Contacts of the strand formed by residues 294 - 300 (chain B) in PDB entry 3DM6


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 GLN 294 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  TRP*     3.8    24.5    -      -       -      -
    190B  TYR      5.3     0.4    +      -       -      -
    288B  MET*     4.5     0.5    -      -       -      +
    289B  GLY*     2.7    41.9    +      -       -      -
    290B  GLU*     2.7    28.3    +      -       -      +
    291B  VAL*     2.6    51.5    +      -       +      +
    292B  THR      4.4     0.2    -      -       -      +
    293B  ASN*     1.3    74.7    -      -       -      +
    295B  SER*     1.3    79.4    +      -       -      +
    296B  PHE*     4.2     2.4    -      -       -      +
    373B  PRO*     3.9    17.3    -      -       +      -
    374B  PHE      3.4     4.5    -      -       -      +
    376B  THR*     5.4     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 295 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204B  VAL*     4.1    19.9    -      -       -      +
    286B  TYR*     4.0     8.3    -      -       -      -
    287B  LEU      3.3    16.8    -      -       -      -
    288B  MET*     4.9     0.4    -      -       -      -
    289B  GLY      3.8     1.6    -      -       -      +
    293B  ASN      4.0     0.4    +      -       -      -
    294B  GLN*     1.3    91.0    +      -       -      +
    296B  PHE*     1.3    63.6    +      -       -      +
    373B  PRO*     3.4     4.3    -      -       -      +
    374B  PHE*     2.9    46.0    +      -       -      +
    375B  VAL      4.4     1.0    +      -       -      -
    376B  THR*     4.4    11.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 296 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  TRP*     3.5    54.5    -      +       +      -
    190B  TYR      3.4    24.2    -      -       -      -
    191B  THR*     3.8     9.9    -      -       -      -
    286B  TYR*     3.1    10.2    -      -       -      +
    287B  LEU*     2.9    61.2    +      -       +      +
    288B  MET      3.8    12.1    -      -       -      -
    294B  GLN*     4.2     8.3    -      -       -      -
    295B  SER*     1.3    77.2    -      -       -      +
    297B  ARG*     1.3    65.5    +      -       -      +
    298B  ILE*     4.1    10.1    -      -       +      -
    354B  PHE*     4.3     7.0    -      +       +      -
    370B  VAL*     4.2     9.4    -      -       +      -
    371B  GLU      3.6    12.6    -      -       -      +
    372B  GLY*     4.2     1.8    -      -       -      -
    374B  PHE*     4.1     6.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 297 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207B  GLU*     3.9     8.5    +      -       -      -
    284B  SER*     4.6     4.7    +      -       -      -
    285B  LEU      3.2    11.7    -      -       -      +
    286B  TYR*     3.1    47.1    +      -       +      -
    287B  LEU      4.7     0.2    -      -       -      +
    296B  PHE*     1.3    76.5    -      -       -      +
    298B  ILE*     1.3    66.3    +      -       -      +
    299B  THR*     4.1    15.7    +      -       -      +
    369B  ALA      3.7     0.3    -      -       -      +
    370B  VAL*     3.2     7.3    -      -       -      +
    371B  GLU*     2.5    75.8    +      -       -      +
    374B  PHE*     3.7    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 298 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283B  ILE      3.8     0.5    -      -       -      +
    284B  SER*     3.3     1.6    -      -       -      -
    285B  LEU*     2.9    49.7    +      -       +      +
    287B  LEU*     4.1     6.7    -      -       +      -
    296B  PHE*     4.1    10.3    -      -       +      -
    297B  ARG*     1.3    77.4    -      -       -      +
    299B  THR*     1.3    61.1    +      -       -      +
    300B  ILE      4.2     0.8    +      -       -      -
    333B  MET*     3.2    35.2    -      -       +      -
    337B  ILE*     3.7    20.9    -      -       +      -
    341B  PHE*     3.6    13.9    -      -       +      -
    354B  PHE*     3.7    39.3    -      -       +      -
    369B  ALA      3.4     3.6    -      -       -      -
    370B  VAL*     4.2     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 299 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282B  VAL*     3.8    28.0    -      -       +      -
    283B  ILE      3.3     4.7    -      -       -      +
    284B  SER*     2.6    27.9    +      -       -      +
    297B  ARG*     4.1    17.7    +      -       -      +
    298B  ILE*     1.3    72.0    -      -       -      +
    300B  ILE*     1.3    61.0    +      -       -      +
    341B  PHE*     3.6     5.0    -      -       -      -
    367B  THR      5.2     4.7    -      -       -      +
    368B  ALA*     3.3    13.5    -      -       -      +
    369B  ALA*     2.7    44.0    +      -       +      +
    371B  GLU*     4.8     1.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 300 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234B  LEU*     5.7     2.5    -      -       +      -
    282B  VAL*     3.4     8.3    -      -       -      +
    283B  ILE*     2.6    58.3    +      -       +      +
    298B  ILE      4.2     1.1    -      -       -      +
    299B  THR*     1.3    73.6    -      -       -      +
    301B  LEU*     1.3    66.3    +      -       -      +
    304B  GLN*     3.2    33.4    -      -       +      +
    305B  TYR*     4.1    12.6    -      -       +      -
    336B  VAL*     3.4    14.4    -      -       +      +
    337B  ILE*     3.3    35.9    -      -       +      +
    340B  GLY*     4.5     0.9    -      -       -      -
    341B  PHE*     3.3    31.9    -      -       +      -
----------------------------------------------------------
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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