Contacts of the strand formed by residues 238 - 245 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    393A  HIS*     5.4     4.2    -      -       -      -
     60B  LEU*     4.4     2.2    -      -       +      -
    205B  GLY*     3.2    10.5    -      -       -      +
    207B  PHE*     3.4    35.9    -      -       -      +
    208B  ALA*     3.4    18.2    -      -       +      +
    234B  MET      4.1     1.0    +      -       -      -
    236B  LYS      3.6     3.0    -      -       -      +
    237B  ALA*     1.3    79.4    +      -       -      +
    239B  GLU*     1.3    66.3    +      -       -      +
    240B  THR      3.2     4.4    +      -       -      +
    241B  THR*     4.0    11.8    -      -       +      +
    267B  HIS*     4.3     4.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 239 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    434A  LYS*     5.2    13.0    -      -       -      +
    205B  GLY      3.1    12.4    +      -       -      +
    206B  ASP*     3.5    13.4    +      -       -      +
    238B  ALA*     1.3    72.6    -      -       -      +
    240B  THR*     1.3    64.8    +      -       -      +
    267B  HIS*     3.6    14.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 240 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206B  ASP      3.0     7.9    +      -       -      -
    207B  PHE*     3.1    30.0    -      -       +      +
    208B  ALA      2.9    21.4    +      -       -      -
    238B  ALA*     4.3     0.4    -      -       -      -
    239B  GLU*     1.3    82.3    +      -       -      +
    241B  THR*     1.3    65.9    +      -       -      +
    242B  VAL*     3.9     2.5    +      -       +      -
    267B  HIS*     3.6    10.5    -      -       +      -
    268B  ARG*     3.6    48.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 241 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208B  ALA*     3.7    17.0    -      -       +      -
    210B  VAL*     5.1     0.7    -      -       -      -
    235B  CYS*     3.0    37.5    -      -       -      +
    238B  ALA*     4.0    10.8    -      -       +      +
    240B  THR*     1.3    75.6    -      -       -      +
    242B  VAL*     1.3    61.7    +      -       -      +
    243B  VAL*     4.0     9.8    -      -       -      +
    265B  TYR      2.5    23.4    +      -       -      +
    266B  VAL*     3.5     9.0    -      -       -      -
    267B  HIS*     2.9    16.1    +      -       +      +
    268B  ARG*     2.9    25.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 242 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  ALA*     3.7    25.4    -      -       +      +
     50B  VAL*     4.6     6.5    -      -       +      -
     73B  LEU*     3.5    35.1    -      -       +      +
    207B  PHE*     4.6    10.3    -      -       +      -
    208B  ALA      2.8    16.4    +      -       -      +
    209B  LEU*     4.3     4.9    -      -       +      -
    210B  VAL*     2.8    32.6    +      -       -      +
    240B  THR*     4.3     9.6    -      -       +      +
    241B  THR*     1.3    76.2    -      -       -      +
    243B  VAL*     1.3    61.0    +      -       -      +
    268B  ARG*     3.4    31.0    -      -       +      +
    269B  LEU      5.1     0.2    -      -       -      +
    270B  ILE*     5.2     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 243 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73B  LEU*     4.2     2.2    -      -       -      -
    210B  VAL*     3.1    22.2    -      -       +      +
    212B  ALA*     3.9    28.7    -      -       +      +
    221B  VAL*     4.1     7.2    -      -       +      -
    235B  CYS*     4.3    12.6    -      -       -      -
    241B  THR*     4.2    11.2    -      -       -      +
    242B  VAL*     1.3    78.8    -      -       -      +
    244B  GLU*     1.3    63.3    +      -       -      +
    245B  VAL*     4.0     1.8    -      -       +      -
    266B  VAL*     3.7    24.2    -      -       +      -
    268B  ARG      2.8     8.8    +      -       -      +
    269B  LEU*     3.3    25.5    -      -       +      +
    270B  ILE*     3.0    24.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 244 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70B  PRO*     2.9    38.7    -      -       -      +
     71B  GLU      3.8     0.3    +      -       -      -
     72B  ASN*     3.0    17.9    +      -       -      +
     73B  LEU*     2.9    19.4    +      -       +      +
    210B  VAL      2.8    17.7    +      -       -      +
    211B  LYS*     3.5     9.7    -      -       +      +
    212B  ALA      2.8    25.3    +      -       -      +
    243B  VAL*     1.3    73.7    -      -       -      +
    245B  VAL*     1.3    61.3    +      -       -      +
    270B  ILE*     3.2    26.9    -      -       +      -
    275B  TYR*     2.8    35.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 245 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212B  ALA*     3.3    22.7    -      -       +      -
    213B  TRP      3.7     6.5    -      -       -      +
    214B  LYS*     3.6    23.6    -      -       -      +
    215B  ALA*     3.6     4.9    -      -       +      +
    221B  VAL*     4.5     0.7    -      -       +      -
    243B  VAL*     4.0     1.8    -      -       +      -
    244B  GLU*     1.3    77.2    -      -       -      +
    246B  GLU*     1.3    58.9    +      -       -      +
    247B  GLU      3.5    21.8    -      -       -      +
    248B  ILE*     4.1    10.5    -      -       +      -
    269B  LEU*     3.8    19.5    -      -       +      -
    270B  ILE      2.9    20.1    +      -       -      +
    271B  LYS*     3.3    13.2    -      -       -      -
    272B  GLY      2.9    23.9    +      -       -      -
    275B  TYR*     3.1     6.4    +      -       -      -
----------------------------------------------------------
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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