Contacts of the strand formed by residues 113 - 119 (chain Y) in PDB entry 5A0Q


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 PRO 113 (chain Y).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8Y  GLN*     2.6    27.6    +      -       +      +
      9Y  GLY      3.8    18.6    -      -       -      +
     10Y  PRO      4.4     7.9    -      -       -      +
     12Y  TYR      3.6     7.2    -      -       -      +
     13Y  VAL*     3.2    24.9    -      -       +      -
    106Y  GLY      3.9     4.7    -      -       -      +
    107Y  TYR*     3.5    39.7    -      -       +      +
    111Y  GLU      4.9     1.0    -      -       -      +
    112Y  GLY*     1.3    86.2    -      -       -      +
    114Y  ALA*     1.3    55.0    +      -       -      +
    126Y  LYS*     4.7     2.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 114 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8Y  GLN*     3.4     9.9    -      -       -      +
     13Y  VAL*     3.8     2.7    -      -       -      +
     77Y  PRO*     4.2     9.1    -      -       +      +
    104Y  LEU      4.1     1.6    -      -       -      +
    105Y  ALA      3.8     0.3    -      -       -      -
    106Y  GLY*     2.7    38.4    +      -       -      +
    111Y  GLU*     5.1     5.8    -      -       -      +
    112Y  GLY      3.6     6.1    +      -       -      +
    113Y  PRO*     1.3    76.7    -      -       -      +
    115Y  LEU*     1.3    59.8    +      -       -      +
    116Y  TYR*     3.5    30.7    -      -       +      +
    126Y  LYS*     4.3     9.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 115 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6Y  GLY*     3.5    39.9    -      -       -      +
      7Y  ILE*     3.5     5.6    -      -       -      +
      8Y  GLN*     2.3    59.4    +      -       +      +
     13Y  VAL*     3.9    13.5    -      -       +      -
    103Y  LEU*     4.2    17.5    -      -       +      -
    104Y  LEU      3.7     4.9    -      -       -      -
    105Y  ALA*     4.3     8.1    -      -       +      -
    114Y  ALA*     1.3    73.7    -      -       -      +
    116Y  TYR*     1.3    68.2    +      -       -      +
    126Y  LYS*     3.9     3.5    -      -       -      +
    127Y  ALA*     3.0    43.3    +      -       +      +
    128Y  PRO      3.8     0.4    -      -       -      +
    129Y  PHE*     4.5     0.9    -      -       -      -
    130Y  ALA      4.3     7.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 116 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77Y  PRO      4.3     2.7    -      -       -      -
     78Y  THR*     2.3    49.4    -      -       +      +
     81Y  ALA*     4.3     7.0    -      -       +      -
     82Y  ASN*     6.3     0.4    -      -       -      -
    102Y  LEU      3.8     0.3    -      -       -      +
    103Y  LEU*     3.3    10.9    -      -       -      -
    104Y  LEU*     3.0    38.4    +      -       +      +
    111Y  GLU*     4.5     0.5    +      -       -      -
    114Y  ALA*     3.5    29.1    -      -       +      +
    115Y  LEU*     1.3    78.1    -      -       -      +
    117Y  TYR*     1.3    62.1    +      -       -      +
    118Y  MET*     4.1     8.2    -      -       +      +
    124Y  LEU*     3.5    38.1    -      -       +      -
    125Y  ALA      3.5     1.8    -      -       -      +
    126Y  LYS*     3.5    41.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 117 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27X  PHE*     4.7     7.2    -      +       -      -
     29X  ILE*     3.6    35.4    -      -       +      +
     34X  VAL*     4.0    35.9    -      -       +      -
    101Y  ASN*     4.1    12.5    +      -       -      -
    103Y  LEU*     3.9     2.9    -      -       -      +
    116Y  TYR*     1.3    74.0    -      -       -      +
    118Y  MET*     1.4    63.3    +      -       -      +
    119Y  ASP*     3.8    27.0    +      -       +      -
    123Y  ALA      4.1     7.9    -      -       -      -
    124Y  LEU*     3.8     0.3    -      -       -      +
    125Y  ALA*     3.1    37.1    +      -       +      +
    127Y  ALA*     4.1     8.7    -      -       +      +
    130Y  ALA*     4.3    15.7    -      -       +      -
    131Y  ALA      3.7    20.4    -      -       -      -
    132Y  HIS*     3.4    27.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with MET 118 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81Y  ALA*     3.5    33.4    -      -       +      +
     84Y  THR*     3.6    24.2    -      -       +      -
     85Y  ARG*     5.3     4.5    -      -       +      -
     88Y  LEU*     5.1     9.2    -      -       +      -
    100Y  VAL      4.3     0.7    -      -       -      +
    101Y  ASN*     2.6    23.7    -      -       -      +
    102Y  LEU*     3.0    40.1    +      -       +      +
    104Y  LEU*     3.3    33.2    -      -       +      -
    116Y  TYR*     4.1     4.3    -      -       +      +
    117Y  TYR*     1.4    82.3    -      -       -      +
    119Y  ASP*     1.3    63.4    +      -       -      +
    122Y  ALA*     6.0     0.7    -      -       -      -
    123Y  ALA      4.2     4.3    -      -       -      +
    124Y  LEU*     3.6    19.7    -      -       +      +
    132Y  HIS*     3.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 119 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27X  PHE*     6.0     1.0    -      -       -      -
     29X  ILE*     3.1    31.5    -      -       -      +
     88Y  LEU*     3.8     9.4    -      -       -      +
    100Y  VAL      4.1     0.2    -      -       -      -
    101Y  ASN*     3.6     7.9    -      -       -      +
    117Y  TYR*     3.8    18.3    +      -       +      -
    118Y  MET*     1.3    76.7    -      -       -      +
    120Y  TYR*     1.3    84.6    +      -       -      +
    121Y  LEU*     4.2    16.7    -      -       +      +
    122Y  ALA*     2.9    21.6    +      -       -      +
    123Y  ALA*     3.7    33.5    +      -       +      +
----------------------------------------------------------
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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