Contacts of the helix formed by residues 202 - 217 (chain 4) 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 THR 202 (chain 4).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2852  CYS      4.7     0.4    -      -       -      +
    2872  ILE*     1.9    51.5    -      -       +      +
    2902  ARG*     1.5    57.6    +      -       -      +
    2014  VAL*     1.3    79.8    -      -       +      +
    2034  THR*     1.3    54.1    +      -       -      -
    2044  ALA*     4.1     0.7    -      -       -      +
    2054  GLU*     2.9    38.8    +      -       -      +
    2064  ARG*     3.1    10.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 203 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2862  ASP*     3.3     3.4    -      -       -      +
    2872  ILE*     1.7    40.2    -      -       +      +
    2882  ASP*     2.1    83.7    +      -       -      +
     624  ARG*     3.7    16.6    +      -       -      -
    2024  THR      1.3    65.7    -      -       -      -
    2044  ALA*     1.3    56.8    +      -       -      -
    2054  GLU      3.2     0.7    -      -       -      -
    2064  ARG*     3.7    11.3    -      -       -      +
    2074  GLU*     3.3    26.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 204 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2872  ILE*     2.6    33.8    -      -       +      +
    2882  ASP*     5.0     3.1    -      -       -      -
    2024  THR*     4.1     1.3    -      -       -      +
    2034  THR*     1.3    70.0    -      -       -      +
    2054  GLU*     1.3    61.7    +      -       -      +
    2074  GLU*     4.6     4.5    -      -       -      -
    2084  ILE*     3.6    12.3    -      -       -      +
    2434  PRO*     3.5    31.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 205 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1994  SER      4.2     4.4    -      -       -      +
    2004  PHE*     3.4    34.7    -      -       +      -
    2014  VAL*     3.5    17.4    -      -       +      +
    2024  THR*     2.9    39.0    +      -       -      +
    2044  ALA*     1.3    87.2    -      -       -      +
    2064  ARG*     1.3    67.4    +      -       -      +
    2084  ILE*     3.1    21.9    -      -       -      +
    2094  VAL*     3.7     2.8    +      -       -      +
    2424  LEU*     3.7    22.6    -      -       -      +
    2434  PRO*     4.4     5.5    -      -       -      +
    2444  ASP*     5.1     2.8    -      -       -      +
    2464  GLN*     5.6     1.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 206 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     624  ARG*     4.4    13.1    -      -       -      +
    1834  ARG*     6.1     2.8    -      -       -      +
    1864  THR*     4.6    11.4    -      -       -      +
    1874  ASP*     3.4    33.4    +      -       -      -
    1904  MET*     3.7    27.9    -      -       +      +
    2004  PHE*     4.2     3.4    -      -       +      +
    2014  VAL      5.9     0.7    -      -       -      +
    2024  THR      3.1     8.2    +      -       -      +
    2034  THR*     3.7    15.7    -      -       -      +
    2054  GLU*     1.3    76.6    -      -       -      +
    2074  GLU*     1.3    67.9    +      -       -      +
    2094  VAL*     3.0    29.9    +      -       -      +
    2104  ARG*     5.1     0.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 207 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2882  ASP*     4.5     6.2    -      -       -      +
     594  GLN*     3.8    12.1    -      -       -      +
     624  ARG*     2.9    38.6    +      -       -      +
    2034  THR      3.3    14.7    +      -       -      +
    2044  ALA*     5.1     4.0    -      -       -      -
    2054  GLU      3.4     0.2    -      -       -      -
    2064  ARG*     1.3    82.6    -      -       -      +
    2084  ILE*     1.3    58.1    +      -       +      +
    2104  ARG*     3.1    39.3    +      -       -      +
    2114  ASP*     3.8     1.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 208 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2004  PHE*     5.4     2.9    -      -       +      -
    2044  ALA      3.6    13.9    +      -       -      +
    2054  GLU*     3.1    19.9    -      -       -      +
    2074  GLU*     1.3    76.2    -      -       -      +
    2094  VAL*     1.4    58.0    +      -       -      +
    2104  ARG      3.1     2.2    -      -       -      -
    2114  ASP*     3.0    11.6    +      -       +      +
    2124  ILE*     2.9    33.6    +      -       +      +
    2404  TYR*     3.2    39.9    -      -       +      +
    2424  LEU*     4.4    14.8    -      -       +      -
    2434  PRO*     3.9    29.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 209 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1864  THR*     3.6    22.4    -      -       +      +
    1894  LEU*     3.5    22.1    -      -       +      +
    1904  MET*     3.2    49.1    -      -       +      +
    1934  LEU*     4.1    13.5    -      -       +      -
    2004  PHE*     5.1     5.6    -      -       +      -
    2054  GLU      3.7     2.7    +      -       -      +
    2064  ARG*     3.0    24.6    +      -       -      +
    2084  ILE*     1.4    79.0    -      -       -      +
    2104  ARG*     1.3    59.1    +      -       -      +
    2124  ILE*     3.2    12.2    +      -       -      +
