Contacts of the strand formed by residues 437 - 448 (chain D) in PDB entry 2VM8


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 MET 437 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284D  GLY*     3.2    30.1    -      -       -      +
    285D  THR*     5.3     1.1    -      -       -      -
    364D  VAL*     4.5    13.2    -      -       +      -
    367D  ASP*     5.3     5.2    -      -       -      +
    368D  LYS*     5.7     4.9    -      -       +      -
    418D  LYS      3.5     0.7    -      -       -      +
    420D  ILE*     2.8    40.4    +      -       +      +
    434D  PHE*     3.0    42.3    +      -       +      +
    435D  GLU      3.3     1.4    +      -       -      +
    436D  GLY*     1.3    75.0    -      -       -      +
    438D  GLU*     1.3    63.4    +      -       -      +
    439D  CYS*     3.2    30.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 438 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367D  ASP*     4.1     6.4    -      -       -      +
    417D  VAL*     4.3    17.0    -      -       +      +
    418D  LYS      4.0     4.0    -      -       -      -
    419D  THR*     2.4    41.2    +      -       -      +
    436D  GLY      3.0    21.5    +      -       -      +
    437D  MET*     1.3    72.6    -      -       -      +
    439D  CYS*     1.3    60.9    +      -       -      +
    440D  ARG      4.2     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 439 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363D  SER*     3.3    49.4    -      -       -      -
    364D  VAL*     4.1     2.2    -      -       -      -
    367D  ASP*     3.6    11.7    -      -       -      -
    417D  VAL*     4.2     1.8    -      -       -      +
    418D  LYS*     3.0    31.8    +      -       -      +
    420D  ILE*     3.9    14.6    -      -       +      -
    437D  MET*     3.2    28.1    +      -       -      -
    438D  GLU*     1.3    74.6    -      -       -      +
    440D  ARG*     1.3    63.9    +      -       -      +
    441D  GLY      3.8     2.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 440 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    487C  ARG*     6.2     1.8    -      -       -      +
    363D  SER      3.6     5.7    -      -       -      +
    366D  TRP*     3.3     9.5    -      -       -      -
    367D  ASP*     2.9    33.1    +      -       -      +
    371D  VAL*     3.5    41.4    -      -       +      +
    414D  PRO*     3.0    24.3    +      -       -      +
    415D  ASP*     3.6    40.1    +      -       -      +
    416D  SER      3.4     4.0    -      -       -      -
    417D  VAL*     4.2    14.4    -      -       +      +
    438D  GLU      4.2     0.4    +      -       -      -
    439D  CYS*     1.3    73.0    -      -       -      +
    441D  GLY*     1.3    60.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 441 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363D  SER*     2.6    30.5    +      -       -      -
    366D  TRP*     3.8    15.7    -      -       -      -
    412D  TRP*     3.6     9.2    -      -       -      -
    413D  ASP      3.6    14.4    -      -       -      -
    414D  PRO      4.4     0.9    +      -       -      -
    416D  SER      2.7    13.9    +      -       -      -
    418D  LYS*     5.6     1.3    -      -       -      +
    439D  CYS*     3.8     3.2    +      -       -      +
    440D  ARG*     1.3    73.9    -      -       -      +
    442D  SER*     1.3    59.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 442 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363D  SER*     3.8     3.4    -      -       -      -
    412D  TRP*     3.4    14.6    -      -       -      -
    413D  ASP*     3.2    29.3    +      -       -      +
    416D  SER*     3.6    13.3    -      -       -      -
    418D  LYS*     3.5    43.0    +      -       -      +
    441D  GLY*     1.3    76.0    -      -       -      -
    443D  PRO*     1.3    74.0    +      -       -      +
    444D  LEU*     4.9     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 443 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98D  ALA      3.7    14.6    -      -       -      +
     99D  GLY*     3.5    34.8    -      -       -      +
    100D  GLY*     4.0     1.8    -      -       -      +
    363D  SER*     4.6     2.9    -      -       -      +
    410D  VAL*     3.6    22.2    -      -       +      -
    411D  ILE      3.9     5.2    -      -       -      +
