Contacts of the strand formed by residues 329 - 334 (chain A) in PDB entry 4LG8


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 TYR 329 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    305A  HIS*     3.3     9.2    -      -       +      -
    325A  SER      3.3    23.9    +      -       -      -
    327A  ASP*     2.9    36.2    +      -       -      +
    328A  GLN*     1.3    82.5    -      -       +      +
    330A  TRP*     1.3    64.0    +      -       -      +
    343A  LYS*     3.8    33.4    -      -       +      -
    344A  VAL      3.3    26.7    -      -       -      -
    345A  THR*     3.5    29.8    -      -       +      +
    353A  LEU*     3.6     6.4    -      -       -      +
    609A  UNX      4.0    12.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 330 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    305A  HIS*     4.2     1.3    -      -       -      -
    322A  LEU*     4.0    13.2    -      -       +      -
    323A  SER      3.1    15.0    -      -       -      +
    329A  TYR*     1.3    74.4    -      -       -      +
    331A  ALA*     1.3    69.7    +      -       -      +
    332A  PHE*     4.4     7.6    -      -       +      -
    342A  THR*     4.0    24.7    -      -       +      -
    343A  LYS*     3.3     5.0    -      -       -      +
    344A  VAL*     2.9    72.4    +      -       +      +
    345A  THR*     5.2     0.7    -      -       -      -
    353A  LEU*     4.1    15.0    -      -       +      -
    365A  PHE*     3.6    35.2    -      +       -      -
    367A  THR*     4.4     6.3    -      -       +      -
    377A  TRP*     3.4    52.5    -      +       +      -
    379A  LEU*     4.5     6.3    -      -       +      -
    382A  ARG*     4.4    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 331 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304A  ALA*     3.8    23.3    -      -       +      -
    305A  HIS*     3.9     4.9    -      -       +      +
    321A  LEU      3.5     0.7    -      -       -      +
    322A  LEU*     3.3     8.1    -      -       -      +
    323A  SER*     2.9    44.6    +      -       -      +
    330A  TRP*     1.3    81.6    -      -       -      +
    332A  PHE*     1.3    60.5    +      -       -      +
    333A  SER*     4.2     3.1    -      -       -      +
    340A  VAL*     4.4     4.3    -      -       +      -
    342A  THR      3.2    11.9    -      -       -      +
    343A  LYS*     4.2     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 332 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315A  HIS*     4.3     4.9    -      +       -      -
    320A  TYR*     3.3    53.8    -      +       +      -
    321A  LEU      3.4     6.3    -      -       -      -
    322A  LEU*     4.8     2.7    -      -       +      -
    330A  TRP*     4.4     7.4    -      -       +      -
    331A  ALA*     1.3    72.9    -      -       -      +
    333A  SER*     1.3    60.7    +      -       -      +
    340A  VAL*     4.1     0.2    -      -       -      -
    341A  LEU*     2.8    44.8    +      -       +      +
    342A  THR*     3.0    28.8    +      -       +      +
    358A  PHE*     3.6    29.2    -      +       -      -
    379A  LEU*     3.8    34.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 333 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288A  ILE*     5.0     6.4    -      -       -      +
    302A  VAL*     3.6    31.1    -      -       -      +
    304A  ALA*     4.4     5.4    -      -       -      +
    320A  TYR*     3.2    11.1    -      -       -      +
    321A  LEU*     2.9    42.8    +      -       -      +
    323A  SER*     5.2     0.2    +      -       -      -
    331A  ALA*     4.6     1.7    -      -       -      +
    332A  PHE*     1.3    78.4    +      -       -      +
    334A  ASP*     1.3    63.7    +      -       -      +
    335A  ILE      3.5     0.5    +      -       -      -
    339A  ARG      3.2     9.9    -      -       -      -
    340A  VAL*     3.8    12.8    -      -       -      +
    341A  LEU*     4.6     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 334 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302A  VAL*     5.2     0.9    -      -       -      +
    319A  ASP*     3.8     7.1    -      -       -      +
    320A  TYR*     3.6    19.6    +      -       -      -
    333A  SER*     1.3    71.5    -      -       -      +
    335A  ILE*     1.3    61.1    +      -       -      +
    336A  GLN*     3.4     9.2    +      -       -      +
    337A  THR*     2.7    45.8    +      -       -      +
    338A  GLY*     2.8    31.4    +      -       -      -
    339A  ARG      2.7    14.1    +      -       -      +
    341A  LEU*     4.1    20.0    -      -       +      +
----------------------------------------------------------
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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