Contacts of the strand formed by residues 47 - 56 (chain B) in PDB entry 5ZX2


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 47 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  SER      3.8     0.6    -      -       -      +
     46B  ILE*     1.3    94.3    -      -       +      +
     48B  GLY*     1.3    57.8    +      -       -      +
    142B  ARG*     4.1    25.5    +      -       +      +
    143B  GLY      3.2    12.6    -      -       -      +
    144B  ARG*     3.6    30.0    -      -       +      +
    170B  PRO*     3.6    11.8    -      -       -      +
    202B  ILE*     5.1     1.4    -      -       -      +
    210B  SER*     5.1     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 48 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  PRO*     1.3    75.5    -      -       -      +
     49B  ALA*     1.3    60.1    +      -       -      -
    142B  ARG*     3.2    12.3    -      -       -      +
    143B  GLY      2.9    32.2    +      -       -      +
    168B  TYR*     3.2    21.9    +      -       -      -
    170B  PRO*     4.2     6.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 49 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  GLY*     1.3    74.1    -      -       -      -
     50B  ALA*     1.3    64.9    +      -       -      +
     83B  LEU      5.4     1.0    -      -       -      +
     85B  VAL*     3.2    41.2    +      -       +      +
     86B  SER*     3.8     1.4    -      -       -      +
     87B  SER*     3.6    33.4    -      -       -      +
    140B  VAL*     4.2     1.8    -      -       +      -
    141B  GLU      3.1    11.0    -      -       -      +
    142B  ARG*     4.8     1.8    -      -       +      -
    167B  ILE      4.0     6.2    -      -       -      +
    168B  TYR      4.0     1.8    +      -       -      +
    199B  LYS*     4.8     5.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  ALA*     1.3    72.2    -      -       -      +
     51B  VAL*     1.3    64.4    +      -       -      +
     52B  THR*     3.7     3.0    +      -       -      -
     83B  LEU      5.7     1.8    -      -       -      -
     85B  VAL*     4.2     4.7    -      -       -      -
    140B  VAL*     3.3     7.8    -      -       -      +
    141B  GLU*     2.9    31.6    +      -       -      +
    166B  SER*     4.1     5.2    -      -       -      -
    167B  ILE      3.1    42.8    -      -       -      +
    168B  TYR*     3.7    14.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  ALA*     1.3    74.8    -      -       -      +
     52B  THR*     1.3    61.7    +      -       -      +
     53B  SER      3.8     6.3    -      -       -      +
     54B  ILE*     3.8    29.4    -      -       +      -
     80B  LEU*     4.4    23.6    -      -       +      +
     81B  LYS*     5.6     2.7    -      -       -      -
     83B  LEU*     4.9    14.5    +      -       +      +
     85B  VAL*     5.2     2.5    -      -       +      -
     95B  MET*     5.2     0.2    -      -       +      -
    138B  LEU*     3.9    21.3    -      -       +      -
    139B  VAL      3.8     5.6    -      -       -      +
    140B  VAL*     3.9    18.8    -      -       +      -
    164B  VAL*     3.4    20.0    -      -       +      +
    165B  ASP      4.1     0.5    -      -       -      +
    166B  SER*     3.0    19.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 52 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  ALA      3.8     3.6    +      -       -      -
     51B  VAL*     1.3    75.3    -      -       -      +
     53B  SER*     1.3    63.5    +      -       -      +
    139B  VAL*     2.9    17.3    +      -       +      -
    141B  GLU*     3.3    38.4    +      -       -      +
    152B  ASN*     3.4    36.3    +      -       +      +
    163B  PRO*     3.8     1.2    -      -       -      +
    164B  VAL*     2.9    33.4    +      -       -      +
    166B  SER*     3.6     4.7    +      -       -      -
    168B  TYR*     3.6    12.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  VAL*     3.8     2.3    -      -       -      +
     52B  THR*     1.3    82.8    -      -       -      +
     54B  ILE*     1.3    68.6    +      -       -      +
    138B  LEU*     3.8     0.2    -      -       -      -
    139B  VAL*     3.0    42.3    +      -       -      +
    152B  ASN      5.5     2.7    -      -       -      -
    161B  ARG*     3.4    38.1    +      -       -      -
    162B  ILE      3.3    14.1    -      -       -      -
    163B  PRO*     4.3     4.7    -      -       -      -
    164B  VAL*     4.5     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  VAL*     3.8    17.3    -      -       +      -
     53B  SER*     1.3    81.5    -      -       -      +
     55B  ARG*     1.3    62.2    +      -       -      +
     56B  ILE*     4.2    20.6    -      -       +      -
     77B  ILE*     4.1    26.5    -      -       +      +
     80B  LEU*     3.7    35.2    -      -       +      -
    136B  VAL*     4.5     3.8    -      -       +      -
    137B  GLU      3.1    12.3    -      -       -      +
    138B  LEU*     3.9     6.1    -      -       +      -
    139B  VAL*     5.9     0.4    -      -       -      -
    160B  GLY      3.9     0.9    -      -       -      +
    161B  ARG*     3.7     1.8    -      -       -      -
    162B  ILE*     2.9    52.1    +      -       +      +
    164B  VAL*     4.2    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 55 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  ILE*     1.3    74.1    -      -       -      +
     56B  ILE*     1.3    62.4    +      -       -      +
     57B  ASP      4.1     0.4    -      -       -      -
     60B  LEU*     5.8     4.2    -      -       -      +
    136B  VAL*     3.0     6.9    -      -       -      +
    137B  GLU*     2.6    76.1    +      -       +      +
    158B  GLU*     2.4    36.8    +      -       -      +
    159B  ILE      3.6    16.9    +      -       -      -
    160B  GLY*     3.7     6.1    +      -       -      -
    161B  ARG*     3.5    39.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 56 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  ILE*     4.2    22.9    +      -       +      -
     55B  ARG*     1.3    78.3    +      -       -      +
     57B  ASP*     1.3    73.8    +      -       -      +
     58B  GLY      3.3     1.9    +      -       -      -
     59B  VAL*     3.2    42.0    +      -       +      +
     66B  VAL*     4.5    16.8    -      -       +      -
     73B  VAL*     4.9    13.2    -      -       +      +
     76B  ILE*     4.3    29.8    -      -       +      -
    134B  LEU*     4.6    12.8    -      -       +      -
    135B  GLU      3.6     6.7    -      -       -      +
    136B  VAL*     3.7    16.4    -      -       +      -
    160B  GLY      4.6     5.9    +      -       -      +
    162B  ILE*     5.2     4.6    -      -       +      +
----------------------------------------------------------
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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