Contacts of the strand formed by residues 229 - 238 (chain B) in PDB entry 1DGH


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 229 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221B  LYS*     4.0     9.6    -      -       +      -
    222B  LEU      3.1    11.9    -      -       -      +
    223B  VAL*     4.1     4.0    -      -       +      -
    227B  GLY      4.0     0.6    +      -       -      -
    228B  GLU*     1.3    76.7    -      -       -      +
    230B  VAL*     1.3    70.3    +      -       -      +
    286B  PHE*     3.5    26.2    +      -       +      -
    421B  HIS*     3.6    33.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 230 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94B  TYR*     4.1    26.0    -      -       +      +
    221B  LYS*     3.5     4.9    -      -       -      +
    222B  LEU*     2.8    49.1    +      -       +      +
    228B  GLU*     5.8     1.3    -      -       +      -
    229B  ALA*     1.3    79.1    -      -       -      +
    231B  TYR*     1.3    65.5    +      -       -      +
    283B  VAL*     4.0    25.8    -      -       +      -
    284B  MET      3.8     9.4    -      -       -      +
    285B  THR*     4.7    13.9    -      -       +      -
    286B  PHE*     3.8     7.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 231 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219B  THR*     3.7    20.4    -      -       +      -
    220B  PHE      3.3    12.3    -      -       -      -
    221B  LYS*     4.1    21.8    -      -       +      -
    230B  VAL*     1.3    76.0    -      -       -      +
    232B  CYS*     1.3    63.0    +      -       -      +
    283B  VAL*     3.4     4.9    -      -       -      +
    284B  MET*     2.7    38.4    +      -       +      +
    286B  PHE*     3.6    33.2    -      +       -      -
    289B  ALA*     4.1    21.1    -      -       +      -
    297B  PHE*     3.5    33.6    -      +       -      -
    303B  TRP*     3.7    10.3    -      -       +      -
    346B  SER*     4.0    11.7    -      -       -      -
    347B  PRO*     4.0     8.8    -      -       +      +
    423B  ILE*     3.7    20.6    -      -       -      +
    425B  TYR*     4.7     2.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 232 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219B  THR*     3.3     8.5    -      -       -      +
    220B  PHE*     2.8    42.8    +      -       -      +
    222B  LEU*     3.4    45.3    -      -       +      -
    231B  TYR*     1.3    76.7    -      -       -      +
    233B  LYS*     1.3    64.9    +      -       -      +
    234B  PHE*     3.7    26.7    -      -       -      -
    281B  ILE*     4.7     3.1    -      -       +      -
    282B  GLN      2.9    16.4    -      -       -      +
    283B  VAL*     4.7     3.1    -      -       +      -
    303B  TRP*     3.7     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 233 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151B  PRO      5.0     0.6    +      -       -      -
    217B  SER*     2.7    25.6    +      -       -      +
    218B  HIS*     3.4    18.2    -      -       -      +
    219B  THR*     3.2    24.1    +      -       -      +
    232B  CYS*     1.3    74.9    -      -       -      +
    234B  PHE*     1.3    63.8    +      -       -      +
    235B  HIS*     3.6     7.5    -      -       +      +
    281B  ILE*     3.1    12.1    -      -       -      +
    282B  GLN*     3.1    47.2    +      -       +      +
    296B  PRO      4.5     2.4    +      -       -      -
    297B  PHE      6.3     0.2    -      -       -      -
    298B  ASP      5.3     3.8    +      -       -      -
    299B  LEU*     5.8     1.8    -      -       -      +
    301B  LYS      4.3    13.9    +      -       -      -
    302B  VAL*     5.5     1.3    -      -       -      +
    303B  TRP*     3.5    47.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 234 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100B  PHE*     4.7     6.3    -      +       -      -
    143B  TRP*     3.8    29.6    -      +       -      -
    145B  LEU*     3.7    29.2    -      -       +      -
    215B  TYR*     3.4     4.4    -      -       -      +
    216B  GLY*     2.9    32.8    +      -       -      +
    217B  SER      4.4     1.1    +      -       -      +
    218B  HIS      4.8     1.6    +      -       -      -
    220B  PHE*     3.5    47.1    -      +       +      -
    222B  LEU*     4.1    15.5    -      -       +      -
    232B  CYS*     3.7    15.9    -      -       -      -
    233B  LYS*     1.3    73.2    -      -       -      +
    235B  HIS*     1.3    66.0    +      -       -      +
    236B  TYR*     4.7     0.9    -      -       -      -
    279B  PHE*     3.8    23.6    -      +       +      -
    280B  TYR      3.9     0.9    -      -       -      -
    281B  ILE*     3.9    17.9    -      -       +      -
    343B  ILE*     4.5     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 235 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151B  PRO*     5.2     6.1    -      -       +      -
    214B  GLY      3.7     5.4    -      -       -      +
    215B  TYR*     3.4    32.8    -      +       +      -
    233B  LYS*     3.6    19.1    -      -       +      +
    234B  PHE*     1.3    78.6    -      -       -      +
    236B  TYR*     1.3    62.6    +      -       -      +
    237B  LYS*     4.0     9.7    -      -       +      -
    278B  THR      4.2     0.2    -      -       -      -
    279B  PHE*     3.4     4.0    -      -       -      -
    280B  TYR*     2.7    53.7    +      -       +      +
    282B  GLN*     2.7    38.0    +      -       +      -
    305B  HIS*     4.1    17.1    +      -       -      -
    310B  LEU*     3.6    19.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 236 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132B  PHE*     2.9    60.7    +      +       -      -
    134B  VAL*     4.0    13.9    -      -       +      +
    145B  LEU*     3.8    22.3    +      -       +      +
    147B  GLY*     3.6    16.8    +      -       -      -
    214B  GLY*     2.8    59.3    +      -       -      -
    215B  TYR*     3.7    14.8    -      -       -      -
    216B  GLY      4.3     1.1    -      -       -      -
    234B  PHE      4.7     0.7    -      -       -      -
    235B  HIS*     1.3    79.9    -      -       -      +
    237B  LYS*     1.3    61.7    +      -       -      +
    277B  TRP*     3.3    22.1    -      -       +      -
    278B  THR      3.1     6.1    -      -       -      +
    279B  PHE*     3.8    24.0    -      +       +      -
    316B  LEU*     3.8     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 237 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213B  ASN*     3.4    29.5    -      -       +      +
    215B  TYR*     4.6    16.6    -      -       +      -
    235B  HIS*     5.0     6.3    -      -       +      -
    236B  TYR*     1.3    74.7    -      -       -      +
    238B  THR*     1.3    65.5    +      -       -      +
    239B  ASP*     3.4     1.7    +      -       -      +
    277B  TRP*     3.1     5.2    -      -       -      -
    278B  THR*     2.9    31.7    +      -       -      +
    280B  TYR*     3.8    28.0    -      -       +      -
    305B  HIS*     4.9    12.4    -      -       -      -
    310B  LEU*     4.0    21.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 238 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210B  ARG      2.8    23.2    +      -       -      -
    212B  MET      3.3    25.6    -      -       -      +
    213B  ASN*     2.9    17.5    +      -       -      +
    237B  LYS*     1.3    73.1    -      -       -      +
    239B  ASP*     1.3    61.5    +      -       -      +
    240B  GLN*     3.1    12.4    +      -       -      -
    241B  GLY*     3.3    32.9    +      -       -      +
    242B  ILE*     3.7     9.0    -      -       +      +
    277B  TRP*     3.4    12.6    -      -       -      -
----------------------------------------------------------
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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