Contacts of the strand formed by residues 47 - 53 (chain B) in PDB entry 5ELI


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 ARG 47 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  GLY      3.9     2.1    +      -       -      +
     46B  ARG*     1.3    75.7    -      -       -      +
     48B  LYS*     1.3    61.9    +      -       -      +
     62B  ARG*     4.6     3.0    -      -       -      +
     65B  SER*     2.7    37.2    +      -       -      -
     66B  THR*     3.5    12.0    +      -       -      +
     67B  HIS      3.4    15.4    +      -       -      +
     68B  ASN*     3.3    48.3    +      -       -      +
     70B  TRP*     4.3    19.1    -      -       +      -
     73B  SER*     6.0     0.4    -      -       -      -
     86B  ASP*     5.3     0.4    -      -       -      -
    112B  SER*     3.5     4.3    -      -       -      -
    113B  LEU*     2.9    47.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 48 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  TYR*     3.3    44.6    +      -       -      -
     43B  HIS*     4.1    13.9    +      -       -      -
     46B  ARG      2.7    23.8    +      -       -      -
     47B  ARG*     1.3    78.3    -      -       -      +
     49B  ALA*     1.3    61.3    +      -       -      +
     65B  SER*     3.3     6.6    -      -       -      -
     66B  THR*     2.9    32.6    +      -       -      +
     70B  TRP*     4.4     3.6    -      -       -      +
     84B  ILE*     4.4     1.3    -      -       -      -
     86B  ASP*     3.2    29.4    +      -       -      +
     88B  THR*     4.7     0.4    -      -       -      +
     93B  LEU*     3.6    25.8    -      -       +      -
    111B  GLN      3.0     8.1    -      -       -      +
    112B  SER*     4.1     3.8    -      -       -      -
    113B  LEU*     4.2     2.9    -      -       -      +
    121B  LEU*     3.8    22.0    -      -       +      -
----------------------------------------------------------
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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  LYS*     1.3    77.4    -      -       -      +
     50B  TRP*     1.3    61.8    +      -       -      +
     51B  CYS      4.2     0.4    -      -       -      -
     62B  ARG*     3.5    40.6    -      -       -      +
     64B  VAL      3.4     6.1    -      -       -      +
     65B  SER*     4.0     0.4    -      -       -      +
     84B  ILE*     4.4     5.6    -      -       -      -
     93B  LEU*     4.6     1.7    -      -       -      +
    109B  GLN      3.8     0.7    -      -       -      +
    110B  CYS*     3.5     5.0    -      -       -      +
    111B  GLN*     2.9    35.4    +      -       +      +
    113B  LEU*     3.7    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  VAL*     3.8    24.5    -      -       +      -
     49B  ALA*     1.3    72.8    -      -       -      +
     51B  CYS*     1.3    59.6    +      -       -      +
     62B  ARG*     4.2     0.7    -      -       -      -
     63B  VAL*     2.9    48.2    +      -       +      +
     64B  VAL*     2.8    19.5    +      -       +      +
     82B  THR*     4.1    10.0    -      -       +      +
     84B  ILE*     4.4     0.9    -      -       +      +
     95B  ILE*     3.4    49.1    -      -       +      +
     97B  LEU*     4.5    17.2    -      -       +      +
    108B  TYR*     3.3    53.9    -      +       +      -
    109B  GLN      3.6    10.8    -      -       -      -
    110B  CYS*     3.9    19.7    -      -       -      -
    124B  VAL*     3.7    24.2    -      -       +      -
    126B  VAL*     5.1     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  TRP*     1.3    75.1    -      -       -      +
     52B  ARG*     1.3    59.9    +      -       -      +
     60B  CYS*     2.1    44.6    -      -       -      +
     61B  GLN      3.2    23.3    -      -       -      +
     62B  ARG*     3.7     8.1    -      -       -      +
     63B  VAL*     3.8     3.4    -      -       -      +
    108B  TYR*     3.2    10.2    -      -       -      +
    109B  GLN*     2.9    35.7    +      -       -      -
    111B  GLN*     3.3    32.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 52 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  CYS*     1.3    75.6    -      -       -      +
     53B  GLN*     1.3    63.1    +      -       -      +
     54B  LEU*     3.4    28.5    -      -       +      +
     60B  CYS*     3.2     4.8    -      -       -      -
     61B  GLN*     2.9    31.4    +      -       +      +
     63B  VAL*     4.1     6.2    -      -       +      +
    103B  HIS*     3.4    19.2    +      -       -      -
    104B  ASP*     4.3     5.5    +      -       -      +
    105B  ALA      3.0    27.3    +      -       -      -
    106B  GLY*     4.3     2.6    -      -       -      -
    107B  LEU      3.4    13.7    -      -       -      +
    108B  TYR*     3.1    43.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  CYS      4.2     0.2    +      -       -      -
     52B  ARG*     1.3    73.8    -      -       -      +
     54B  LEU*     1.3    69.9    +      -       -      +
     55B  GLY      2.9    24.6    +      -       -      +
     56B  GLU      2.9    17.2    +      -       -      -
     57B  LYS      4.7     4.2    -      -       -      -
     58B  GLY*     5.0     3.4    -      -       -      -
     59B  PRO      3.7    10.8    -      -       -      +
     60B  CYS*     4.0    10.0    -      -       +      -
    107B  LEU*     2.9    49.2    +      -       +      +
    108B  TYR*     5.2     0.4    -      -       -      -
    109B  GLN*     3.0    27.3    +      -       +      +
    123B  LYS*     3.4    28.3    +      -       -      +
----------------------------------------------------------
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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