Contacts of the strand formed by residues 35 - 41 (chain B) in PDB entry 1DIZ


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 TYR 35 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  LEU*     4.2     9.0    -      -       +      -
     19B  LEU*     4.3    23.8    -      -       +      +
     28B  GLU*     2.8    34.2    +      -       +      +
     29B  THR      3.7     5.6    -      -       -      -
     30B  VAL*     4.2    25.1    -      -       +      -
     34B  TYR*     1.3    78.3    -      -       -      +
     36B  ALA*     1.3    61.3    +      -       -      +
     37B  ARG*     3.4    40.2    +      -       +      -
     48B  VAL      5.5     0.7    -      -       -      -
     49B  THR*     3.3     3.6    -      -       -      +
     50B  ALA*     2.7    40.9    +      -       +      +
     52B  PRO*     6.3     0.2    -      -       +      -
     78B  MET*     4.9     4.9    -      -       -      -
     81B  LEU*     3.6    23.7    -      -       +      +
     82B  PHE*     3.6    28.3    -      +       +      -
----------------------------------------------------------
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Residues in contact with ALA 36 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  GLU*     3.2     1.7    -      -       -      +
     29B  THR*     2.5    42.4    +      -       -      +
     34B  TYR*     4.1    17.7    -      -       +      -
     35B  TYR*     1.3    78.3    -      -       -      +
     37B  ARG*     1.3    61.8    +      -       -      +
     47B  VAL*     4.6     3.6    -      -       +      -
     48B  VAL      3.2    11.2    -      -       -      +
     49B  THR*     4.0    12.1    -      -       +      +
    152B  TYR*     3.5    20.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 37 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  VAL*     3.1    35.7    -      -       -      +
     28B  GLU*     3.6    17.3    +      -       +      +
     35B  TYR*     3.4    34.9    +      -       +      +
     36B  ALA*     1.3    76.8    -      -       -      +
     38B  SER*     1.3    83.5    +      -       -      +
     39B  LEU*     4.9     2.2    -      -       +      +
     47B  VAL*     3.5     3.3    -      -       -      +
     48B  VAL*     3.1    33.1    +      -       +      +
     78B  MET*     4.9     7.6    -      -       +      -
     81B  LEU*     6.1     0.2    -      -       -      +
    111B  VAL*     4.0    34.5    -      -       -      +
    115B  GLU*     2.9    40.0    +      -       -      -
    119B  ARG*     4.7     2.6    -      -       -      +
    152B  TYR*     4.0     8.2    -      -       -      -
    155B  PHE*     4.3     5.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 38 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27B  VAL*     2.9    19.4    +      -       -      +
     37B  ARG*     1.3   100.5    +      -       -      +
     39B  LEU*     1.3    60.6    +      -       -      +
     46B  GLY      3.2     9.4    -      -       -      -
     47B  VAL*     4.5     1.3    -      -       -      +
    146B  LEU*     4.1    14.8    -      -       -      -
    152B  TYR*     3.9    10.7    -      -       -      -
    153B  ILE      2.7    33.6    +      -       -      -
    154B  CYS*     3.6    11.2    -      -       -      -
    155B  PHE      4.3     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 39 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  ARG*     4.5     3.8    -      -       +      +
     38B  SER*     1.3    78.6    -      -       -      +
     40B  ALA*     1.3    66.1    +      -       -      +
     41B  VAL*     4.2     4.7    -      -       +      -
     45B  ARG*     3.1     5.0    -      -       -      +
     46B  GLY      2.7    33.3    +      -       -      -
     48B  VAL*     3.3    35.2    -      -       +      -
     67B  LEU*     3.7     7.8    -      -       +      +
     74B  CYS*     3.7    24.7    -      -       +      -
     77B  LYS*     4.1    22.0    -      -       +      -
     78B  MET*     4.3     9.2    -      -       +      -
    111B  VAL*     3.3    37.0    -      -       +      -
    154B  CYS*     4.8     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 40 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  LEU*     1.3    80.7    -      -       -      +
     41B  VAL*     1.3    63.5    +      -       -      +
     42B  GLY      3.6     8.9    +      -       -      +
     44B  TYR      3.1     4.9    -      -       -      +
     45B  ARG*     3.4    24.2    -      -       +      -
     77B  LYS*     4.8     6.9    +      -       -      -
    144B  GLU*     5.3     2.0    -      -       -      +
    154B  CYS*     4.4     9.6    -      -       +      -
    157B  THR*     5.9     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 41 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  LEU*     4.2     3.3    -      -       +      -
     40B  ALA*     1.3    74.0    -      -       -      +
     42B  GLY*     1.3    60.9    +      -       -      +
     44B  TYR*     2.8    27.2    +      -       -      +
     67B  LEU*     4.5     3.4    -      -       +      -
     70B  VAL*     3.6    33.1    -      -       +      +
     73B  GLU*     4.0    31.4    -      -       +      +
     74B  CYS*     4.0    18.2    -      -       -      -
     77B  LYS*     3.7    25.1    -      -       +      +
----------------------------------------------------------
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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