Contacts of the strand formed by residues 314 - 320 (chain B) in PDB entry 5JMO


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 314 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274B  PHE*     3.6    24.9    -      -       +      -
    289B  PHE*     3.3     9.4    -      -       +      -
    291B  TRP*     3.6    34.3    -      -       +      +
    308B  TYR      2.7    26.3    +      -       -      +
    309B  THR*     3.5     2.8    +      -       -      -
    311B  SER*     3.4     7.4    +      -       -      +
    312B  ILE      3.3     4.5    -      -       -      +
    313B  TYR*     1.3    80.3    -      -       -      +
    315B  LEU*     1.3    59.9    +      -       -      +
    316B  SER      3.5     0.3    +      -       -      -
    337B  LEU*     5.8     0.2    -      -       -      +
    394B  GLN*     4.1     6.3    +      -       -      +
    486B  HIS*     5.6     0.2    +      -       -      -
    534B  MET*     5.4     0.7    -      -       -      +
    606B   NA      2.4    45.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 315 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288B  ILE*     3.6    28.0    -      -       +      -
    289B  PHE      2.8    25.4    +      -       -      +
    290B  VAL*     3.7     8.3    -      -       +      -
    291B  TRP      2.9    22.9    +      -       -      -
    313B  TYR      5.3     0.7    -      -       -      +
    314B  THR*     1.3    71.3    -      -       -      +
    316B  SER*     1.3    63.7    +      -       -      +
    317B  ILE*     3.5    17.4    -      -       +      +
    337B  LEU*     3.9    21.8    -      -       +      -
    378B  ILE*     4.2    12.3    -      -       +      -
    390B  TRP      5.6     0.4    -      -       -      +
    393B  MET*     4.5     6.3    -      -       +      -
    394B  GLN*     3.8    34.8    -      -       +      +
    397B  VAL*     4.0    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 316 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291B  TRP*     3.5     6.7    -      -       -      -
    293B  SER*     3.5    17.3    -      -       -      -
    309B  THR*     3.4    45.2    -      -       -      +
    314B  THR      3.5     4.9    +      -       -      -
    315B  LEU*     1.3    71.0    -      -       -      +
    317B  ILE*     1.3    61.8    +      -       -      +
    335B  SER*     4.1     3.6    +      -       -      -
    336B  THR*     3.7    19.4    +      -       -      +
    337B  LEU*     2.9    29.4    +      -       -      +
    338B  ALA      3.6     5.4    +      -       -      -
    606B   NA      3.9     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 317 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    290B  VAL*     3.8    10.5    -      -       +      -
    291B  TRP      2.8    13.5    +      -       -      +
    292B  ALA*     3.8     2.8    -      -       -      -
    293B  SER*     2.9    23.6    +      -       -      -
    315B  LEU*     3.5    26.5    -      -       +      +
    316B  SER*     1.3    80.1    -      -       -      +
    318B  SER*     1.3    75.1    +      -       -      +
    337B  LEU*     5.4     1.1    -      -       +      -
    338B  ALA*     3.4    23.3    -      -       +      +
    339B  THR      4.3     0.4    -      -       -      -
    340B  THR*     3.9    16.2    -      -       +      +
    367B  THR*     4.3     4.0    -      -       -      -
    370B  SER*     3.9    22.7    -      -       -      +
    371B  ALA*     4.3     5.8    -      -       -      -
    374B  ALA*     3.7    22.4    -      -       +      -
    378B  ILE*     5.9     1.3    -      -       +      -
    397B  VAL*     5.9     1.8    -      -       +      -
    429B  LEU*     4.7     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 318 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293B  SER*     2.7    23.3    +      -       -      -
    317B  ILE*     1.3    73.6    -      -       -      +
    319B  SER*     1.3    63.2    +      -       -      +
    330B  SER*     5.3     4.0    -      -       -      -
    331B  GLU      4.3     6.2    +      -       -      -
    336B  THR*     3.4    23.1    +      -       -      +
    338B  ALA      3.0     7.7    +      -       -      -
    339B  THR*     3.3     7.4    -      -       -      -
    340B  THR      3.0    23.7    +      -       -      -
    367B  THR*     4.5     1.3    -      -       -      -
    370B  SER*     3.4     7.0    +      -       -      -
    423B  SER      3.3    25.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 319 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318B  SER*     1.3    74.8    -      -       -      +
    320B  ALA*     1.3    60.4    +      -       -      +
    327B  PRO*     3.2    18.2    -      -       -      +
    329B  TYR*     3.4    31.1    -      -       -      -
    330B  SER*     5.0     4.4    +      -       -      -
    339B  THR*     3.5     4.4    -      -       -      +
    340B  THR      3.3     4.5    -      -       -      -
    342B  SER*     3.6     6.4    -      -       -      -
    366B  GLY      3.6     0.3    +      -       -      -
    367B  THR*     3.4    26.3    -      -       -      +
    370B  SER*     2.7    19.8    +      -       -      -
    423B  SER      4.8     0.9    -      -       -      +
    424B  TYR*     3.6    13.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 320 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319B  SER*     1.3    75.4    -      -       -      +
    321B  THR*     1.3    67.5    +      -       -      +
    324B  GLY*     4.8     0.9    -      -       -      -
    325B  ASN      3.6     8.5    -      -       -      +
    327B  PRO*     4.0     2.9    -      -       -      -
    339B  THR*     3.8    11.2    -      -       +      -
    340B  THR      3.1     8.6    +      -       -      +
    341B  TYR*     3.3     8.5    -      -       +      -
    342B  SER      2.8    25.1    +      -       -      -
    406B  LEU*     3.7    30.5    -      -       +      -
    424B  TYR*     3.8     9.6    -      -       +      +
    428B  LEU*     5.5     0.4    -      -       +      -
----------------------------------------------------------
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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