -       -      -
     80B  CYS*     3.8    18.8    -      -       +      +
     81B  CYS*     1.3    80.8    -      -       -      +
     83B  PRO*     1.3    80.3    -      -       +      +
     84B  THR*     3.0     3.5    +      -       -      +
    114B  GLY*     2.6    45.3    +      -       -      +
    115B  CYS      4.7     0.2    -      -       -      -
    116B  SER*     4.0    19.7    -      -       -      +
     82D  VAL*     4.1    31.2    -      -       +      -
    116D  SER*     5.0     9.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 83 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  CYS*     3.2    17.6    -      -       +      +
     82B  VAL*     1.3    92.8    -      -       +      +
     84B  THR*     1.3    60.7    +      -       -      +
     85B  LYS      3.4     0.4    -      -       -      -
     86B  LEU*     4.1    15.8    -      -       +      +
    110B  VAL*     3.7    33.4    -      -       +      -
    112B  GLU      3.4     7.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 84 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82B  VAL*     3.0     5.4    +      -       -      +
     83B  PRO*     1.3    72.9    -      -       -      +
     85B  LYS*     1.3    65.8    +      -       +      +
     86B  LEU*     5.0     0.9    -      -       -      -
    112B  GLU*     2.7    21.6    +      -       +      +
    113B  CYS      4.1     1.3    -      -       -      -
    114B  GLY*     3.5    30.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 85 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  GLN*     5.1    13.6    -      -       -      +
     83B  PRO      3.4     1.2    -      -       -      -
     84B  THR*     1.3    88.1    -      -       +      +
     86B  LEU*     1.3    76.5    +      -       -      +
    110B  VAL*     3.7     1.4    -      -       -      +
    111B  GLU*     2.8    61.9    +      -       +      +
    112B  GLU*     3.3    36.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 86 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  PRO*     4.1    26.2    -      -       +      +
     84B  THR      5.0     0.4    -      -       -      -
     85B  LYS*     1.3    97.4    -      -       -      +
     87B  ARG*     1.3    62.9    +      -       -      +
    107B  ASN*     3.4    52.7    -      -       +      +
    108B  MET      5.7     0.2    -      -       -      -
    109B  ILE      3.4     8.7    -      -       -      +
    110B  VAL*     4.5     9.4    -      -       +      -
    111B  GLU*     3.9     1.3    -      -       -      +
    107D  ASN*     6.1     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 87 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  LYS*     4.1    29.5    -      -       -      +
     80A  ASP*     4.5    22.2    +      -       -      +
     85A  TYR*     5.3     3.0    +      -       -      -
     13B  LYS*     5.0     5.9    -      -       -      +
     36B  HIS*     5.7     5.7    +      -       -      -
     38B  ASN*     4.8     5.7    -      -       -      +
     86B  LEU*     1.3    76.3    -      -       -      +
     88B  PRO*     1.3    80.2    +      -       +      +
    107B  ASN      4.3     2.7    -      -       -      +
    108B  MET      3.0     8.6    +      -       -      -
    109B  ILE*     2.8    68.9    +      -       +      +
    111B  GLU*     3.7    37.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 88 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  GLU*     6.0     5.4    -      -       +      -
     79A  LEU*     3.5    33.3    -      -       +      +
     80A  ASP      5.3     3.1    -      -       -      +
     86B  LEU      4.8     0.2    -      -       -      +
     87B  ARG*     1.3   101.1    +      -       +      +
     89B  MET*     1.3    59.0    +      -       -      +
     90B  SER      4.2     0.2    -      -       -      -
    104B  ASP*     4.7     3.8    -      -       +      -
    105B  ILE      2.8    21.5    -      -       -      +
    106B  GLN*     3.1    33.0    -      -       -      +
    107B  ASN      4.8     0.4    -      -       -      +
    109B  ILE*     4.5     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 89 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  LEU*     4.8     0.2    -      -       -      -
     80A  ASP      6.0     1.3    -      -       -      -
     20B  PHE*     4.5     4.3    -      -       +      -
     32B  PRO*     4.1    20.9    -      -       +      -
     35B  TYR*     3.3    30.5    -      -       +      -
     87B  ARG      4.1     0.4    +      -       -      -
     88B  PRO*     1.3    74.1    -      -       -      +
     90B  SER*     1.3    64.0    +      -       -      +
     91B  MET*     3.5    33.2    -      -       +      -
    104B  ASP*     4.6     0.9    -      -       -      -
