Contacts of the strand formed by residues 673 - 681 (chain J) in PDB entry 5LS6


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 673 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121J  MET*     3.9    30.7    -      -       +      -
    298J  PRO*     5.0     9.0    -      -       +      -
    299J  PHE*     6.3     1.1    -      +       -      -
    519J  ASN*     3.6    42.6    -      -       +      -
    645J  ILE*     3.7    26.7    -      -       +      -
    646J  ILE*     3.5    13.2    -      -       -      -
    647J  SER*     4.3     7.9    -      -       -      -
    669J  LEU*     3.2    17.2    +      -       +      -
    670J  ASN*     3.1    34.9    +      -       -      +
    672J  ASP*     1.3    92.1    -      -       +      +
    674J  VAL*     1.3    67.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 674 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    644J  GLU      3.5     0.2    -      -       -      +
    645J  ILE*     3.4     4.1    -      -       -      -
    646J  ILE*     2.8    41.6    +      -       +      +
    648J  GLN*     3.2    36.1    -      -       +      +
    651J  ALA*     3.9    23.1    -      -       +      -
    666J  LEU*     4.1    14.6    -      -       +      -
    667J  PHE      3.2    28.9    -      -       -      +
    668J  ASN*     4.0     4.9    -      -       +      +
    669J  LEU*     4.2     1.3    -      -       -      +
    673J  PHE*     1.3    73.1    -      -       -      +
    675J  VAL*     1.3    72.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 675 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119J  ASN*     4.2    14.8    -      -       -      +
    641J  TYR*     3.9    20.0    -      -       +      +
    642J  CYS      3.9     3.6    -      -       -      +
    643J  GLY*     3.8    24.9    -      -       -      +
    644J  GLU      3.0     9.9    -      -       -      +
    645J  ILE*     4.4     1.8    -      -       +      -
    665J  PHE      4.0     0.4    -      -       -      +
    666J  LEU*     3.3     4.5    -      -       -      -
    667J  PHE*     2.8    39.4    +      -       +      +
    669J  LEU*     3.9    25.9    -      -       +      +
    674J  VAL*     1.3    74.9    -      -       -      +
    676J  ASP*     1.3    63.3    +      -       -      +
    677J  ALA      4.4     1.3    -      -       -      +
    708J  ILE*     4.0    24.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 676 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    643J  GLY*     4.3     0.2    -      -       -      -
    644J  GLU*     2.7    40.6    +      -       +      +
    646J  ILE*     4.4     8.5    -      -       +      -
    654J  ARG*     3.0    32.4    +      -       -      +
    658J  TYR*     2.8    21.1    +      -       -      -
    665J  PHE      3.3     7.8    -      -       -      +
    666J  LEU*     3.3    21.1    -      -       +      +
    675J  VAL*     1.3    73.1    -      -       -      +
    677J  ALA*     1.3    61.2    +      -       -      +
    678J  THR*     2.9    29.1    +      -       -      -
    679J  ARG      4.0     0.7    +      -       -      -
    680J  LYS      3.5     2.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 677 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    641J  TYR*     3.8    23.8    -      -       +      +
    642J  CYS      3.6    20.0    -      -       -      +
    665J  PHE*     3.2     9.9    +      -       +      +
    675J  VAL*     4.1     2.4    -      -       -      +
    676J  ASP*     1.3    71.5    -      -       -      +
    678J  THR*     1.3    58.4    +      -       -      +
    679J  ARG      3.4     0.2    -      -       -      -
    680J  LYS      3.3    20.2    -      -       -      +
    681J  GLY*     3.7     3.3    +      -       -      -
    685J  ARG*     2.6    46.1    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 678 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112J  SER      4.7     2.8    -      -       -      +
    113J  TRP*     3.9     3.8    -      -       -      +
    658J  TYR*     3.5    32.8    -      -       +      +
    665J  PHE*     3.7    23.9    +      -       -      +
    676J  ASP*     2.9    19.7    +      -       -      -
    677J  ALA*     1.3    78.7    -      -       -      +
    679J  ARG*     1.3    69.4    +      -       +      +
    685J  ARG*     3.1    18.2    +      -       -      +
    809J  74D      4.0    46.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 679 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112J  SER      4.4     3.0    -      -       -      +
    113J  TRP*     3.1    26.4    -      -       -      -
    114J  SER*     3.1     4.5    +      -       -      -
    122J  VAL*     5.3     4.9    -      -       -      +
    125J  GLU*     4.4    13.1    +      -       -      +
    644J  GLU*     3.2    30.4    +      -       -      +
    650J  GLU*     4.8     0.6    +      -       -      -
    654J  ARG*     3.5    40.0    -      -       -      +
    658J  TYR*     5.0     2.3    +      -       -      +
    676J  ASP      4.0     2.8    +      -       -      -
    677J  ALA      3.4     0.2    -      -       -      -
    678J  THR*     1.3    83.8    -      -       +      +
    680J  LYS*     1.3    66.9    +      -       +      +
    809J  74D      6.1     0.8    -      -       -      -
    236K  ARG*     3.4    47.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 680 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113J  TRP*     4.6     1.3    -      -       -      -
    114J  SER*     3.0    26.7    -      -       -      +
    116J  LEU*     3.8    16.6    -      -       +      -
    120J  PHE*     4.1    26.9    -      -       +      -
    122J  VAL*     4.9     2.0    -      -       -      +
    643J  GLY*     3.2    18.4    -      -       -      -
    644J  GLU*     3.3    36.1    +      -       +      -
    676J  ASP      3.5     2.5    +      -       -      +
    677J  ALA*     3.3    12.9    -      -       -      +
    679J  ARG*     1.3    83.1    -      -       -      +
    681J  GLY*     1.3    56.2    +      -       -      +
    232K  VAL*     3.9    31.9    -      -       -      +
    591L  TRP*     4.1    20.7    -      -       +      -
    595L  LYS*     6.2     0.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 681 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113J  TRP*     3.8     9.7    -      -       -      -
    114J  SER      3.2     4.6    +      -       -      -
    115J  PRO*     3.4     6.4    -      -       -      +
    116J  LEU*     2.6    35.6    +      -       -      +
    642J  CYS      3.5    16.4    -      -       -      -
    643J  GLY*     4.0     3.4    -      -       -      -
    677J  ALA*     3.7    11.3    +      -       -      -
    680J  LYS*     1.3    73.2    -      -       -      +
    682J  ASN*     1.3    58.8    +      -       -      -
    685J  ARG*     4.5     2.0    -      -       -      -
----------------------------------------------------------
 Back to top of page


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