Contacts of the strand formed by residues 545 - 553 (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 GLY 545 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    470B  THR*     3.3    11.6    -      -       -      -
    471B  VAL*     2.8    41.3    +      -       -      +
    508B  PRO*     3.6     5.8    -      -       -      -
    544B  SER*     1.3    75.7    -      -       -      +
    546B  GLU*     1.3    63.1    +      -       -      -
    547B  TRP*     3.5     2.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 546 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    468B  ARG*     3.2    52.4    +      -       +      +
    469B  LYS      3.5     9.1    +      -       -      +
    470B  THR*     3.8    16.0    +      -       -      +
    506B  VAL*     4.1     0.3    -      -       -      +
    507B  SER      3.9     2.4    -      -       -      +
    508B  PRO*     3.3    26.9    -      -       +      +
    545B  GLY*     1.3    69.8    -      -       -      -
    547B  TRP*     1.3    71.1    +      -       -      +
    548B  VAL*     4.1     7.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 547 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454B  ILE*     6.1     1.1    -      -       +      -
    467B  VAL      3.8     0.7    -      -       -      +
    468B  ARG*     3.5     1.7    -      -       -      -
    469B  LYS*     3.0    32.7    +      -       +      +
    471B  VAL*     3.6    24.8    -      -       +      +
    484B  LEU*     4.0    17.5    -      -       +      -
    487B  ALA*     4.2    10.3    -      -       +      -
    505B  LEU*     3.7    39.5    -      -       +      -
    506B  VAL      3.4    17.5    -      -       -      -
    507B  SER*     3.7    20.9    -      -       -      -
    508B  PRO*     3.4    18.3    -      -       +      +
    535B  THR*     5.6     1.6    -      -       +      -
    538B  SER*     4.7     4.3    -      -       -      -
    543B  PRO*     2.8    34.8    +      -       +      +
    545B  GLY      3.8     0.4    -      -       -      -
    546B  GLU*     1.3    74.5    -      -       -      +
    548B  VAL*     1.3    64.5    +      -       -      +
    566B  PHE*     5.8     5.2    -      -       +      -
    568B  LEU*     3.7    26.3    -      -       +      +
    570B  LEU*     3.8    16.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 548 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    466B  GLU*     3.7    35.2    -      -       +      +
    467B  VAL      3.4     5.4    -      -       -      +
    468B  ARG*     3.9    32.5    -      -       +      +
    504B  HIS      3.8     0.5    -      -       -      +
    505B  LEU*     3.4     7.0    -      -       -      +
    506B  VAL*     2.8    56.6    +      -       +      +
    546B  GLU*     4.2    11.2    -      -       +      +
    547B  TRP*     1.3    81.4    -      -       -      +
    549B  LEU*     1.3    64.8    +      -       -      +
    550B  GLU*     4.3     9.9    -      -       +      +
    566B  PHE*     5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 549 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    465B  LEU      3.8     0.5    -      -       -      +
    466B  GLU*     3.3     4.3    -      -       -      -
    467B  VAL*     2.8    43.3    +      -       +      +
    489B  ALA*     4.7     0.7    -      -       +      -
    491B  LEU*     4.0    20.2    -      -       +      -
    503B  ILE*     3.8    17.3    -      -       +      -
    504B  HIS      3.5    12.6    -      -       -      +
    505B  LEU*     4.3    13.0    -      -       +      -
    515B  LEU*     4.3     9.4    -      -       +      -
    547B  TRP      4.3     0.4    -      -       -      -
    548B  VAL*     1.3    74.0    -      -       -      +
    550B  GLU*     1.3    62.2    +      -       -      +
    551B  ILE*     4.0    26.0    -      -       +      -
    563B  LEU*     4.1    10.5    -      -       +      -
    566B  PHE*     3.7    40.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 550 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    464B  ARG*     3.9    35.1    +      -       +      +
    465B  LEU      3.4     6.3    -      -       -      +
    466B  GLU*     4.4     6.8    -      -       +      +
    502B  ALA      3.8     1.0    -      -       -      +
    503B  ILE*     3.2     7.4    -      -       -      +
    504B  HIS*     2.8    50.9    +      -       +      +
    506B  VAL*     3.9     7.2    -      -       -      +
    512B  ARG*     2.8    44.3    +      -       -      -
    548B  VAL*     4.3    14.8    -      -       +      +
    549B  LEU*     1.3    77.6    -      -       -      +
    551B  ILE*     1.3    62.7    +      -       -      +
    552B  GLU*     4.6     5.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 551 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461B  ILE*     3.8    18.3    -      -       +      +
    464B  ARG*     3.4     2.7    -      -       -      +
    465B  LEU*     2.7    50.7    +      -       +      +
    491B  LEU*     4.8     1.1    -      -       +      -
    493B  LEU*     4.2    12.8    -      -       +      -
    501B  LEU*     3.7    28.3    -      -       +      -
    502B  ALA      3.5     3.1    -      -       -      -
    503B  ILE*     4.2    19.7    -      -       +      -
    549B  LEU*     4.0    25.4    -      -       +      -
    550B  GLU*     1.3    79.2    -      -       -      +
    552B  GLU*     1.3    63.6    +      -       -      +
    563B  LEU*     4.1    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 552 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461B  ILE*     5.6     1.3    -      -       -      -
    463B  LYS      3.6     9.2    -      -       -      +
    464B  ARG*     3.2    32.9    +      -       +      -
    501B  LEU*     3.4    11.2    -      -       -      -
    502B  ALA*     2.8    57.1    +      -       +      +
    504B  HIS*     4.4    13.7    -      -       -      -
    550B  GLU*     4.6     8.1    -      -       +      +
    551B  ILE*     1.3    75.9    -      -       -      +
    553B  ASN*     1.3    63.3    +      -       -      +
    554B  THR*     4.2    11.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 553 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462B  GLY      3.9     4.8    +      -       -      +
    463B  LYS*     2.8    49.3    +      -       +      +
    495B  TYR*     3.2    22.3    +      -       -      +
    500B  ASP*     3.6     6.9    -      -       -      +
    552B  GLU*     1.3    73.0    -      -       -      +
    554B  THR*     1.3    59.1    +      -       -      +
    555B  SER*     3.0    22.1    +      -       -      -
    557B  ALA      2.9    28.1    +      -       -      -
    559B  ASN*     3.1    30.4    +      -       -      +
----------------------------------------------------------
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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