Contacts of the strand formed by residues 354 - 358 (chain B) in PDB entry 1M2V


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 ILE 354 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348B  LEU*     4.1    18.8    -      -       +      -
    349B  CYS      3.8     2.2    -      -       -      -
    350B  VAL*     4.4    12.6    -      -       +      -
    353B  ALA*     1.3    76.4    -      -       -      +
    355B  HIS*     1.3    62.4    +      -       -      +
    356B  TYR*     3.4    30.0    -      -       +      +
    376B  MET      3.5     1.9    -      -       -      +
    377B  ASP*     3.9     0.5    -      -       -      -
    378B  ILE*     2.9    41.1    +      -       +      +
    380B  ASP      5.9     0.4    -      -       -      +
    381B  LEU*     4.2    12.1    -      -       +      -
    423B  ALA*     5.0     2.7    -      -       +      +
    426B  PRO*     3.7    11.0    -      -       +      -
    427B  ALA*     3.6    26.5    -      -       +      +
    430B  SER*     3.1    25.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 355 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178A  ARG*     3.9     7.4    -      -       -      -
    348B  LEU*     3.5     7.2    -      -       -      +
    349B  CYS*     2.8    52.1    +      -       +      +
    351B  ASP*     3.0    30.7    +      -       -      -
    352B  ASN*     5.5     0.4    -      -       -      -
    353B  ALA*     3.2    15.8    +      -       +      +
    354B  ILE*     1.3    72.9    -      -       -      +
    356B  TYR*     1.3    63.3    +      -       -      +
    357B  PHE*     3.3     8.6    -      -       +      -
    375B  MET*     3.6    20.9    -      -       +      -
    376B  MET      3.6     4.0    -      -       -      -
    377B  ASP*     2.6    28.8    +      -       -      +
    414B  PHE*     3.4    32.5    -      +       -      -
----------------------------------------------------------
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Residues in contact with TYR 356 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    347B  ILE      4.3     0.2    -      -       -      -
    348B  LEU*     3.8    19.3    -      -       +      -
    354B  ILE*     3.4    29.7    -      -       +      +
    355B  HIS*     1.3    74.4    -      -       -      +
    357B  PHE*     1.3    77.2    +      -       -      +
    375B  MET*     3.4     1.4    -      -       -      +
    376B  MET*     3.0    38.1    +      -       +      +
    378B  ILE*     3.9    11.6    -      -       +      +
    385B  PHE      3.7    12.5    +      -       -      -
    386B  LEU*     3.4    24.4    -      -       +      +
    387B  PRO*     3.5    33.9    -      -       +      -
    392B  MET*     3.6    23.3    -      -       +      -
    430B  SER*     2.9    30.3    +      -       -      -
    434B  LEU*     4.2     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 357 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176A  ILE*     4.6     1.8    -      -       +      -
    347B  ILE*     3.2    34.7    +      -       +      +
    349B  CYS*     3.7    30.3    -      -       +      -
    355B  HIS*     3.3    17.0    -      -       +      -
    356B  TYR*     1.3    81.4    -      -       -      +
    358B  LYS*     1.3    63.6    +      -       -      +
    359B  ILE*     3.3    10.5    +      -       +      +
    373B  ILE*     5.2     0.2    -      -       +      -
    374B  ASN      3.3    13.9    -      -       -      +
    375B  MET*     3.2    44.6    -      -       +      -
    376B  MET*     3.9     2.0    -      -       -      -
    391B  SER      3.4     5.2    -      -       -      +
    392B  MET*     3.8    14.0    -      -       -      +
    406B  LEU*     3.4    46.2    -      -       +      -
    410B  ILE*     4.6     3.4    -      -       +      -
    413B  ILE*     4.6     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 358 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  SER*     5.9     0.8    +      -       -      -
    357B  PHE*     1.3    71.2    -      -       -      +
    359B  ILE*     1.3    62.8    +      -       -      +
    360B  PRO*     3.7    16.7    -      -       -      +
    372B  GLN      3.9    20.6    -      -       -      +
    373B  ILE*     3.5    10.6    -      -       -      +
    374B  ASN*     3.1    49.3    +      -       -      +
    376B  MET*     3.2    22.8    -      -       +      +
    388B  ARG*     3.9    30.0    -      -       -      +
    391B  SER*     3.0    27.4    -      -       -      -
    392B  MET*     4.6     0.4    -      -       -      -
----------------------------------------------------------
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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