Contacts of the strand formed by residues 326 - 335 (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 PHE 326 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236B  PHE*     3.7    14.6    -      +       -      +
    237B  VAL*     3.2     2.8    -      -       -      -
    238B  GLU*     2.9    60.1    +      -       +      +
    325B  GLY*     1.3    71.0    -      -       -      -
    327B  TYR*     1.3    74.1    +      -       -      +
    328B  GLY*     3.8    17.3    -      -       -      -
    376B  ARG*     3.5    44.6    -      -       +      +
    378B  PRO*     4.2    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 327 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236B  PHE      3.3     4.0    -      -       -      -
    237B  VAL*     3.7    16.8    -      -       +      +
    251B  PHE*     3.7    35.9    -      +       -      -
    308B  TRP*     3.5    26.1    +      +       -      -
    325B  GLY      3.6    22.2    +      -       -      -
    326B  PHE*     1.3    79.9    -      -       -      +
    328B  GLY*     1.3    58.8    +      -       -      +
    378B  PRO*     3.7     4.9    -      -       -      +
    379B  MET*     2.9    37.3    +      -       +      +
    384B  VAL*     3.6    46.4    -      -       +      -
    387B  LEU*     4.4     7.4    -      -       +      -
    388B  HIS*     5.4     5.7    +      -       -      +
    391B  ARG*     4.8     4.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 328 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235B  ALA*     3.4     3.5    -      -       -      +
    236B  PHE*     2.9    46.4    +      -       -      -
    326B  PHE*     3.8    19.1    +      -       -      -
    327B  TYR*     1.3    74.2    -      -       -      +
    329B  VAL*     1.3    66.4    +      -       -      +
    376B  ARG      5.0     0.2    -      -       -      -
    377B  SER      3.3     9.0    -      -       -      -
    379B  MET*     4.1     2.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 329 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233B  PHE*     3.8    24.7    -      -       +      -
    234B  SER      3.4    10.1    -      -       -      +
    235B  ALA*     4.3     2.7    -      -       +      -
    236B  PHE*     4.2     0.2    -      -       -      -
    328B  GLY*     1.3    79.2    -      -       -      +
    330B  SER*     1.3    65.6    +      -       -      +
    331B  SER*     4.4     4.7    -      -       -      +
    374B  LEU      3.7     2.3    -      -       -      +
    376B  ARG      3.5     0.3    +      -       -      -
    377B  SER*     2.7    47.4    +      -       -      +
    379B  MET*     4.0    22.9    -      -       +      -
    380B  P1L      4.1    41.1    -      -       +      +
    410B  GLN*     5.5     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 330 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232B  GLU*     4.5     1.7    -      -       -      +
    233B  PHE*     3.4     4.7    -      -       -      -
    234B  SER*     2.9    45.2    +      -       -      +
    236B  PHE*     3.6    14.6    -      -       -      -
    248B  ARG*     5.2     2.7    +      -       -      -
    329B  VAL*     1.3    71.2    -      -       -      +
    331B  SER*     1.3    65.3    +      -       -      +
    374B  LEU      3.5     3.1    -      -       -      -
    375B  LEU*     3.5    18.3    -      -       -      +
    376B  ARG*     2.8    24.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 331 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230B  LEU*     5.2     0.7    -      -       -      -
    232B  GLU      3.5     6.3    -      -       -      -
    233B  PHE*     3.2    27.6    -      -       -      -
    329B  VAL*     4.4     4.3    -      -       -      +
    330B  SER*     1.3    73.2    -      -       -      +
    332B  GLN*     1.3    63.4    +      -       -      +
    333B  TYR*     3.9    26.1    +      -       -      -
    343B  CYS*     6.2     1.3    -      -       -      -
    372B  TYR      4.0     0.4    -      -       -      +
    374B  LEU*     2.9    46.6    +      -       -      +
    375B  LEU*     3.8     4.3    -      -       -      +
    410B  GLN*     4.6     5.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 332 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230B  LEU*     3.7     4.8    -      -       -      +
    231B  VAL*     2.8    49.3    +      -       +      +
    232B  GLU*     2.9    18.8    +      -       +      +
    331B  SER*     1.3    77.3    -      -       -      +
    333B  TYR*     1.3    65.9    +      -       -      +
    371B  VAL*     3.5    24.2    -      -       +      +
    372B  TYR      3.2    11.4    -      -       -      +
    373B  ARG*     3.8    31.3    +      -       +      +
    375B  LEU*     4.4    13.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 333 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228B  LEU*     3.8    28.3    -      -       +      -
    229B  GLN      3.2    16.2    -      -       -      +
    230B  LEU*     3.7    27.2    -      -       +      +
    231B  VAL*     4.2     3.4    -      -       -      +
    233B  PHE*     5.7     0.3    -      -       -      -
    331B  SER*     3.9    24.6    +      -       -      -
    332B  GLN*     1.3    76.1    -      -       -      +
    334B  GLU*     1.3    63.0    +      -       -      +
    341B  LEU*     4.4    10.3    -      -       +      -
    343B  CYS*     4.3    11.7    -      -       +      -
    371B  VAL*     3.6     5.2    -      -       -      +
    372B  TYR*     2.9    37.0    +      -       +      -
    374B  LEU*     4.3    19.3    -      -       +      -
    410B  GLN*     4.2    14.0    +      -       -      -
    412B  VAL*     3.8    24.5    -      -       +      +
    422B  LEU*     4.2    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 334 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228B  LEU*     3.6     2.8    -      -       -      -
    229B  GLN*     2.9    55.7    +      -       +      +
    231B  VAL*     3.5    24.8    -      -       +      +
    333B  TYR*     1.3    75.1    -      -       -      +
    335B  SER*     1.3    65.4    +      -       -      +
    369B  ARG*     5.3     7.4    -      -       +      +
    370B  PHE      3.3    11.2    -      -       -      +
    371B  VAL*     4.8    11.7    -      -       +      +
    372B  TYR*     4.3     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 335 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227B  ARG      2.9    24.2    +      -       -      -
    228B  LEU*     4.0     5.4    -      -       -      -
    229B  GLN*     4.5     6.5    -      -       -      +
    334B  GLU*     1.3    78.0    -      -       -      +
    336B  LEU*     1.3    73.9    +      -       -      +
    337B  GLU*     3.0    18.7    +      -       -      +
    339B  MET*     3.5     6.9    -      -       -      +
    369B  ARG*     3.6     6.4    -      -       -      +
    370B  PHE      2.9    29.7    +      -       -      -
    372B  TYR*     3.8    20.6    -      -       -      -
----------------------------------------------------------
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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