Contacts of the strand formed by residues 78 - 83 (chain L) in PDB entry 1MWA


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 TYR 78 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9L  VAL*     5.3     0.4    -      -       -      -
     23L  LEU*     3.1    33.2    -      -       +      -
     40L  LEU      3.1    11.2    -      -       -      -
     41L  LYS*     3.2    45.0    +      -       +      +
     46L  ILE*     4.5    12.6    -      -       +      -
     70L  PHE*     3.4    41.6    -      +       +      +
     71L  THR      4.1    12.0    +      -       -      -
     72L  PRO*     4.7     6.5    -      -       +      -
     76L  ASP*     3.8    22.2    +      -       +      +
     77L  THR*     1.3    78.1    -      -       -      +
     79L  ALA*     1.3    56.9    +      -       -      +
     94L  TYR*     3.2     8.5    -      -       -      +
     95L  TRP*     2.7    53.9    +      +       +      +
----------------------------------------------------------
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Residues in contact with ALA 79 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9L  VAL*     5.1     3.8    -      -       -      -
     23L  LEU*     5.6     1.3    -      -       -      +
     39L  MET*     3.3     6.7    -      -       -      +
     40L  LEU*     2.6    55.3    +      -       +      +
     43L  GLY*     6.4     0.2    -      -       -      -
     78L  TYR*     1.3    77.2    -      -       -      +
     80L  CYS*     1.3    60.6    +      -       -      +
     92L  THR*     4.6     7.2    -      -       -      +
     93L  VAL      3.3    13.2    -      -       -      +
     94L  TYR*     3.8    24.9    -      -       +      +
     95L  TRP      4.4     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 80 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7L  ILE*     4.6     2.4    -      -       +      +
      9L  VAL*     3.7    17.3    -      -       +      -
     25L  CYS*     2.0    50.5    -      -       +      -
     37L  ILE*     3.8    15.7    -      -       -      -
     38L  GLN      3.3     9.2    -      -       -      -
     39L  MET*     4.0     6.7    -      -       +      +
     79L  ALA*     1.3    75.3    -      -       -      +
     81L  ARG*     1.3    62.9    +      -       -      +
     82L  VAL*     4.1     7.9    +      -       -      +
     91L  LYS      3.6     1.6    -      -       -      +
     92L  THR*     3.0     3.2    -      -       -      -
     93L  VAL*     2.8    31.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 81 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36L  GLU*     3.7     7.2    -      -       -      +
     38L  GLN*     2.5    57.5    +      -       +      +
     40L  LEU*     3.1    42.4    -      -       +      +
     43L  GLY      5.5     0.6    +      -       -      -
     45L  LYS*     2.8    37.8    -      -       -      +
     80L  CYS*     1.3    72.3    -      -       -      +
     82L  VAL*     1.3    64.1    +      -       -      +
     83L  LYS*     4.1     0.8    +      -       +      +
     90L  PRO*     4.2    24.9    -      -       +      -
     91L  LYS      3.2     7.6    -      -       -      +
     92L  THR*     4.0    15.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 82 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5L  PRO*     4.2     8.7    -      -       +      -
      7L  ILE*     3.2    37.2    -      -       +      -
     27L  VAL*     4.2    17.0    -      -       +      -
     35L  ILE*     4.8     7.9    -      -       +      -
     36L  GLU      3.3     6.5    -      -       -      +
     37L  ILE*     4.4     8.5    -      -       +      -
     80L  CYS*     4.2    17.9    -      -       -      -
     81L  ARG*     1.3    79.9    -      -       -      +
     83L  LYS*     1.3    59.4    +      -       -      +
     87L  MET*     3.2    24.9    -      -       +      +
     90L  PRO*     3.4     2.2    -      -       -      +
     91L  LYS*     2.7    33.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 83 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35L  ILE*     3.3     7.0    -      -       -      +
     36L  GLU*     2.9    59.1    +      -       +      +
     81L  ARG*     4.1     1.5    +      -       +      -
     82L  VAL*     1.3    72.3    -      -       -      +
     84L  HIS*     1.3    67.8    +      -       -      +
     85L  ASP*     6.0     2.5    -      -       -      +
     87L  MET      4.0    12.6    +      -       -      -
     88L  ALA      3.6    22.4    +      -       -      -
     89L  GLU      5.0     0.4    -      -       -      -
     90L  PRO*     3.9    33.2    -      -       +      +
----------------------------------------------------------
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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