Contacts of the strand formed by residues 369 - 378 (chain B) in PDB entry 5EMV


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 ARG 369 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334B  GLU*     5.3    10.5    -      -       +      +
    335B  SER      3.6    13.7    -      -       -      +
    336B  LEU*     4.0    13.5    -      -       +      -
    364B  GLN      3.5     0.3    -      -       -      +
    365B  LEU*     3.7     2.2    -      -       -      -
    366B  GLU*     2.8    35.8    +      -       -      +
    367B  ASP      3.3     3.0    -      -       -      +
    368B  GLY*     1.3    79.6    -      -       -      +
    370B  PHE*     1.3    69.2    +      -       -      +
    371B  VAL*     3.9     2.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 370 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334B  GLU*     3.3     5.9    -      -       -      +
    335B  SER      2.9    32.1    +      -       -      +
    336B  LEU*     3.2    24.5    -      -       -      -
    337B  GLU*     3.2    27.1    -      -       -      +
    338B  HIS*     3.4    44.6    -      -       +      -
    363B  ALA*     3.9    15.0    -      -       +      -
    364B  GLN      3.3     1.6    -      -       -      -
    365B  LEU*     3.7    44.0    -      -       +      -
    368B  GLY      5.1     4.0    -      -       -      -
    369B  ARG*     1.3    74.1    -      -       -      +
    371B  VAL*     1.3    61.1    +      -       -      +
    372B  TYR*     3.7     4.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 371 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332B  GLN*     3.5    31.4    -      -       +      +
    333B  TYR      3.6     7.6    -      -       -      +
    334B  GLU*     4.9    12.6    -      -       +      +
    362B  ARG      4.2     0.2    -      -       -      +
    363B  ALA      3.7     2.8    -      -       -      -
    364B  GLN*     2.8    36.6    +      -       +      +
    366B  GLU*     3.8    29.4    -      -       +      +
    369B  ARG*     4.3     4.5    -      -       +      +
    370B  PHE*     1.3    79.6    -      -       -      +
    372B  TYR*     1.3    65.1    +      -       -      +
    373B  ARG*     3.6    26.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 372 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228B  LEU*     4.0     5.4    -      -       +      -
    331B  SER      4.0     0.2    -      -       -      +
    332B  GLN*     3.2     8.3    -      -       -      +
    333B  TYR*     2.9    53.5    +      -       +      +
    335B  SER*     3.8    16.6    -      -       -      -
    337B  GLU      3.0    22.6    +      -       -      -
    339B  MET*     3.1    42.0    +      -       -      +
    341B  LEU*     3.5    42.6    -      -       +      -
    361B  GLU*     3.7    21.5    -      -       +      -
    362B  ARG      4.1     0.4    -      -       -      -
    363B  ALA*     3.4    19.6    -      -       +      +
    370B  PHE      3.7    16.2    -      -       -      -
    371B  VAL*     1.3    75.1    -      -       -      +
    373B  ARG*     1.3    61.6    +      -       -      +
    374B  LEU*     4.1     4.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 373 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331B  SER      3.9     2.9    -      -       -      -
    332B  GLN*     3.8    32.7    +      -       -      +
    361B  GLU*     3.1    29.9    +      -       -      +
    364B  GLN*     4.8    11.0    -      -       +      +
    366B  GLU*     2.7    43.7    +      -       -      -
    371B  VAL*     3.6    18.5    +      -       +      +
    372B  TYR*     1.3    73.9    -      -       -      +
    374B  LEU*     1.3    62.3    +      -       -      +
    375B  LEU*     3.6    27.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 374 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329B  VAL      3.7     4.2    -      -       -      +
    330B  SER*     3.5     4.0    -      -       -      -
    331B  SER*     2.9    42.2    +      -       -      +
    333B  TYR*     4.3    24.7    -      -       +      -
    341B  LEU*     5.6     2.9    -      -       +      -
    343B  CYS*     4.3    19.3    -      -       +      -
    359B  GLU*     3.9    40.8    -      -       +      +
    360B  THR      5.3     0.7    -      -       -      +
    361B  GLU*     3.8    30.3    -      -       +      +
    372B  TYR*     4.3     5.6    -      -       +      +
    373B  ARG*     1.3    76.8    -      -       -      +
    375B  LEU*     1.3    60.9    +      -       -      +
    377B  SER*     4.6     6.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 375 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330B  SER*     3.5    19.3    -      -       -      +
    331B  SER      3.8    18.4    -      -       -      +
    332B  GLN*     4.4    15.3    -      -       +      +
    373B  ARG*     3.6    31.4    +      -       +      +
    374B  LEU*     1.3    73.7    -      -       -      +
    376B  ARG*     1.3    78.7    +      -       +      +
    377B  SER*     3.1     5.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 376 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236B  PHE*     4.2    18.0    -      -       +      -
    238B  GLU*     2.8    42.2    +      -       -      -
    246B  TYR*     4.4     3.0    +      -       -      -
    248B  ARG*     4.9     4.9    -      -       -      +
    326B  PHE*     3.5    32.4    -      -       +      -
    329B  VAL      3.5     2.2    +      -       -      -
    330B  SER*     2.8    21.7    +      -       -      +
    375B  LEU*     1.3    79.2    -      -       +      +
    377B  SER*     1.3    65.4    +      -       -      +
    378B  PRO*     3.3     6.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 377 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    328B  GLY*     3.3     0.9    -      -       -      -
    329B  VAL*     2.7    48.5    +      -       -      +
    357B  LYS*     3.3    14.0    +      -       -      +
    359B  GLU*     2.8    31.0    +      -       -      -
    374B  LEU*     4.6     8.3    -      -       -      -
    375B  LEU      3.1     4.0    +      -       -      -
    376B  ARG*     1.3    75.4    -      -       -      +
    378B  PRO*     1.3    71.4    +      -       -      +
    380B  P1L      5.5     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 378 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326B  PHE*     4.2    17.3    -      -       +      -
    327B  TYR      3.7     7.0    -      -       -      +
    329B  VAL*     5.5     0.4    -      -       -      +
    357B  LYS*     4.8     8.6    +      -       -      +
    376B  ARG      3.3     7.4    -      -       -      +
    377B  SER*     1.3    92.3    +      -       -      +
    379B  MET*     1.3    67.3    +      -       -      +
    380B  P1L      3.4     9.0    +      -       -      +
----------------------------------------------------------
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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