Contacts of the strand formed by residues 116 - 120 (chain A) in PDB entry 3MR3


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 GLU 116 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  LEU*     4.1    18.7    -      -       +      +
     12A  VAL      3.0    18.6    -      -       -      +
     13A  ASP*     3.2    12.0    -      -       +      +
    100A  MET*     3.7     7.3    -      -       -      +
    103A  MET*     5.8     0.2    -      -       -      -
    112A  ALA*     2.9    35.9    +      -       +      +
    113A  SER*     2.7    31.5    +      -       -      +
    114A  ILE      3.8     0.2    -      -       -      -
    115A  ASP*     1.3    78.5    -      -       -      +
    117A  ALA*     1.3    60.3    +      -       -      +
    118A  TYR*     5.1     1.2    +      -       -      -
    224A  LYS*     4.4    13.7    +      -       -      +
    435A   MG      2.1    30.6    -      -       -      -
      9P    T      2.8    20.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  LEU*     3.2     6.7    -      -       -      +
     12A  VAL      3.0    29.3    +      -       -      +
    100A  MET*     3.9    20.6    -      -       -      -
    103A  MET*     3.7    27.0    -      -       +      +
    109A  ILE*     4.3     6.7    -      -       +      -
    110A  GLU      3.2    17.3    -      -       -      +
    112A  ALA      4.1     1.1    -      -       -      +
    116A  GLU*     1.3    76.3    -      -       -      +
    118A  TYR*     1.3    64.7    -      -       -      +
    119A  VAL*     4.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  VAL*     4.3     2.9    -      -       +      -
     10A  ALA      3.2    11.9    -      -       -      +
     11A  LEU*     3.6    26.2    -      -       +      +
    109A  ILE*     3.1     9.5    -      -       -      +
    110A  GLU*     2.9    40.2    +      -       +      +
    112A  ALA*     3.6    28.9    -      -       +      -
    116A  GLU*     5.1     1.3    +      -       -      -
    117A  ALA*     1.3    73.0    -      -       -      +
    119A  VAL*     1.3    61.6    -      -       -      +
    220A  LYS*     3.4    51.4    -      -       +      -
    224A  LYS*     3.6    15.6    -      -       -      +
    256A  ARG*     2.8    39.8    +      -       -      -
    310A  VAL*     3.9    21.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  VAL*     3.3     6.9    -      -       -      +
     10A  ALA*     2.7    46.5    +      -       +      +
     12A  VAL*     4.4     6.7    -      -       +      -
    103A  MET*     3.2    34.8    -      -       +      -
    107A  ALA*     3.7    16.4    -      -       +      +
    108A  VAL      3.7     5.2    -      -       -      +
    109A  ILE*     4.2     5.2    -      -       +      -
    117A  ALA      4.1     1.8    -      -       -      +
    118A  TYR*     1.3    76.6    -      -       -      +
    120A  ASP*     1.3    61.9    +      -       -      +
    121A  LEU*     3.6    28.6    +      -       +      -
    200A  MET*     4.1    17.9    -      -       +      -
    310A  VAL*     4.3     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ARG*     4.6    11.5    -      -       -      -
      8A  VAL      3.9     4.0    -      -       -      +
      9A  VAL*     4.8     4.5    -      -       -      +
    107A  ALA*     3.7    15.1    -      -       -      +
    108A  VAL*     3.3    21.2    +      -       +      +
    119A  VAL*     1.3    70.1    -      -       -      +
    121A  LEU*     1.3    59.8    +      -       -      +
    122A  THR*     3.0    28.6    +      -       -      -
    123A  SER*     4.8     7.1    +      -       -      -
    124A  ALA      5.4     0.2    +      -       -      -
    310A  VAL*     3.9    33.7    +      -       +      +
----------------------------------------------------------
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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