    105B  ILE*     2.6    40.6    +      -       +      +
    108B  MET*     3.1    42.6    -      -       +      +
    109B  ILE*     4.0    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 90 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  TRP*     3.6    35.5    -      -       -      -
     79A  LEU*     3.1    31.5    +      -       -      +
     80A  ASP      5.9     0.6    +      -       -      -
     32B  PRO*     3.4    14.0    -      -       -      +
     88B  PRO      4.2     0.8    +      -       -      -
     89B  MET*     1.3    77.1    -      -       -      +
     91B  MET*     1.3    67.5    +      -       -      +
    102B  LYS*     3.5     5.7    +      -       -      -
    103B  LYS      3.6     4.0    -      -       -      -
    104B  ASP*     2.7    24.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 91 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  TRP*     4.0     5.3    -      -       -      -
     20B  PHE*     4.6     7.6    -      -       -      -
     28B  TRP*     5.9     6.7    -      -       +      -
     29B  ILE*     4.5    28.9    -      -       +      -
     31B  ALA      3.7     2.9    -      -       -      -
     32B  PRO*     3.9     6.7    -      -       +      -
     89B  MET*     3.5    26.9    -      -       +      -
     90B  SER*     1.3    81.0    -      -       -      +
     92B  LEU*     1.3    60.7    +      -       -      +
     93B  TYR*     4.0    19.0    -      -       +      -
    101B  ILE      3.7     0.5    -      -       -      +
    102B  LYS*     3.2     7.6    -      -       -      +
    103B  LYS      2.8    38.8    +      -       -      +
    105B  ILE*     3.0    36.1    -      -       +      -
    108B  MET*     5.1     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 92 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  TYR*     4.4     5.2    -      -       +      -
     62A  SER*     3.8    28.7    -      -       -      +
     74A  LYS*     4.3     8.1    -      -       +      -
     78A  TRP*     4.2    12.6    -      -       +      -
     99A  VAL*     5.0     1.6    -      -       +      -
    101A  PHE*     4.0    16.8    -      -       +      -
     29B  ILE*     3.7     0.8    -      -       -      +
     30B  ILE*     2.7    47.5    +      -       +      +
     31B  ALA*     2.8    21.2    +      -       +      +
     91B  MET*     1.3    73.4    -      -       -      +
     93B  TYR*     1.3    55.0    +      -       -      +
    100B  ILE*     3.8    22.7    -      -       +      -
    101B  ILE      3.2    16.2    -      -       -      +
    102B  LYS*     3.5    22.4    -      -       +      -
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Residues in contact with TYR 93 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  TRP*     3.1    34.3    -      +       +      +
     29B  ILE*     3.8    16.6    -      -       +      -
     30B  ILE*     3.5    10.5    -      -       -      -
     91B  MET*     4.0    35.4    -      -       +      -
     92B  LEU*     1.3    77.0    -      -       -      +
     94B  TYR*     1.3    76.5    +      -       -      +
     95B  ASP*     4.7     5.6    -      -       +      -
    100B  ILE*     3.4     2.1    -      -       -      +
    101B  ILE*     2.5    74.4    +      -       +      +
    103B  LYS*     4.1    16.4    -      -       +      +
    105B  ILE*     4.9     5.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 94 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ARG*     5.2     6.0    +      -       -      -
     98A  GLN*     4.5    10.6    -      -       -      +
     99A  VAL*     3.5    20.4    -      -       -      +
     27B  ASP      4.1    11.0    -      -       -      -
     28B  TRP*     2.7    53.6    +      -       +      +
     30B  ILE*     3.6    19.0    -      -       +      +
     93B  TYR*     1.3    85.9    -      -       -      +
     95B  ASP*     1.3    69.0    +      -       -      +
     98B  GLN*     3.9    42.2    -      -       -      +
     99B  ASN      3.2     5.4    -      -       -      +
    100B  ILE*     3.4    31.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 95 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93B  TYR*     4.1     6.7    +      -       +      -
     94B  TYR*     1.3    81.0    -      -       -      +
     96B  ASP*     1.3    66.7    +      -       -      +
     97B  GLY*     2.9    12.0    +      -       -      -
     98B  GLN*     3.1    10.0    +      -       -      -
     99B  ASN*     2.5    55.2    +      -       -      +
    101B  ILE*     3.8    17.1    -      -       +      +
----------------------------------------------------------
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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