Contacts of the strand formed by residues 379 - 383 (chain B) in PDB entry 3LPJ


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 ASP 379 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220B  PHE*     6.0     1.7    -      -       -      +
    221B  PRO*     5.6     7.3    -      -       -      +
    330B  CYS*     3.4     0.5    -      -       -      -
    331B  TRP*     2.9    31.9    +      -       -      +
    332B  GLN      5.0     0.4    -      -       -      +
    333B  ALA*     4.2     2.8    -      -       -      +
    334B  GLY*     2.9    32.7    +      -       -      +
    336B  THR*     3.8     9.4    +      -       -      +
    377B  GLN      4.2     3.8    -      -       -      +
    378B  ASP*     1.3    75.2    -      -       -      +
    380B  CYS*     1.3    62.1    +      -       -      +
    381B  TYR*     3.6    28.8    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 380 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221B  PRO*     5.1     2.8    -      -       -      +
    328B  LEU*     4.1    11.9    -      -       +      -
    329B  VAL      3.2     5.2    -      -       -      +
    330B  CYS*     2.0    46.9    -      -       -      -
    369B  PRO*     3.5     2.3    -      -       -      +
    370B  VAL*     3.1    35.1    +      -       -      +
    372B  ASP*     3.4    25.6    -      -       -      -
    378B  ASP*     3.8     9.3    +      -       -      -
    379B  ASP*     1.3    75.2    -      -       -      +
    381B  TYR*     1.3    73.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 381 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219B  GLY      4.7     6.4    +      -       -      -
    322B  PHE*     4.3     5.6    -      -       +      -
    327B  GLN      4.3     0.2    -      -       -      +
    328B  LEU*     3.1     5.0    -      -       -      -
    329B  VAL*     3.0    30.2    +      -       +      +
    331B  TRP*     3.7    19.5    -      +       +      -
    336B  THR*     2.9    35.5    +      -       +      -
    338B  TRP*     3.3    30.3    -      +       -      -
    367B  LEU*     3.9    31.4    -      -       +      -
    368B  ARG      3.1     8.7    -      -       -      +
    369B  PRO*     3.7    31.2    -      -       +      -
    370B  VAL*     4.0     4.9    -      -       -      -
    379B  ASP*     3.6    26.9    +      -       +      +
    380B  CYS*     1.3    85.8    -      -       -      +
    382B  LYS*     1.3    64.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 382 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322B  PHE*     4.3     2.9    -      -       -      -
    325B  GLY      4.0    18.7    +      -       -      +
    326B  GLU*     3.6    21.8    +      -       -      +
    327B  GLN      4.3     6.5    -      -       -      +
    328B  LEU*     4.2    20.2    -      -       +      +
    367B  LEU*     3.5     3.9    -      -       -      -
    368B  ARG*     2.9    60.2    +      -       +      +
    370B  VAL*     4.1    16.8    -      -       +      -
    381B  TYR*     1.3    79.9    -      -       -      +
    383B  PHE*     1.3    64.5    +      -       -      +
    384B  ALA*     3.2     1.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 383 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294B  ASN*     4.1     3.8    +      -       -      -
    306B  VAL*     4.1    16.2    -      -       +      -
    309B  ILE*     4.1    11.9    -      -       +      -
    322B  PHE*     3.2    36.7    +      +       +      +
    323B  TRP*     3.5    60.8    -      +       -      -
    325B  GLY*     3.5    20.2    -      -       -      +
    327B  GLN      5.0     0.2    +      -       -      -
    341B  PHE*     6.0     0.2    -      +       -      -
    366B  TYR*     4.0    15.9    -      +       -      -
    367B  LEU*     4.1    16.2    -      -       +      -
    382B  LYS*     1.3    71.8    -      -       -      +
    384B  ALA*     1.3    59.9    +      -       -      +
    385B  ILE*     3.3    58.5    +      -       +      +
----------------------------------------------------------
 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