Contacts of the strand formed by residues 247 - 254 (chain M) 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 GLY 247 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246M  PHE*     1.3    83.7    -      -       -      +
    248M  MLY      1.3    67.5    +      -       -      +
    267M  THR*     3.6     1.4    -      -       -      -
    268M  TYR*     3.0    36.8    +      -       -      -
    269M  LEU*     4.4     0.6    +      -       -      +
    463M  ASP*     3.3    10.8    -      -       -      -
    464M  ILE*     4.2    16.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MLY 248 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186M  THR*     3.3    33.0    -      -       -      -
    189M  THR*     4.8    13.5    -      -       -      -
    190M  MLY      4.8     9.6    -      -       -      -
    193M  ILE*     5.6     1.8    -      -       -      -
    226M  ASN*     2.8    42.1    -      -       -      -
    229M  LEU*     5.4     9.7    -      -       +      +
    230M  GLU*     5.0     5.6    -      -       -      -
    234M  ASN*     5.9     0.2    -      -       -      -
    244M  SER*     4.6     7.2    -      -       -      -
    246M  PHE*     4.0    25.2    -      -       +      -
    247M  GLY*     1.3    78.2    -      -       -      +
    249M  PHE*     1.3    64.4    +      -       -      +
    250M  ILE*     3.8    32.8    -      -       +      -
    265M  ILE*     4.5    14.4    -      -       +      -
    266M  GLU      3.3    11.7    -      -       -      +
    267M  THR*     4.9     0.4    -      -       -      -
    268M  TYR*     4.1     6.6    -      -       -      -
    461M  VAL      3.7     1.0    -      -       -      +
    462M  LEU*     3.5     3.3    -      -       -      +
    463M  ASP*     2.4    64.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 249 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174M  SER*     5.5     2.0    -      -       -      -
    248M  MLY      1.3    77.8    -      -       -      +
    250M  ILE*     1.3    60.5    +      -       -      +
    251M  ARG*     4.0    26.5    -      -       +      -
    264M  ASP      3.0    12.6    -      -       -      +
    265M  ILE*     3.5     0.3    -      -       -      -
    266M  GLU*     3.1    24.6    +      -       +      +
    268M  TYR*     3.8    23.8    -      -       +      +
    458M  PHE*     4.7     5.4    -      +       -      -
    460M  GLY*     3.9    28.7    -      -       -      -
    461M  VAL      3.5     6.5    -      -       -      -
    462M  LEU*     3.6    28.0    -      -       +      -
    660M  LEU*     3.9    18.8    -      -       +      -
    663M  ASN*     4.2    21.1    -      -       +      -
    664M  LEU*     4.0    24.0    -      -       +      -
    667M  THR*     6.0     0.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 250 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189M  THR*     5.0     3.6    -      -       +      -
    193M  ILE*     3.1    34.5    -      -       +      -
    222M  ILE*     6.0     0.9    -      -       +      -
    226M  ASN*     5.4     0.7    -      -       -      +
    248M  MLY      3.8    39.7    -      -       +      -
    249M  PHE*     1.3    75.6    -      -       -      +
    251M  ARG*     1.3    71.2    +      -       -      +
    252M  ILE*     4.3    14.3    -      -       +      +
    263M  ALA*     4.3     6.1    -      -       +      -
    264M  ASP      3.2    17.9    -      -       -      +
    265M  ILE*     4.3    16.4    -      -       +      -
    459M  ILE      3.5     2.4    -      -       -      +
    460M  GLY*     3.3     4.7    -      -       -      -
    461M  VAL*     3.1    38.3    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 251 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249M  PHE*     4.0    21.3    -      -       +      -
    250M  ILE*     1.3    79.0    -      -       -      +
    252M  ILE*     1.3    62.4    +      -       -      +
    253M  HIS*     3.1    45.8    +      -       +      -
    263M  ALA*     3.0    22.5    -      -       -      -
    264M  ASP*     3.0    42.1    +      -       +      -
    458M  PHE*     3.7    35.3    -      -       +      -
    459M  ILE      4.0     2.2    -      -       -      -
    663M  ASN*     3.6    34.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 252 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193M  ILE*     3.9    32.8    -      -       +      -
    196M  PHE*     4.6    20.2    -      -       +      -
    222M  ILE*     5.0     6.7    -      -       +      -
    250M  ILE*     4.3    12.3    -      -       +      -
    251M  ARG*     1.3    71.4    -      -       -      +
    253M  HIS*     1.3    61.4    +      -       -      +
    254M  PHE*     3.3    24.1    -      -       +      -
    260M  LEU*     3.2    35.0    -      -       +      -
    262M  SER      3.4     5.8    -      -       -      +
    263M  ALA*     4.6     7.0    -      -       +      -
    458M  PHE*     3.0     3.1    -      -       -      -
    459M  ILE      2.7    44.5    +      -       -      +
    461M  VAL*     4.6    10.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 253 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251M  ARG*     3.1    66.5    +      -       +      -
    252M  ILE*     1.3    71.6    -      -       -      +
    254M  PHE*     1.3    64.0    +      -       -      +
    260M  LEU*     4.4     0.3    -      -       -      -
    261M  ALA*     2.9    24.6    +      -       -      +
    262M  SER*     2.4    39.2    +      -       -      +
    263M  ALA      4.3     0.4    +      -       -      -
    264M  ASP*     3.6    10.3    +      -       -      -
    455M  ARG*     4.2    33.3    +      -       +      -
    457M  TYR      3.5     5.8    -      -       -      +
    458M  PHE*     3.6    20.0    -      +       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 254 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163M  TYR*     4.1    11.7    -      +       -      -
    166M  MET*     3.0    40.4    -      -       +      -
    196M  PHE*     3.6    31.9    -      +       +      -
    200M  ALA*     4.3     7.6    -      -       +      -
    252M  ILE*     3.3    36.8    -      -       +      -
    253M  HIS*     1.3    76.0    -      -       -      +
    255M  GLY*     1.3    66.6    +      -       -      +
    258M  GLY*     3.9    20.4    -      -       -      +
    259M  LYS      4.2     1.1    -      -       -      -
    260M  LEU*     3.7    30.1    -      -       +      -
    261M  ALA*     4.2     0.4    -      -       -      -
    455M  ARG*     3.8     3.5    -      -       -      -
    456M  GLN      3.4    11.8    +      -       -      -
    457M  TYR*     2.7    18.7    +      -       +      +
    459M  ILE*     3.3    25.4    -      -       +      -
----------------------------------------------------------
 Back to top of page


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