Contacts of the strand formed by residues 339 - 343 (chain C) in PDB entry 3DLX


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 VAL 339 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    313C  PHE*     3.8    26.7    -      -       +      -
    314C  GLU      3.8     7.0    -      -       -      +
    317C  MET*     3.7    12.1    -      -       +      +
    319C  ALA*     4.2     7.2    -      -       +      -
    333C  ILE*     3.8    25.7    -      -       +      +
    337C  ILE*     3.5    31.1    +      -       +      -
    338C  THR*     1.3    77.3    -      -       -      +
    340C  HIS*     1.3    64.8    +      -       -      +
    341C  LEU*     3.5    32.3    +      -       +      +
    350C  LEU      5.3     1.4    -      -       -      +
    374C  LEU*     5.2     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 340 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316C  GLY*     3.8    20.2    -      -       -      -
    317C  MET      2.9    16.7    +      -       -      -
    318C  TYR*     3.3    46.7    +      +       +      +
    319C  ALA      3.0    24.9    +      -       -      +
    338C  THR*     3.6    25.9    -      -       +      +
    339C  VAL*     1.3    70.0    -      -       -      +
    341C  LEU*     1.3    63.0    +      -       -      +
    342C  GLN      3.7     0.5    +      -       -      -
    348C  LEU*     4.1    10.2    -      -       +      +
    349C  GLY*     5.1     7.2    -      -       -      +
    218D  ALA*     6.2     0.9    -      -       +      -
    263D  GLN*     3.4    28.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 341 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319C  ALA*     3.4    14.1    -      -       +      +
    321C  LEU*     3.9    26.2    -      -       +      +
    330C  SER*     4.1    24.5    -      -       -      -
    333C  ILE*     4.2    10.3    -      -       +      -
    339C  VAL*     3.5    31.2    +      -       +      +
    340C  HIS*     1.3    72.7    -      -       -      +
    342C  GLN*     1.3    58.9    +      -       -      +
    348C  LEU*     3.7     1.8    -      -       -      -
    349C  GLY*     2.8    30.3    +      -       -      +
    350C  LEU*     3.3    45.7    +      -       +      +
    351C  GLY      5.9     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 342 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318C  TYR*     6.0     0.7    -      -       +      -
    319C  ALA      2.8    19.0    +      -       -      +
    320C  ASN*     3.1    40.4    +      -       +      +
    321C  LEU      4.4     2.9    +      -       -      -
    340C  HIS      3.7     1.1    +      -       -      +
    341C  LEU*     1.3    74.7    -      -       -      +
    343C  SER*     1.3    71.6    +      -       -      +
    344C  GLU      3.6     0.9    +      -       -      -
    347C  VAL      3.5    10.3    -      -       -      +
    348C  LEU*     4.0    14.1    -      -       +      -
    350C  LEU*     4.4     5.4    -      -       -      +
    380C  PHE*     4.0     2.8    -      -       -      -
    385C  SER*     3.2    32.1    +      -       -      +
    388C  MET*     3.5    33.1    -      -       -      -
    389C  ILE*     3.8    14.5    -      -       -      +
    394C  VAL*     4.6    13.7    -      -       +      -
    264D  ILE*     5.3     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 343 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    320C  ASN*     4.2     2.0    -      -       -      +
    341C  LEU      4.3     0.2    +      -       -      -
    342C  GLN*     1.3    81.6    -      -       -      +
    344C  GLU*     1.3    59.5    +      -       -      +
    345C  ASN*     2.5    22.5    +      -       -      -
    346C  GLY*     3.1    17.5    +      -       -      -
    347C  VAL*     3.0    28.8    +      -       -      +
    350C  LEU*     4.0    16.2    -      -       -      +
    365C  ASN*     3.6     8.4    -      -       -      +
    366C  ALA*     3.5    19.0    +      -       -      +
    385C  SER*     3.8     0.7    +      -       -      -
----------------------------------------------------------
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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