Contacts of the strand formed by residues 71 - 75 (chain M) in PDB entry 2WWA


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 71 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12M  TYR      4.0     0.2    -      -       -      +
     13M  THR*     3.4     6.4    -      -       -      -
     14M  ILE*     3.4    39.6    +      -       +      -
     16M  LEU*     3.7    24.7    -      -       +      -
     36M  ILE*     4.1    15.7    -      -       +      -
     55M  LEU*     4.2    12.8    -      -       +      -
     58M  ALA*     5.4     9.2    -      -       +      +
     59M  ILE*     5.0    10.3    -      -       +      -
     68M  GLU*     4.7    11.2    -      -       +      +
     69M  TYR      4.4     3.1    -      -       -      +
     70M  ARG*     1.3    74.5    -      -       -      +
     72M  ARG*     1.3    75.4    +      -       -      +
     73M  LEU*     3.6    33.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 72 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11M  GLU*     3.8    23.1    -      -       -      +
     12M  TYR      3.7     6.1    -      -       -      +
     13M  THR*     3.9    18.0    -      -       +      +
     68M  GLU*     3.2    26.1    +      -       -      -
     70M  ARG*     3.5    25.7    +      -       -      +
     71M  LEU*     1.3    88.4    -      -       -      +
     73M  LEU*     1.3    69.2    +      -       -      +
     74M  ARG*     5.7     2.9    -      -       -      +
     90M  PHE      5.4     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 73 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11M  GLU*     3.5     8.8    -      -       -      +
     12M  TYR*     3.3    31.4    +      -       +      +
     14M  ILE*     3.8    23.1    -      -       +      -
     36M  ILE*     4.0     5.8    -      -       +      -
     55M  LEU*     4.3    15.5    -      -       +      -
     71M  LEU*     3.6    24.9    +      -       +      -
     72M  ARG*     1.3    79.8    -      -       -      +
     74M  ARG*     1.3    60.0    -      -       -      +
     75M  ILE*     4.3     3.0    +      -       +      +
     89M  LEU*     3.6    50.7    -      -       +      +
     90M  PHE*     3.7    19.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 74 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9M  THR*     4.1    18.0    +      -       +      +
     10M  ARG      3.7    11.4    -      -       -      +
     11M  GLU*     3.2    38.7    +      -       +      +
     72M  ARG*     5.7     3.0    -      -       -      +
     73M  LEU*     1.3    74.7    -      -       -      +
     75M  ILE*     1.3    64.5    +      -       -      +
     88M  PRO      3.7     5.0    -      -       -      +
     89M  LEU*     3.9     2.3    -      -       -      -
     90M  PHE      3.2    33.7    +      -       -      +
     91M  SER*     3.6    16.1    +      -       -      -
     92M  TYR*     3.6    36.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 75 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9M  THR*     3.5     7.9    -      -       -      +
     10M  ARG*     3.2    53.5    +      -       +      +
     11M  GLU*     5.1     0.4    -      -       -      -
     12M  TYR*     4.2    17.5    -      -       +      -
     40M  ALA*     4.3    11.9    -      -       +      +
     43M  HIS*     5.2     4.9    -      -       +      -
     44M  MET*     3.7    27.4    -      -       +      +
     73M  LEU*     5.1     2.2    -      -       +      +
     74M  ARG*     1.3    78.1    -      -       -      +
     76M  SER*     1.4    60.2    +      -       -      +
     87M  ASN*     3.1    29.2    -      -       -      +
     88M  PRO*     3.6     8.1    -      -       -      +
     89M  LEU*     3.8    20.0    -      -       +      -
     92M  TYR*     5.2     0.6    -      -       -      +
----------------------------------------------------------
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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