Contacts of the strand formed by residues 111 - 116 (chain B) in PDB entry 5E1M


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 VAL 111 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76B  THR*     4.1    15.5    -      -       +      -
     81B  LEU*     4.4     6.1    -      -       +      -
     87B  VAL*     3.1    14.4    -      -       +      +
     89B  MET*     4.2     9.0    -      -       +      -
    104B  LEU*     3.8    26.7    -      -       +      -
    108B  GLY*     2.9    21.1    +      -       -      +
    109B  LYS      3.9     7.8    -      -       -      +
    110B  ARG*     1.3    78.0    -      -       -      +
    112B  ARG*     1.3    63.7    +      -       -      +
    113B  ASN      3.7    17.3    -      -       -      +
    114B  TYR*     3.7    34.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 112 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  CYS*     3.7    16.0    -      -       -      +
     86B  GLU*     3.5    40.9    +      -       +      +
     87B  VAL      2.7    11.3    +      -       -      +
     88B  ASP*     2.7    37.2    +      -       -      +
    110B  ARG      3.3     1.9    +      -       -      +
    111B  VAL*     1.3    74.7    -      -       -      +
    113B  ASN*     1.3    75.7    +      -       -      +
    114B  TYR*     5.4     2.1    -      -       -      -
    125B  GLU*     6.3     0.2    -      -       -      +
    128B  SER*     4.5    13.3    +      -       -      -
    129B  TYR*     3.7    16.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 113 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  ASP*     3.0    28.8    +      -       -      +
     89B  MET      2.9    25.5    +      -       -      +
    111B  VAL*     3.7     3.7    -      -       -      +
    112B  ARG*     1.3    99.1    +      -       -      +
    114B  TYR*     1.3    62.7    +      -       -      +
    115B  PHE*     3.4    35.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 114 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89B  MET*     3.5    34.1    -      -       -      -
     97B  LEU*     4.0    34.5    -      -       +      +
    100B  ALA*     4.0     6.3    -      -       +      -
    101B  LYS*     3.6    55.5    -      -       +      +
    104B  LEU*     4.2     4.2    -      -       -      +
    108B  GLY      3.9     9.2    +      -       -      -
    111B  VAL*     3.7    32.6    -      -       +      +
    112B  ARG      5.4     1.3    -      -       -      -
    113B  ASN*     1.3    72.1    -      -       -      +
    115B  PHE*     1.3    63.7    +      -       -      +
    116B  CYS      3.9     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 115 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66B  LEU*     4.6     0.7    -      -       +      -
     88B  ASP*     3.7    19.3    -      -       +      -
     89B  MET      2.8    19.5    +      -       -      +
     90B  VAL*     3.3     7.8    -      -       +      +
     91B  ASP      3.0    25.3    +      -       -      +
     97B  LEU*     3.3     4.6    -      -       -      +
    113B  ASN*     3.4    38.8    -      -       +      -
    114B  TYR*     1.3    74.2    -      -       -      +
    116B  CYS*     1.3    59.4    +      -       -      +
    117B  CYS      3.5     0.9    +      -       -      -
    122B  PHE*     3.6    26.5    -      +       +      -
    125B  GLU*     6.0     2.5    -      -       +      -
    129B  TYR*     3.9    10.5    -      -       -      -
    314B  UNX      3.9    15.9    -      -       -      -
    315B  UNX      3.7    22.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 116 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  ASP      3.2     6.5    -      -       -      -
     92B  ILE      3.5    23.1    -      -       -      -
     94B  GLU*     3.3    46.7    -      -       -      +
     97B  LEU*     3.7     6.0    -      -       +      +
    114B  TYR      3.9     2.4    +      -       -      -
    115B  PHE*     1.3    68.1    -      -       -      +
    117B  CYS*     1.3    62.4    +      -       -      +
----------------------------------------------------------
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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