Contacts of the strand formed by residues 102 - 108 (chain E) in PDB entry 5MGX


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 LEU 102 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95E  ASP*     4.0     3.1    -      -       -      +
     96E  ILE*     3.1    48.5    +      -       +      +
     97E  LEU*     3.7    33.3    +      -       +      -
     99E  ASN*     4.1     2.6    +      -       -      -
    100E  GLY      3.5     0.6    -      -       -      -
    101E  LEU*     1.3    79.6    -      -       -      +
    103E  ARG*     1.4    59.6    +      -       -      +
    155E  ALA*     4.2    15.7    -      -       +      +
    158E  LEU*     3.6    34.5    -      -       +      -
    159E  SER*     4.8     0.2    -      -       -      -
    171E  VAL*     3.8    18.6    -      -       +      -
    172E  THR      3.3     1.6    -      -       -      -
    173E  ALA*     3.7    25.8    -      -       +      -
    177E  TYR*     4.5     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 103 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93E  TRP*     3.4    55.2    -      -       +      +
     94E  LEU      3.2    10.5    -      -       -      +
     95E  ASP*     4.4    12.6    -      -       +      +
     96E  ILE*     4.5     1.6    -      -       -      -
    100E  GLY*     3.6    28.6    +      -       -      +
    102E  LEU*     1.4    75.8    -      -       -      +
    104E  LYS*     1.3    59.0    +      -       -      +
    171E  VAL*     3.2     6.1    -      -       -      +
    172E  THR*     2.9    49.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 104 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92E  GLU      3.8     1.6    -      -       -      +
     93E  TRP*     3.5     3.9    -      -       -      -
     94E  LEU*     2.8    48.2    +      -       +      +
     96E  ILE*     3.8    19.9    -      -       +      +
    103E  ARG*     1.3    73.6    -      -       -      +
    105E  LYS*     1.3    62.7    +      -       -      +
    106E  THR*     2.9    28.7    +      -       -      +
    116E  ARG*     5.3     2.6    -      -       -      +
    159E  SER      4.3     7.2    -      -       -      +
    162E  LEU*     3.4    38.9    +      -       +      -
    163E  MET*     3.7    14.8    -      -       +      -
    167E  GLU*     2.9    16.6    +      -       -      -
    169E  ALA*     3.9     7.6    -      -       +      -
    170E  MET      3.4     2.9    -      -       -      -
    171E  VAL*     4.0    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 105 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92E  GLU*     3.7    42.8    -      -       +      +
     93E  TRP*     3.6    48.6    -      -       +      +
    104E  LYS*     1.3    74.1    -      -       -      +
    106E  THR*     1.3    66.9    +      -       -      +
    107E  LEU*     3.5    11.1    +      -       +      +
    169E  ALA*     3.3     3.5    -      -       -      -
    170E  MET*     2.8    40.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 106 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92E  GLU*     4.6    18.6    +      -       -      +
    104E  LYS*     2.9    12.7    +      -       -      +
    105E  LYS*     1.3    77.5    -      -       -      +
    107E  LEU*     1.3    65.9    +      -       -      +
    108E  VAL      3.8    14.8    -      -       -      +
    109E  PRO*     4.0    12.8    -      -       +      -
    167E  GLU*     2.7    41.1    +      -       +      +
    168E  THR      3.9     3.1    -      -       -      -
    169E  ALA*     4.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 107 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105E  LYS*     4.1    24.7    -      -       +      +
    106E  THR*     1.3    77.9    -      -       -      +
    108E  VAL*     1.3    64.5    -      -       +      +
    109E  PRO*     4.3     4.3    -      -       -      +
    168E  THR*     2.8    28.5    +      -       +      +
    170E  MET*     4.2    27.8    -      -       +      +
    197E  GLU*     3.3    26.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 108 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106E  THR*     3.9     2.7    -      -       -      -
    107E  LEU*     1.3    82.5    -      -       +      +
    109E  PRO*     1.3    81.1    -      -       +      +
    166E  GLY      4.9     4.9    -      -       -      +
    167E  GLU*     3.4     3.8    -      -       -      +
    168E  THR*     2.8    49.6    +      -       +      +
----------------------------------------------------------
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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