Contacts of the strand formed by residues 253 - 260 (chain A) in PDB entry 3DB4


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 ARG 253 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214A  TRP*     3.5    56.1    -      -       +      +
    247A  ARG      3.7     3.4    -      -       -      -
    248A  GLU*     3.8    18.4    -      -       +      +
    251A  THR      4.4     0.2    +      -       -      -
    252A  ALA*     1.3    75.4    -      -       -      +
    254A  GLU*     1.3    62.0    +      -       -      +
    255A  LEU      4.1     1.2    +      -       -      -
    270A  ARG*     3.7    12.3    +      -       -      +
    271A  ILE      5.5     0.2    -      -       -      +
    274A  VAL*     3.9    19.1    -      -       +      +
    275A  ASP*     2.7    43.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 254 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214A  TRP*     3.3     7.1    -      -       -      -
    245A  ARG*     4.5     0.5    +      -       -      -
    246A  LYS*     3.5     2.4    -      -       -      -
    247A  ARG*     2.6    85.4    +      -       +      +
    249A  THR*     4.6     4.5    +      -       -      -
    252A  ALA*     4.0    19.3    -      -       +      +
    253A  ARG*     1.3    75.2    -      -       -      +
    255A  LEU*     1.3    60.7    +      -       -      +
    256A  TYR*     4.0    23.1    +      -       +      -
    270A  ARG*     3.5    30.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214A  TRP*     3.8    12.1    -      -       +      -
    217A  LEU*     3.9    26.7    -      -       +      -
    225A  LEU*     5.0     2.5    -      -       +      -
    243A  ILE*     3.7    37.9    -      -       +      -
    245A  ARG      3.6     7.9    -      -       -      +
    246A  LYS*     4.3     9.9    -      -       +      -
    253A  ARG      4.1     1.4    +      -       -      -
    254A  GLU*     1.3    74.9    -      -       -      +
    256A  TYR*     1.3    64.8    +      -       -      +
    257A  ALA*     5.5     0.4    -      -       +      -
    269A  CYS      3.5     0.3    -      -       -      +
    270A  ARG*     3.7     9.8    -      -       -      +
    271A  ILE*     2.8    45.1    +      -       +      -
    274A  VAL*     3.6    26.9    -      -       +      +
    277A  VAL*     4.3    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 256 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243A  ILE*     3.7     4.5    -      -       -      +
    244A  SER*     2.7    30.1    +      -       -      -
    245A  ARG*     2.8    70.8    +      -       +      +
    247A  ARG*     5.5     2.5    -      -       +      -
    254A  GLU*     4.0    29.9    +      -       +      -
    255A  LEU*     1.3    77.2    -      -       -      +
    257A  ALA*     1.3    58.2    +      -       -      +
    268A  ASP*     3.6    21.3    -      -       -      +
    269A  CYS      3.1    16.4    -      -       -      +
    270A  ARG*     3.3    44.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 257 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  LEU*     4.4     4.7    -      -       +      -
    241A  ALA*     3.8    20.6    -      -       +      -
    242A  GLU      3.1    15.0    -      -       -      +
    243A  ILE*     4.2     4.5    -      -       +      -
    244A  SER*     3.9     2.2    -      -       -      -
    255A  LEU*     5.5     0.7    -      -       +      -
    256A  TYR*     1.3    76.8    -      -       -      +
    258A  ASN*     1.3    64.1    +      -       -      +
    259A  VAL      3.5     0.7    +      -       -      -
    268A  ASP      3.5     2.1    +      -       -      -
    269A  CYS*     2.8    36.9    +      -       -      +
    271A  ILE*     3.8    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 258 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241A  ALA*     3.1     2.3    -      -       -      -
    242A  GLU*     2.7    69.3    +      -       +      +
    244A  SER*     3.9    16.7    +      -       -      +
    257A  ALA*     1.3    69.9    -      -       -      +
    259A  VAL*     1.3    63.1    +      -       -      +
    260A  VAL*     3.8     3.8    +      -       -      +
    265A  SER*     5.2     5.8    -      -       -      -
    266A  LEU      3.4     5.6    -      -       -      -
    267A  ASN*     3.1    30.7    +      -       -      +
    268A  ASP      3.3    15.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 259 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  LEU*     4.4     2.2    -      -       +      -
    227A  TYR*     4.1    15.3    -      -       +      -
    239A  TYR*     3.5    33.7    -      -       +      -
    240A  ASP      3.6     3.8    -      -       -      +
    241A  ALA*     3.9    12.3    -      -       +      -
    257A  ALA      4.0     2.0    -      -       -      +
    258A  ASN*     1.3    74.3    -      -       -      +
    260A  VAL*     1.3    61.5    +      -       -      +
    261A  LEU*     3.6    15.3    +      -       +      -
    265A  SER*     3.3     1.6    -      -       -      -
    266A  LEU*     2.5    48.8    +      -       +      +
    269A  CYS*     3.9    28.5    -      -       +      -
    271A  ILE*     4.1    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 260 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  ARG*     5.2     5.4    -      -       -      +
    149A  GLY      4.0     6.9    -      -       -      +
    239A  TYR*     3.7    19.9    -      -       -      +
    240A  ASP*     2.8    36.0    +      -       +      +
    241A  ALA*     4.8     1.6    -      -       -      +
    242A  GLU*     5.5     1.6    -      -       +      +
    258A  ASN      4.4     6.3    -      -       -      +
    259A  VAL*     1.3    70.9    -      -       -      +
    261A  LEU*     1.3    64.1    +      -       -      +
    263A  ASP*     3.4    32.5    -      -       +      +
    264A  ASP      4.7     0.4    -      -       -      +
    265A  SER*     4.2    12.8    -      -       -      +
----------------------------------------------------------
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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