Contacts of the helix formed by residues 381 - 391 (chain G) in PDB entry 1MVW


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 381 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    379G  GLY*     3.6     4.1    -      -       -      -
    380G  THR*     1.3    78.1    -      -       -      +
    382G  VAL*     1.3    73.8    +      -       +      +
    383G  ALA      3.5     0.2    -      -       -      -
    384G  ASP*     3.4    11.4    -      -       -      +
    385G  MLY      2.9    57.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 382 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360G  HIS*     3.4    46.0    -      -       +      +
    363G  ASN*     4.1    23.8    -      -       +      +
    364G  LEU*     3.6    13.7    -      -       +      -
    379G  GLY      5.2     0.6    +      -       -      -
    381G  GLU*     1.3    91.8    -      -       +      +
    383G  ALA*     1.3    67.9    +      -       -      +
    384G  ASP      2.9     1.8    -      -       -      -
    385G  MLY      3.0    11.6    +      -       +      +
    386G  ALA*     2.9    20.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 383 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    364G  LEU*     3.9    18.0    -      -       +      +
    379G  GLY      4.6     3.9    +      -       -      +
    380G  THR*     4.5     8.5    -      -       -      -
    381G  GLU      3.5     1.0    -      -       -      +
    382G  VAL*     1.3    78.1    -      -       -      +
    384G  ASP*     1.3    53.9    +      -       -      +
    386G  ALA*     3.1     3.4    +      -       -      +
    387G  ALA*     2.6    38.7    +      -       -      +
    394G  SER*     3.6     8.7    -      -       -      +
    397G  LEU*     4.6     3.2    -      -       +      +
    398G  LEU*     3.6    42.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 384 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    380G  THR*     2.4    33.6    +      -       -      +
    381G  GLU*     3.4    11.7    -      -       -      +
    383G  ALA*     1.3    81.0    -      -       -      +
    385G  MLY      1.3    59.4    +      -       +      +
    387G  ALA*     3.6     2.3    -      -       -      +
    388G  TYR*     3.0    29.6    +      -       -      +
    394G  SER*     2.3    38.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with MLY 385 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304G  LEU*     4.1    47.8    -      -       +      -
    360G  HIS*     4.1    26.7    -      -       +      +
    381G  GLU*     2.9    56.3    -      -       -      +
    382G  VAL*     3.0    14.0    +      -       +      +
    384G  ASP*     1.3    77.0    +      -       +      -
    386G  ALA*     1.3    67.5    +      -       -      +
    388G  TYR*     3.8     2.4    -      -       -      +
    389G  LEU*     2.9    31.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 386 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357G  ALA*     4.5     4.9    -      -       -      +
    360G  HIS*     4.2    14.3    -      -       +      +
    361G  TYR*     3.6    34.8    -      -       +      -
    364G  LEU*     4.6     4.9    -      -       +      -
    382G  VAL      2.9    14.8    +      -       -      +
    383G  ALA*     3.6     6.3    -      -       -      +
    385G  MLY      1.3    77.5    +      -       -      +
    387G  ALA*     1.3    64.3    +      -       -      +
    389G  LEU*     3.7     4.3    -      -       -      +
    390G  MET*     3.1    28.2    +      -       -      +
    397G  LEU*     5.1     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 387 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    383G  ALA      2.6    21.5    +      -       -      +
    384G  ASP      3.6     5.4    -      -       -      +
    386G  ALA*     1.3    74.5    -      -       -      +
    388G  TYR*     1.3    58.9    +      -       -      +
    391G  GLY      3.1     2.8    +      -       -      -
    392G  LEU*     2.6    50.0    +      -       +      +
    393G  ASN      3.9     2.7    -      -       -      -
    394G  SER*     3.5    34.8    -      -       -      +
    397G  LEU*     4.6     5.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 388 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302G  MET      4.8     3.8    -      -       -      -
    304G  LEU*     3.9    20.4    -      -       +      -
    353G  MLY      3.1    41.4    -      -       -      -
    384G  ASP      3.0    18.5    +      -       -      +
    385G  MLY      3.8     2.0    -      -       -      +
    387G  ALA*     1.3    75.1    -      -       -      +
    389G  LEU*     1.3    88.9    +      -       +      +
    391G  GLY*     3.1    12.6    +      -       -      -
    392G  LEU      4.6     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 389 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302G  MET      3.6    22.9    -      -       -      +
    303G  LEU*     3.1    26.2    -      -       +      +
    304G  LEU*     4.0     4.3    -      -       +      -
    353G  MLY      3.4    65.3    -      -       +      +
    354G  LEU*     4.4     4.2    -      -       -      +
    356G  GLY      4.7     0.7    -      -       -      -
    357G  ALA*     4.4    10.1    -      -       +      +
    360G  HIS*     3.9    17.9    -      -       +      +
    385G  MLY      2.9    20.1    +      -       -      +
    386G  ALA      3.7     3.8    -      -       -      +
    388G  TYR*     1.3    98.8    -      -       +      +
    390G  MET*     1.3    58.6    +      -       -      +
    616G  VAL*     4.4     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 390 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354G  LEU*     4.1    16.8    -      -       +      +
    357G  ALA*     3.7    23.3    -      -       +      -
    358G  VAL*     5.3     3.6    -      -       +      -
    361G  TYR*     2.8    43.1    -      -       +      +
    386G  ALA      3.1    15.2    +      -       -      +
    387G  ALA      4.1     0.2    -      -       -      +
    388G  TYR      3.1     0.6    -      -       -      -
    389G  LEU*     1.3    78.6    -      -       -      +
    391G  GLY*     1.3    50.1    +      -       -      +
    392G  LEU*     4.1    14.0    -      -       +      +
    433G  VAL*     4.2    25.8    -      -       +      -
    611G  TYR*     4.2    19.3    -      -       +      +
    614G  SER*     2.4    28.6    +      -       -      -
    616G  VAL*     3.4    11.4    -      -       -      +
    619G  LEU*     3.6    18.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 391 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353G  MLY      4.9     0.9    -      -       -      -
    387G  ALA      3.7     0.7    -      -       -      -
    388G  TYR*     3.1    13.8    +      -       -      -
    389G  LEU      3.5     0.2    -      -       -      -
    390G  MET*     1.3    80.8    -      -       -      +
    392G  LEU*     1.3    59.8    +      -       -      +
    613G  MLY      4.9     0.5    -      -       -      +
    614G  SER*     3.2     8.7    +      -       -      -
    615G  SER*     2.7    39.1    +      -       -      -
    616G  VAL*     3.6    11.8    -      -       -      +
----------------------------------------------------------
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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