    2134  LYS*     3.0    24.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 210 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     164  LEU*     6.1     2.2    -      -       -      +
    1864  THR*     3.7    31.9    -      -       +      +
    2064  ARG*     6.2     0.2    -      -       -      +
    2074  GLU*     3.1    23.3    +      -       -      +
    2094  VAL*     1.3    82.7    -      -       +      +
    2114  ASP*     1.3    61.4    +      -       -      +
    2134  LYS*     3.4    12.7    -      -       -      +
    2144  GLU*     2.8    68.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 211 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2074  GLU      3.8     1.5    +      -       -      +
    2084  ILE*     3.0    19.6    +      -       +      +
    2104  ARG*     1.3    82.3    +      -       -      +
    2124  ILE*     1.3    60.7    +      -       -      +
    2144  GLU*     4.0    13.9    -      -       -      +
    2154  LYS*     2.7    63.4    +      -       -      +
    2404  TYR*     2.9    21.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 212 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1894  LEU*     3.7    17.3    -      -       +      -
    1934  LEU*     4.2    23.8    -      -       +      -
    2004  PHE*     5.1     7.4    -      -       +      -
    2084  ILE*     2.9    21.3    +      -       +      +
    2094  VAL*     3.3    12.6    -      -       -      +
    2114  ASP*     1.3    73.4    -      -       -      +
    2134  LYS*     1.4    61.2    -      -       -      +
    2154  LYS      3.2     0.7    +      -       -      -
    2164  LEU*     2.9    42.8    +      -       +      +
    2174  CYS*     3.7     2.8    +      -       -      -
    2404  TYR*     3.9    38.6    -      -       +      -
    2424  LEU*     5.2     1.3    -      -       +      -
    2484  ILE*     4.3    15.3    -      -       +      -
    2504  ILE*     4.5    15.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 213 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1574  ASP*     5.8     0.2    +      -       -      -
    1824  GLY*     2.8    25.6    +      -       -      +
    1854  LEU*     4.1     2.9    -      -       +      -
    1864  THR*     2.7    42.0    +      -       -      +
    1894  LEU*     3.6    17.3    -      -       +      -
    2094  VAL      3.0     8.7    +      -       -      +
    2104  ARG*     3.4    19.9    -      -       -      +
    2124  ILE*     1.4    74.0    -      -       -      +
    2144  GLU*     1.3    77.6    +      -       -      +
    2174  CYS*     3.0    32.0    +      -       -      +
    2574  CYS*     4.2    13.5    -      -       -      -
    3034  THR*     5.1     0.6    +      -       -      -
    3064  TYR*     3.7    32.8    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 214 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2104  ARG*     2.8    57.0    +      -       -      +
    2114  ASP*     4.2    10.4    -      -       -      +
    2124  ILE      3.3     0.4    -      -       -      -
    2134  LYS*     1.3    95.4    +      -       -      +
    2154  LYS*     1.3    64.0    +      -       +      +
    2174  CYS      4.3     5.7    +      -       -      +
    3064  TYR*     5.6     4.1    -      -       -      -
    3074  PRO*     5.7     2.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 215 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2114  ASP*     2.7    53.5    +      -       -      +
    2124  ILE*     4.1     0.7    -      -       -      +
    2144  GLU*     1.3    78.7    -      -       +      +
    2164  LEU*     1.3    72.2    +      -       +      +
    2174  CYS      4.9     0.7    -      -       -      +
    2184  TYR*     4.8     7.3    -      -       -      -
    2404  TYR*     4.1    15.1    +      -       +      -
    2544  ARG*     5.4     0.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 216 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2124  ILE*     2.9    27.7    +      -       +      +
    2154  LYS*     1.3    85.3    -      -       +      +
    2174  CYS*     1.3    62.1    +      -       -      +
    2184  TYR*     3.3     5.6    -      -       -      -
    2384  LYS*     3.8    46.9    -      -       +      +
    2394  SER      5.8     0.7    -      -       -      +
    2404  TYR*     3.9    32.8    -      -       +      +
    2504  ILE*     4.6    11.4    -      -       +      -
    2544  ARG*     2.9    43.6    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 217 (chain 4). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1894  LEU*     4.6     7.9    -      -       -      -
    2124  ILE*     3.7     2.9    +      -       -      -
    2134  LYS*     3.0    36.8    +      -       -      +
    2144  GLU      4.6     3.3    -      -       -      +
    2154  LYS      3.8     1.1    -      -       -      +
    2164  LEU*     1.3    72.4    -      -       -      +
    2184  TYR*     1.4    73.2    +      -       -      +
    2504  ILE*     6.2     0.4    -      -       -      -
    2534  GLU      4.7     0.4    -      -       -      -
    2544  ARG*     2.9    27.6    -      -       -      +
    2574  CYS*     4.2    19.3    -      -       -      -
    2584  PRO*     4.1     3.1    -      -       +      -
    3064  TYR*     4.0    21.2    -      -       +      -
    3074  PRO*     3.4    18.2    -      -       -      +
----------------------------------------------------------
 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