    412D  TRP*     3.7     9.4    -      -       +      -
    418D  LYS*     4.6     6.2    +      -       -      -
    442D  SER*     1.3    93.2    -      -       -      +
    444D  LEU*     1.3    65.3    +      -       -      +
    446D  VAL*     3.8    16.2    -      -       +      -
    454D  LEU*     4.1     9.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 444 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63D  ARG*     3.5    41.3    -      -       -      +
    411D  ILE*     3.0    20.3    +      -       +      +
    413D  ASP*     3.6    31.2    -      -       +      +
    416D  SER*     4.5     2.7    -      -       -      +
    418D  LYS*     5.1     6.7    -      -       -      +
    442D  SER*     4.4     4.5    -      -       -      +
    443D  PRO*     1.3    78.8    -      -       -      +
    445D  VAL*     1.3    71.7    +      -       +      +
    454D  LEU*     3.9    17.5    -      -       -      +
    455D  GLU*     4.1     6.8    -      -       -      -
    456D  ASP      4.4     4.7    +      -       -      -
    457D  GLY      5.0     2.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 445 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58D  ILE*     4.5    13.2    -      -       +      -
    409D  LEU      5.6     0.2    -      -       -      +
    410D  VAL*     3.3    10.3    -      -       -      +
    411D  ILE*     2.9    55.7    +      -       +      -
    444D  LEU*     1.3    86.4    -      -       +      +
    446D  VAL*     1.3    64.8    -      -       -      +
    447D  ILE*     4.1    21.5    -      -       +      -
    452D  ILE*     4.1    14.6    -      -       +      -
    454D  LEU      3.4    13.2    -      -       -      +
    455D  GLU*     4.5    14.6    -      -       +      +
    456D  ASP      5.7     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 446 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97D  LEU*     3.2    55.0    -      -       +      +
    100D  GLY*     4.3     4.7    -      -       -      -
    102D  THR*     4.0    12.3    -      -       +      -
    409D  LEU      3.9     1.8    -      -       -      -
    410D  VAL*     4.4     7.0    -      -       +      +
    443D  PRO*     3.8    13.5    -      -       +      -
    445D  VAL*     1.3    80.2    -      -       -      +
    447D  ILE*     1.3    59.5    +      -       -      +
    452D  ILE*     3.6     3.3    -      -       -      -
    453D  VAL*     2.8    35.8    +      -       +      +
    454D  LEU*     3.3    34.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 447 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17D  LEU*     4.2    12.6    -      -       +      -
     19D  ILE*     3.7    32.5    -      -       +      -
     37D  MET*     4.3     9.4    -      -       +      -
     58D  ILE*     4.5     3.6    -      -       +      -
    102D  THR*     3.6     6.6    -      -       -      +
    407D  ALA      3.4    17.0    -      -       -      +
    408D  ASP*     3.1     5.5    -      -       -      -
    409D  LEU*     2.7    46.5    +      -       +      +
    411D  ILE*     5.7     2.0    -      -       +      -
    445D  VAL*     4.1    13.9    -      -       +      -
    446D  VAL*     1.3    75.8    -      -       -      +
    448D  SER*     1.3    60.8    -      -       -      +
    450D  GLY*     3.9    18.6    -      -       -      +
    451D  LYS      3.4     8.1    -      -       -      +
    452D  ILE*     3.7    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 448 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97D  LEU*     3.7    25.4    -      -       -      -
    102D  THR*     4.2     4.6    +      -       -      -
    132D  CYS      4.0    14.2    +      -       -      -
    133D  CYS*     4.2    10.2    -      -       -      +
    134D  ASP      4.8     1.2    +      -       -      -
    408D  ASP*     3.6     9.4    +      -       -      -
    446D  VAL      4.3     0.4    +      -       -      -
    447D  ILE*     1.3    74.5    -      -       -      +
    449D  GLN*     1.3    78.9    +      -       -      +
    450D  GLY      3.2     0.7    -      -       -      -
    451D  LYS*     2.8    26.6    +      -       -      +
    453D  VAL*     4.3    11.9    -      -       -      +
----------------------------------------------------------
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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