Contacts of the strand formed by residues 745 - 748 (chain A) in PDB entry 3MP6


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 745 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    744A  LYS*     1.3    81.5    -      -       -      +
    746A  VAL*     1.3    64.6    +      -       -      +
    747A  ILE*     4.7     6.1    -      -       +      -
    765A  PHE*     4.0    20.0    -      -       +      -
    771A  ILE*     5.2     0.2    -      -       +      -
    772A  LYS      2.9    11.8    +      -       -      +
    773A  VAL*     3.4    16.3    -      -       +      -
    774A  THR*     2.9    26.8    +      -       -      -
    796A  ASP*     3.3    24.0    -      -       +      -
    797A  ILE*     4.7     5.4    -      -       +      -
   1010A  ASN*     4.0    10.1    -      -       +      +
   1013A  LEU*     3.9    24.7    -      -       +      +
   1014A  ALA*     3.9    22.4    -      -       +      +
   1017A  PHE*     3.9    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 746 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    741A  GLU*     6.5     1.3    -      -       +      -
    744A  LYS*     4.3    25.6    -      -       +      +
    745A  LEU*     1.3    78.8    -      -       -      +
    747A  ILE*     1.3    62.3    +      -       -      +
    748A  TRP*     4.1    10.8    -      -       +      +
    774A  THR*     3.4    13.9    -      -       -      +
    776A  GLU*     3.8    32.1    -      -       -      +
    794A  GLY      5.4     1.6    -      -       -      +
    795A  PRO*     3.5    13.2    -      -       +      +
    796A  ASP*     2.8    38.3    +      -       -      +
    797A  ILE      3.3     6.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 747 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    745A  LEU*     4.7     3.8    -      -       +      -
    746A  VAL*     1.3    80.1    -      -       -      +
    748A  TRP*     1.3    65.2    +      -       -      +
    758A  LEU*     3.9    12.1    -      -       +      -
    773A  VAL*     3.7    27.6    -      -       +      -
    774A  THR      2.9     9.4    +      -       -      +
    775A  VAL*     3.4    10.3    -      -       +      +
    776A  GLU*     2.8    32.4    +      -       -      +
    797A  ILE*     3.4    22.0    -      -       +      +
    799A  PHE*     3.5    33.0    -      -       +      -
   1017A  PHE*     3.6    37.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 748 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    746A  VAL*     4.1     4.4    -      -       +      +
    747A  ILE*     1.3    81.4    -      -       -      +
    749A  ILE*     1.3    60.3    +      -       -      +
    776A  GLU*     2.9    37.1    +      -       +      +
    778A  PRO*     3.8    19.9    -      -       +      +
    781A  LEU*     4.0    33.0    -      -       +      -
    784A  LYS*     4.0    18.8    -      -       +      -
    785A  PHE*     3.8    31.0    -      +       +      -
    788A  VAL*     3.9    22.4    -      -       +      -
    794A  GLY*     5.3     1.3    -      -       -      -
    795A  PRO*     3.5    37.9    -      -       +      +
    797A  ILE      3.0     8.5    +      -       -      +
    798A  ILE*     4.6     3.4    -      -       +      -
    799A  PHE*     2.8    33.8    +      -       -      +
----------------------------------------------------------
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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