Contacts of the strand formed by residues 49 - 57 (chain B) in PDB entry 2ERY


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 ASP 49 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43B  TYR*     4.1    18.2    +      -       -      +
     47B  ILE*     4.1     6.5    +      -       +      +
     48B  GLU*     1.3    73.2    -      -       -      +
     50B  SER*     1.3    82.3    +      -       -      +
     51B  TYR*     3.9    18.7    +      -       +      -
     67B  LEU*     3.5     3.7    -      -       -      +
     68B  ASP*     3.0    35.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  ARG*     3.3    26.1    +      -       -      -
     49B  ASP*     1.3    89.0    +      -       -      +
     51B  TYR*     1.3    72.5    +      -       -      +
     66B  ILE      3.2     8.7    -      -       -      -
     67B  LEU*     3.4    10.0    -      -       -      +
     80B  GLU*     4.7     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  THR*     3.4    27.4    -      -       +      -
     32B  ILE*     3.9    22.6    -      -       +      +
     35B  ILE*     3.6    37.0    -      -       +      -
     36B  GLN*     4.0    20.2    -      -       -      -
     43B  TYR*     3.5    24.1    +      -       -      -
     49B  ASP*     3.9    30.5    +      -       +      +
     50B  SER*     1.3    80.2    -      -       -      +
     52B  THR*     1.3    62.5    +      -       -      +
     65B  ASP*     3.5     5.0    -      -       -      +
     66B  ILE*     2.8    35.0    +      -       +      +
     68B  ASP*     4.2     9.1    +      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
     35B  ILE*     3.8    16.5    -      -       -      +
     51B  TYR*     1.3    77.6    -      -       -      +
     53B  LYS*     1.3    65.2    +      -       -      +
     63B  ARG*     3.5    15.9    -      -       -      +
     64B  LEU      3.3     6.9    +      -       -      -
     65B  ASP*     2.9    23.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  ASP*     2.8    37.1    +      -       -      +
     34B  PHE*     2.7    53.4    +      -       +      +
     35B  ILE*     3.7    20.9    -      -       +      +
     37B  SER*     5.7     0.4    +      -       -      -
     52B  THR*     1.3    80.7    +      -       -      +
     54B  GLN*     1.3    70.3    +      -       -      +
     55B  CYS*     3.9     4.5    +      -       -      -
     63B  ARG*     3.7     3.5    -      -       -      -
     64B  LEU*     2.8    33.4    +      -       +      +
    161B  ARG*     4.1     3.4    -      -       -      +
    165B  ASP*     3.5    11.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  ASP*     5.2     2.3    -      -       -      +
     53B  LYS*     1.3    79.8    -      -       -      +
     55B  CYS*     1.3    64.6    +      -       -      +
     56B  VAL*     6.3     1.1    -      -       +      -
     61B  ALA*     3.7    25.8    -      -       +      +
     62B  ALA*     3.7    16.9    +      -       -      +
     63B  ARG*     3.5    23.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 55 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  ASP*     3.7    31.6    -      -       -      +
     34B  PHE*     3.9    20.6    -      -       -      -
     53B  LYS*     4.0     9.9    -      -       -      -
     54B  GLN*     1.3    82.6    +      -       -      +
     56B  VAL*     1.3    65.1    +      -       -      +
     57B  ILE*     4.1    20.4    -      -       +      -
     61B  ALA*     3.4     5.2    -      -       -      +
     62B  ALA      2.8    35.1    +      -       -      +
     64B  LEU*     4.1    15.0    -      -       +      -
    169B  HIS*     4.2     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 56 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  ARG*     6.0     6.1    -      -       +      -
    117A  ARG      5.5     0.9    -      -       -      +
    118A  ASP*     4.6     3.3    +      -       -      +
     54B  GLN*     6.3     0.9    -      -       +      -
     55B  CYS*     1.3    76.3    -      -       -      +
     57B  ILE*     1.3    64.9    +      -       -      +
     58B  ASP      4.4     0.2    +      -       -      -
     59B  ASP*     3.6    37.9    -      -       -      +
     60B  ARG      3.7     4.0    -      -       -      +
     61B  ALA*     4.6    11.0    -      -       +      +
    169B  HIS*     3.8    13.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 57 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  CYS*     4.1     5.8    -      -       +      -
     56B  VAL*     1.3    79.5    -      -       -      +
     58B  ASP*     1.3    69.9    +      -       -      +
     59B  ASP      3.1     0.2    -      -       -      -
     60B  ARG      3.0    14.9    +      -       -      +
     62B  ALA*     4.4     5.4    -      -       +      -
     64B  LEU*     4.1    15.3    -      -       +      -
    169B  HIS*     3.8    45.5    -      -       +      +
    172B  VAL*     3.7    36.6    -      -       +      -
    173B  ARG*     4.1    25.1    -      -       +      +
    176B  ARG*     2.9    36.7    +      -       -      +
----------------------------------------------------------
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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