Contacts of the strand formed by residues 238 - 245 (chain D) 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 ALA 238 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    393C  HIS*     5.5     4.2    -      -       -      -
     60D  LEU*     4.0     4.3    -      -       +      -
    205D  GLY      3.2     9.0    -      -       -      +
    207D  PHE*     3.4    35.0    -      -       -      +
    208D  ALA*     3.5    18.4    -      -       +      +
    234D  MET      3.9     1.6    +      -       -      -
    235D  CYS      4.7     0.9    +      -       -      +
    236D  LYS      3.6     4.2    -      -       -      +
    237D  ALA*     1.3    80.7    -      -       -      +
    239D  GLU*     1.3    65.9    +      -       -      +
    240D  THR      3.4     3.4    -      -       -      +
    241D  THR*     4.3     8.4    +      -       -      +
    267D  HIS*     4.4     6.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 239 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    434C  LYS*     5.5    11.7    -      -       -      +
    205D  GLY      2.9    13.8    +      -       -      +
    206D  ASP*     3.4    13.0    +      -       -      +
    238D  ALA*     1.3    72.8    -      -       -      +
    240D  THR*     1.3    64.1    +      -       -      +
    267D  HIS*     3.6    14.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 240 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206D  ASP      2.9     8.8    +      -       -      -
    207D  PHE*     3.1    31.6    -      -       +      +
    208D  ALA      3.0    23.3    +      -       -      +
    238D  ALA*     4.5     1.1    -      -       -      -
    239D  GLU*     1.3    80.1    +      -       -      +
    241D  THR*     1.3    62.7    +      -       -      +
    242D  VAL*     4.1     3.4    -      -       +      -
    267D  HIS*     3.6     8.9    +      -       +      +
    268D  ARG*     3.6    46.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 241 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208D  ALA*     3.8    12.7    -      -       +      +
    210D  VAL*     4.7     4.3    -      -       +      -
    234D  MET      4.1     0.3    +      -       -      -
    235D  CYS*     2.8    39.6    +      -       -      -
    238D  ALA*     4.3     7.1    +      -       -      +
    240D  THR*     1.3    71.7    -      -       -      +
    242D  VAL*     1.3    63.4    +      -       -      +
    243D  VAL*     3.6    24.5    -      -       +      -
    265D  TYR      3.1    22.4    +      -       -      +
    266D  VAL*     4.3     1.8    -      -       -      -
    267D  HIS*     3.0    16.4    +      -       -      +
    268D  ARG      3.1    23.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 242 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49D  ALA*     3.9    24.9    -      -       +      +
     50D  VAL*     4.5     2.5    -      -       +      -
     73D  LEU*     3.3    33.7    -      -       +      +
    207D  PHE*     4.5     7.4    -      -       +      -
    208D  ALA      2.9    15.9    +      -       -      +
    209D  LEU*     4.1    12.3    -      -       +      -
    210D  VAL*     3.0    24.1    +      -       -      +
    240D  THR*     4.1    11.0    -      -       +      +
    241D  THR*     1.3    75.1    -      -       -      +
    243D  VAL*     1.3    63.4    +      -       -      +
    268D  ARG*     3.3    33.7    -      -       +      +
    270D  ILE*     5.0     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 243 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73D  LEU*     4.3     2.5    -      -       -      -
    210D  VAL*     3.3    20.4    -      -       +      +
    212D  ALA*     3.8    28.9    -      -       +      -
    221D  VAL*     4.0     9.2    -      -       +      -
    235D  CYS*     4.5     3.6    -      -       -      -
    241D  THR*     3.6    26.2    -      -       +      -
    242D  VAL*     1.3    73.2    -      -       -      +
    244D  GLU*     1.3    65.8    +      -       -      +
    245D  VAL*     4.0     0.7    -      -       +      -
    266D  VAL*     3.9    20.9    -      -       +      -
    268D  ARG      2.8    10.2    +      -       -      +
    269D  LEU*     3.3    23.8    -      -       +      +
    270D  ILE*     3.0    26.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 244 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70D  PRO*     2.9    29.3    -      -       +      +
     72D  ASN*     3.1    14.2    +      -       -      -
     73D  LEU*     2.7    35.0    +      -       +      +
    210D  VAL      2.8    19.6    +      -       -      +
    211D  LYS*     3.5     8.6    -      -       +      +
    212D  ALA      2.9    25.8    +      -       -      +
    243D  VAL*     1.3    73.7    -      -       -      +
    245D  VAL*     1.3    61.1    +      -       -      +
    270D  ILE*     3.3    23.1    -      -       +      -
    272D  GLY      4.7     0.2    -      -       -      +
    275D  TYR*     2.6    39.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 245 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212D  ALA*     3.4    22.2    -      -       +      +
    213D  TRP      4.0     2.5    -      -       -      +
    214D  LYS      3.7    21.3    -      -       -      +
    215D  ALA*     3.8    11.7    -      -       +      +
    243D  VAL*     4.0     1.3    -      -       +      -
    244D  GLU*     1.3    79.0    -      -       -      +
    246D  GLU*     1.3    60.1    +      -       -      +
    247D  GLU      3.5    23.1    -      -       -      +
    248D  ILE*     3.9    19.7    -      -       +      -
    269D  LEU*     3.8    13.5    -      -       +      -
    270D  ILE      3.0    18.0    +      -       -      +
    271D  LYS*     3.4     4.9    -      -       -      -
    272D  GLY*     2.7    26.0    +      -       -      -
    275D  TYR*     3.4     6.9    +      -       -      -
----------------------------------------------------------
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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