Contacts of the strand formed by residues 229 - 238 (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 GLN 229 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223B  LEU      4.6     2.9    -      -       -      +
    224B  GLY*     4.1     5.2    -      -       -      -
    225B  THR      2.6    29.8    +      -       -      +
    226B  ALA*     3.3    21.6    +      -       -      +
    227B  ARG      4.1     0.8    -      -       -      -
    228B  LEU*     1.3    76.2    -      -       -      +
    230B  LEU*     1.3    65.6    +      -       -      +
    231B  VAL*     4.3     0.6    -      -       +      +
    256B  GLN*     5.3     1.3    -      -       -      +
    333B  TYR*     3.2    10.2    -      -       -      +
    334B  GLU*     2.9    64.7    +      -       +      +
    335B  SER*     4.4     4.1    +      -       -      +
    336B  LEU      5.7     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 230 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223B  LEU*     3.1    51.1    +      -       +      +
    224B  GLY*     4.4     0.8    -      -       -      -
    228B  LEU      4.3     0.4    +      -       -      -
    229B  GLN*     1.3    74.4    -      -       -      +
    231B  VAL*     1.3    61.3    +      -       -      +
    232B  GLU      3.7    17.9    -      -       -      +
    233B  PHE*     4.1    19.5    -      -       +      -
    254B  ILE*     4.0    24.9    -      -       +      -
    256B  GLN*     2.7    29.8    +      -       -      +
    331B  SER*     5.2     1.3    -      -       -      -
    332B  GLN      3.7    16.2    -      -       -      +
    333B  TYR*     3.7    30.0    -      -       +      +
    422B  LEU*     4.6     2.3    -      -       +      +
    426B  TYR*     5.4     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 231 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229B  GLN*     5.6     0.4    -      -       +      -
    230B  LEU*     1.3    76.6    -      -       -      +
    232B  GLU*     1.3    67.4    +      -       +      +
    255B  SER*     3.8     0.7    +      -       -      -
    256B  GLN*     2.8    41.5    +      -       -      +
    332B  GLN*     2.8    41.1    +      -       +      +
    333B  TYR      4.2     1.8    -      -       -      -
    334B  GLU*     3.5    46.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 232 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230B  LEU*     3.7     5.6    -      -       -      +
    231B  VAL*     1.3    88.6    -      -       +      +
    233B  PHE*     1.3    67.3    +      -       -      +
    234B  SER*     4.9     5.7    +      -       -      +
    248B  ARG*     5.6     4.0    +      -       -      -
    253B  HIS*     3.3    27.1    -      -       +      -
    254B  ILE      3.2    13.0    -      -       -      +
    255B  SER*     3.7    13.6    +      -       -      -
    330B  SER*     4.5     2.0    -      -       -      +
    331B  SER*     3.5     2.8    -      -       -      -
    332B  GLN*     2.9    34.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 233 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230B  LEU*     4.1    23.1    -      -       +      -
    232B  GLU*     1.3    76.7    -      -       -      +
    234B  SER*     1.3    66.4    +      -       -      +
    252B  VAL*     4.1    14.8    -      -       +      -
    253B  HIS*     3.3     2.2    +      -       -      -
    254B  ILE*     2.6    46.9    +      -       +      +
    302B  PHE*     4.1    31.4    -      +       -      -
    329B  VAL*     3.8    17.0    -      -       +      -
    330B  SER      3.4     6.1    -      -       -      -
    331B  SER*     3.2    27.1    -      -       -      -
    333B  TYR*     5.7     0.7    -      -       -      -
    380B  P1L      3.8    29.6    -      -       +      -
    410B  GLN*     3.9    20.2    -      -       -      -
    426B  TYR*     4.3    18.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with SER 234 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232B  GLU*     4.9     5.2    +      -       -      +
    233B  PHE*     1.3    83.1    -      -       -      +
    235B  ALA*     1.3    60.6    +      -       -      +
    236B  PHE*     4.1     8.9    -      -       -      -
    248B  ARG*     5.2     4.7    +      -       -      -
    250B  LEU*     4.3    14.4    -      -       -      +
    252B  VAL*     3.4    12.3    -      -       -      -
    253B  HIS*     3.5    20.0    -      -       -      -
    328B  GLY      4.1     0.2    -      -       -      +
    329B  VAL*     3.4     7.2    -      -       -      +
    330B  SER*     2.9    46.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 235 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234B  SER*     1.3    72.9    -      -       -      +
    236B  PHE*     1.3    65.1    +      -       -      +
    250B  LEU*     3.6     1.7    -      -       -      +
    251B  PHE*     2.8    28.2    +      -       +      -
    252B  VAL*     3.2    19.3    +      -       +      +
    328B  GLY      3.4     5.4    -      -       -      +
    329B  VAL*     4.3     2.2    -      -       +      -
    379B  MET*     3.9    18.4    -      -       +      -
    380B  P1L      3.6    35.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 236 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234B  SER*     4.1    12.6    -      -       -      -
    235B  ALA*     1.3    78.3    -      -       -      +
    237B  VAL*     1.3    61.1    +      -       -      +
    238B  GLU*     3.6    22.4    -      -       +      -
    248B  ARG*     2.7    51.4    -      -       +      +
    249B  HIS      3.1    12.6    -      -       -      +
    250B  LEU*     3.9     6.1    -      -       +      -
    251B  PHE*     3.5    10.5    -      -       -      -
    326B  PHE*     4.0    20.4    -      +       -      -
    327B  TYR*     3.3     4.3    -      -       -      +
    328B  GLY*     2.9    54.3    +      -       -      -
    329B  VAL      4.2     0.2    -      -       -      -
    330B  SER*     3.6    26.5    -      -       -      -
    376B  ARG*     4.2    13.2    -      -       +      -
    379B  MET*     4.7     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 237 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236B  PHE*     1.3    76.7    -      -       -      +
    238B  GLU*     1.3    74.5    +      -       -      +
    239B  PRO*     3.8     6.1    -      -       +      +
    248B  ARG*     3.5     1.8    -      -       -      -
    249B  HIS*     2.9    51.9    +      -       +      +
    251B  PHE*     3.5    25.8    -      -       +      -
    308B  TRP*     3.7    19.3    -      -       +      +
    325B  GLY*     4.7     3.1    -      -       -      -
    326B  PHE      3.2    10.1    -      -       -      +
    327B  TYR*     3.7    31.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 238 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236B  PHE*     3.6    12.6    -      -       +      -
    237B  VAL*     1.3    74.3    -      -       -      +
    239B  PRO*     1.3    70.5    -      -       +      +
    242B  ALA*     4.2    10.1    -      -       +      +
    246B  TYR*     2.4    38.4    +      -       +      +
    247B  GLN      3.8     4.7    -      -       -      +
    248B  ARG*     3.7    17.9    -      -       +      -
    325B  GLY*     3.2     1.9    -      -       -      -
    326B  PHE*     2.9    44.2    +      -       +      +
    376B  ARG*     2.8    42.1    +      -       -      -
----------------------------------------------------------
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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