Contacts of the strand formed by residues 367 - 370 (chain A) in PDB entry 1LV5


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 LYS 367 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    314A  ASP      3.6    21.3    +      -       -      +
    315A  LYS*     3.3    20.3    +      -       +      -
    316A  ALA      3.0    22.7    +      -       -      -
    360A  TRP*     4.3     3.6    -      -       -      -
    364A  GLU*     3.4    25.8    +      -       -      +
    365A  THR*     3.5    10.7    +      -       -      +
    366A  LYS*     1.3    72.2    -      -       -      +
    368A  LYS*     1.3    64.5    +      -       -      +
    389A  GLY*     3.4    11.9    +      -       -      +
    391A  SER*     4.0    19.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 368 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315A  LYS*     3.8     3.6    -      -       -      -
    316A  ALA      3.3     5.4    -      -       -      +
    318A  LEU*     4.2    15.9    -      -       +      -
    360A  TRP*     2.6    53.9    +      -       +      -
    361A  LEU*     2.6    29.8    +      -       -      +
    363A  ASP      2.9     4.4    +      -       -      -
    366A  LYS*     2.7    30.9    +      -       -      +
    367A  LYS*     1.3    76.9    -      -       -      +
    369A  SER*     1.3    60.0    +      -       -      +
    370A  MET*     4.2    20.0    -      -       +      -
    387A  LEU*     4.8     2.0    -      -       +      -
    388A  CYS      2.7    18.7    +      -       -      +
    389A  GLY      2.9     9.6    +      -       -      +
    390A  VAL*     3.2     8.0    -      -       -      +
    391A  SER*     2.9    24.6    +      -       -      -
    392A  PHE      3.6     1.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 369 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315A  LYS*     3.4    18.1    -      -       -      +
    316A  ALA      2.8    11.4    +      -       -      -
    317A  ALA*     3.3     6.5    -      -       -      -
    318A  LEU      3.0    24.8    +      -       -      -
    368A  LYS*     1.3    71.3    -      -       -      +
    370A  MET*     1.3    60.6    +      -       -      +
    392A  PHE*     3.1    32.2    -      -       -      +
    454A  ILE*     3.6    18.4    +      -       -      +
    455A  TRP*     5.6     2.7    -      -       -      -
    458A  GLU*     3.1    14.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 370 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318A  LEU*     3.7    47.8    -      -       +      +
    320A  VAL*     4.7     4.0    -      -       +      +
    368A  LYS*     4.2     4.7    -      -       +      +
    369A  SER*     1.3    85.6    +      -       -      +
    371A  PHE*     1.3    57.2    +      -       -      +
    372A  ASP      5.4     0.4    -      -       -      +
    373A  SER*     4.2    17.3    -      -       -      -
    376A  ALA*     4.0    18.4    -      -       +      -
    387A  LEU*     4.0    16.6    -      -       +      -
    390A  VAL*     3.4    31.4    -      -       +      -
    392A  PHE*     2.8    14.2    +      -       -      +
    393A  ASP*     3.2     4.7    -      -       -      -
    394A  LEU*     2.6    35.0    +      -       -      +
    454A  ILE*     3.8    13.9    -      -       -      +
----------------------------------------------------------
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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