Contacts of the strand formed by residues 412 - 418 (chain A) 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 ARG 412 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251A  TYR*     3.5    47.0    +      -       +      -
    252A  THR      3.3    13.9    -      -       -      +
    253A  PRO*     4.5     0.7    -      -       +      -
    254A  ILE*     3.6     5.6    -      -       -      +
    351A  GLU*     2.8    48.8    +      -       -      +
    407A  ASP*     2.9    58.2    +      -       +      +
    410A  ARG*     3.2    55.2    -      -       -      +
    411A  LYS*     1.3    79.0    -      -       -      +
    413A  ILE*     1.3    65.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 413 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250A  TRP      3.8     0.7    -      -       -      +
    251A  TYR*     3.3     3.0    -      -       -      -
    252A  THR*     2.8    43.5    +      -       +      +
    254A  ILE*     3.7    17.9    -      -       +      -
    260A  TYR*     3.8    29.6    -      -       +      +
    262A  VAL*     3.7    24.5    -      -       +      -
    288A  VAL*     4.0     8.7    -      -       +      -
    404A  VAL*     3.7    19.7    -      -       +      -
    405A  VAL      3.2    11.0    -      -       -      +
    406A  PHE*     4.5    11.0    -      -       +      -
    412A  ARG*     1.3    79.0    -      -       -      +
    414A  GLY*     1.3    62.3    +      -       -      +
    415A  PHE*     3.6    24.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 414 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249A  LEU*     4.1     6.7    -      -       -      -
    250A  TRP      3.2     8.5    -      -       -      -
    251A  TYR*     3.3    23.4    -      -       -      -
    404A  VAL*     3.3     7.6    -      -       -      +
    405A  VAL*     2.8    39.2    +      -       -      -
    413A  ILE*     1.3    74.3    -      -       -      +
    415A  PHE*     1.3    64.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 415 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249A  LEU*     3.4     4.2    -      -       -      +
    250A  TRP      2.8    33.7    +      -       -      +
    252A  THR*     4.2     8.3    -      -       +      -
    262A  VAL*     5.5     0.4    -      -       +      -
    288A  VAL*     4.3    13.7    -      -       +      -
    348A  LEU*     3.7    22.9    -      -       +      -
    357A  PHE*     4.2     7.0    -      +       +      -
    359A  ILE*     4.0    29.2    -      -       +      -
    394A  MET*     3.9    29.6    -      -       +      -
    398A  ILE*     5.9     0.7    -      -       +      -
    399A  MET*     6.1     2.2    -      -       +      -
    402A  PHE*     4.2    13.7    -      +       +      -
    403A  TYR      3.5     3.1    -      -       -      -
    404A  VAL*     4.1    25.6    -      -       +      -
    413A  ILE*     3.6    29.8    -      -       +      -
    414A  GLY*     1.3    76.2    -      -       -      -
    416A  ALA*     1.3    60.1    +      -       -      +
    431A  VAL*     3.4    13.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 416 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245A  TYR*     3.4    37.2    -      -       +      -
    246A  THR      4.2     0.2    -      -       -      +
    248A  SER      3.6    14.1    -      -       -      +
    249A  LEU*     3.5    15.7    -      -       +      -
    402A  PHE*     3.2     6.4    -      -       -      +
    403A  TYR      2.9    30.7    +      -       -      +
    415A  PHE*     1.3    75.1    -      -       -      +
    417A  VAL*     1.3    61.3    +      -       -      +
    431A  VAL*     3.7     8.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 417 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245A  TYR*     3.2     6.4    -      -       -      +
    246A  THR*     3.1    48.9    +      -       -      +
    247A  GLY*     6.1     0.9    -      -       -      -
    248A  SER      4.9     0.2    +      -       -      -
    401A  GLY      4.0     6.3    -      -       -      +
    402A  PHE*     4.2     2.5    -      -       +      -
    416A  ALA*     1.3    71.5    -      -       -      +
    418A  SER*     1.3    64.5    +      -       -      +
    421A  HIS*     3.4    30.7    -      -       +      +
    428A  THR*     4.5     1.3    -      -       -      +
    429A  ALA*     3.7     8.7    -      -       +      +
    430A  ALA*     3.5    34.3    -      -       -      +
    431A  VAL*     3.6    11.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 418 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214A  GLN*     3.8     9.4    -      -       -      +
    215A  LEU      4.9     0.2    +      -       -      -
    244A  LEU      3.9     4.7    -      -       -      -
    246A  THR*     5.1     1.0    +      -       -      +
    400A  GLU      4.1     4.2    +      -       -      -
    401A  GLY      3.0    31.5    +      -       -      -
    402A  PHE      3.6    13.0    +      -       -      -
    403A  TYR      4.0     3.8    -      -       -      +
    416A  ALA      3.3     1.8    +      -       -      -
    417A  VAL*     1.3    74.5    -      -       -      +
    419A  ALA*     1.3    62.7    +      -       -      +
    420A  CYS*     3.0    31.7    +      -       -      -
    421A  HIS*     2.9    30.0    +      -       -      -
----------------------------------------------------------
 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