Contacts of the strand formed by residues 336 - 344 (chain A) in PDB entry 1LW0


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 GLN 336 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    277A  ARG*     4.0    31.9    -      -       -      +
    331A  LYS*     3.3     6.1    -      -       -      +
    332A  GLN*     2.6    49.9    +      -       -      +
    333A  GLY*     3.1    24.8    +      -       -      +
    334A  GLN      3.3    11.4    +      -       -      +
    335A  GLY*     1.3    78.6    -      -       -      +
    337A  TRP*     1.3    65.7    +      -       -      +
    353A  LYS*     5.4     7.9    -      -       +      -
    354A  TYR      3.8     1.8    -      -       -      +
    355A  ALA*     3.8    22.2    -      -       +      +
   1301A  PO4      4.8     5.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 337 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329A  ILE*     3.9    19.3    -      -       +      -
    330A  GLN      3.0    21.3    -      -       -      +
    331A  LYS*     3.8    25.8    -      -       +      -
    335A  GLY*     3.9     7.8    -      -       -      -
    336A  GLN*     1.3    84.1    -      -       -      +
    338A  THR*     1.3    66.5    +      -       -      +
    339A  TYR*     5.7     0.4    -      -       -      -
    353A  LYS*     3.2     6.5    -      -       -      +
    354A  TYR*     2.9    61.3    +      +       +      +
    364A  ASP*     3.8    31.4    -      -       +      -
    367A  GLN*     3.0    35.4    +      -       +      +
    368A  LEU*     3.8    33.9    -      -       +      -
    371A  ALA*     4.7     4.7    -      -       +      -
    392A  PRO*     4.8     4.0    -      -       +      -
    423A  VAL*     4.0    21.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 338 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273A  GLY      5.6     4.3    -      -       -      +
    329A  ILE*     3.4     2.5    -      -       -      +
    330A  GLN*     2.7    62.9    +      -       -      +
    332A  GLN*     3.3    41.4    -      -       +      +
    337A  TRP*     1.3    80.3    -      -       -      +
    339A  TYR*     1.3    64.1    +      -       -      +
    340A  GLN*     5.1     2.9    -      -       -      -
    352A  GLY      3.3     6.7    -      -       -      -
    353A  LYS*     3.9    13.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 339 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    327A  ALA*     5.9     0.2    -      -       +      -
    328A  GLU      3.1    13.0    -      -       -      +
    329A  ILE*     4.3     6.3    -      -       +      -
    337A  TRP      5.7     0.2    -      -       -      -
    338A  THR*     1.3    77.9    -      -       -      +
    340A  GLN*     1.3    78.4    +      -       -      +
    341A  ILE*     3.9    22.7    -      -       +      -
    350A  LYS*     2.8    17.7    +      -       -      -
    351A  THR*     3.2    13.0    -      -       -      -
    352A  GLY*     2.7    69.1    +      -       -      +
    353A  LYS*     3.7     9.0    -      -       -      -
    354A  TYR*     5.4     3.6    -      -       +      -
    374A  LYS*     3.6    21.8    +      -       +      -
    375A  ILE*     3.4    31.6    -      -       +      -
    378A  GLU*     2.5    33.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 340 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272A  PRO*     5.1     8.9    -      -       -      +
    326A  ILE      3.7     0.9    -      -       -      +
    327A  ALA*     3.3     1.9    -      -       -      +
    328A  GLU*     2.8    36.8    +      -       +      +
    330A  GLN*     2.4    40.8    +      -       -      +
    338A  THR*     4.7     2.8    -      -       -      -
    339A  TYR*     1.3    94.7    +      -       -      +
    341A  ILE*     1.3    63.8    +      -       -      +
    342A  TYR*     4.3    11.4    +      -       +      -
    348A  ASN*     3.6    21.7    -      -       -      +
    350A  LYS      3.5     5.8    -      -       -      -
    351A  THR*     3.7    15.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 341 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325A  LEU*     3.3    29.8    -      -       +      -
    326A  ILE      2.9    12.8    -      -       -      +
    327A  ALA*     4.0    11.0    -      -       +      -
    339A  TYR*     3.9    22.2    -      -       +      -
    340A  GLN*     1.3    77.8    -      -       -      +
    342A  TYR*     1.3    61.9    +      -       -      +
    348A  ASN*     3.9     1.3    -      -       -      -
    349A  LEU*     3.0    25.1    +      -       -      +
    350A  LYS*     2.7    18.5    +      -       +      +
    375A  ILE*     3.9    24.2    -      -       +      +
    378A  GLU*     4.7     6.1    -      -       -      +
    379A  SER*     4.2     3.6    -      -       -      +
    383A  TRP*     3.9    33.2    -      -       +      -
    387A  PRO*     4.7     4.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 342 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325A  LEU*     3.5     2.8    -      -       -      -
    326A  ILE*     2.5    78.7    +      -       +      +
    328A  GLU*     3.1    37.0    +      -       +      -
    340A  GLN*     4.4    12.1    -      -       +      -
    341A  ILE*     1.3    78.7    -      -       -      +
    343A  GLN*     1.3    63.1    +      -       -      +
    344A  GLU      3.6    20.2    -      -       -      +
    345A  PRO*     4.3    15.7    -      -       +      -
    346A  PHE*     4.4    10.5    -      -       -      -
    347A  LYS      3.5    23.6    -      -       -      +
    348A  ASN*     4.0    11.4    -      -       -      +
    349A  LEU*     4.0     5.2    -      -       -      -
    390A  LYS*     4.1     9.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 343 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318A  TYR      4.0     1.4    -      -       -      +
    319A  TYR*     3.4    22.0    -      -       -      -
    320A  ASP*     2.6    58.5    +      -       -      +
    323A  LYS*     2.9    39.9    +      -       +      +
    324A  ASP*     2.8    23.1    +      -       -      +
    325A  LEU*     4.2     2.7    -      -       +      -
    326A  ILE*     4.8     5.8    -      -       -      +
    342A  TYR*     1.3    79.7    -      -       -      +
    344A  GLU*     1.3    65.5    +      -       -      +
    345A  PRO*     4.5     1.7    -      -       -      +
    347A  LYS      4.0     4.2    +      -       -      -
    349A  LEU*     3.8    20.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 344 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323A  LYS*     3.2    36.2    +      -       +      -
    342A  TYR*     3.6     9.0    -      -       -      +
    343A  GLN*     1.3    82.2    -      -       -      +
    345A  PRO*     1.3    64.2    -      -       +      +
    346A  PHE      3.3     0.9    +      -       -      -
    347A  LYS*     2.7    76.9    +      -       +      +
----------------------------------------------------------
 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