Contacts of the strand formed by residues 36 - 41 (chain A) in PDB entry 4M83


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 ARG 36 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ALA      3.0    13.7    +      -       -      +
      8A  HIS*     3.3    38.9    +      -       -      +
      9A  ILE      2.8    26.0    +      -       -      -
     34A  GLY      3.9     0.8    +      -       -      -
     35A  HIS*     1.3    70.5    -      -       -      +
     37A  VAL*     1.3    61.3    +      -       -      +
     38A  THR*     4.8    10.6    -      -       +      +
     55A  ARG*     5.6     2.8    -      -       -      +
    102A  ASP*     2.6    40.5    +      -       -      -
    103A  ILE      5.5     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  ILE*     3.2    29.4    -      -       +      +
     11A  MET*     5.1     1.6    -      -       +      -
     27A  ILE*     3.8    32.3    -      -       +      +
     30A  LEU*     4.2     8.1    -      -       +      -
     31A  VAL*     3.6    31.9    -      -       +      +
     35A  HIS*     3.6    17.0    +      -       +      +
     36A  ARG*     1.3    80.1    -      -       -      +
     38A  THR*     1.3    71.3    +      -       -      +
     53A  GLY      4.6     0.5    -      -       -      +
     54A  ALA*     3.2     7.6    -      -       +      -
     55A  ARG*     2.8    22.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  HIS*     2.9    33.9    -      -       +      +
      9A  ILE      2.9     7.0    +      -       -      +
     10A  ALA*     3.3     1.2    -      -       -      +
     11A  MET*     2.7    33.1    +      -       -      +
     36A  ARG*     4.2    11.2    +      -       +      +
     37A  VAL*     1.3    81.9    -      -       -      +
     39A  TYR*     1.3    58.4    +      -       -      +
     55A  ARG*     3.1    40.2    -      -       +      +
     57A  VAL*     3.9     6.3    -      -       -      -
     99A  TYR*     2.6    26.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  MET*     3.3    45.9    -      -       +      +
     13A  SER*     3.7    21.0    -      -       -      -
     20A  VAL*     3.6    25.5    +      -       +      +
     23A  SER*     4.3     2.9    +      -       -      -
     24A  LEU*     5.1     6.1    -      -       +      -
     27A  ILE*     4.2    25.8    -      -       +      -
     38A  THR*     1.3    76.3    -      -       -      +
     40A  ALA*     1.3    80.5    +      -       -      +
     41A  ILE*     3.5    11.0    +      -       +      +
     49A  VAL*     3.5    42.2    -      -       +      -
     52A  THR*     5.4     0.2    -      -       -      -
     54A  ALA*     4.2     6.7    -      -       +      -
     55A  ARG      2.8    10.0    +      -       -      +
     56A  PRO*     3.3     4.0    -      -       -      +
     57A  VAL*     2.8    24.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 40 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  MET      2.8     9.8    +      -       -      +
     12A  PHE*     3.7    33.0    -      -       +      -
     13A  SER      3.2    26.0    +      -       -      +
     38A  THR      4.3     0.2    -      -       -      -
     39A  TYR*     1.3    70.1    -      -       -      +
     41A  ILE*     1.3    63.9    +      -       -      +
     57A  VAL*     3.2    12.8    -      -       +      +
     59A  TYR*     4.0     4.7    -      -       +      -
     95A  LEU*     3.7    23.6    -      -       +      -
     99A  TYR*     4.4     6.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  SER      4.2     7.2    -      -       -      +
     14A  ILE      3.4    27.1    -      -       -      +
     20A  VAL*     4.0    12.8    -      -       +      -
     39A  TYR*     3.8    18.4    -      -       +      +
     40A  ALA*     1.3    74.5    -      -       -      +
     42A  PRO*     1.3    84.8    -      -       +      +
     45A  PHE*     3.3    31.2    -      -       +      -
     46A  ALA*     4.0    20.4    -      -       -      -
     49A  VAL*     4.2    17.0    -      -       +      -
     56A  PRO*     4.5     1.8    -      -       +      -
     57A  VAL      3.1     4.2    +      -       -      -
     58A  LEU*     3.3    26.5    -      -       +      -
     59A  TYR*     3.4     8.1    +      -       -      -
----------------------------------------------------------
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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