Contacts of the strand formed by residues 33 - 40 (chain R) in PDB entry 2ZJQ


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 THR 33 (chain R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21R  THR*     3.1    22.5    -      -       +      +
     22R  VAL      3.0    16.1    +      -       -      -
     23R  ILE*     3.9    14.1    -      -       +      -
     24R  VAL*     5.0     0.7    -      -       -      -
     31R  GLY      4.5     4.5    -      -       -      +
     32R  GLN*     1.3    89.7    +      -       -      +
     34R  GLY*     1.3    73.2    +      -       -      +
     48R  VAL*     4.3     4.7    -      -       -      -
     49R  GLU      5.1     0.9    -      -       -      -
     50R  GLY*     4.5     5.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 34 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21R  THR*     4.3     3.6    -      -       -      -
     22R  VAL      3.2    18.7    +      -       -      -
     33R  THR*     1.3    89.0    +      -       -      +
     35R  LYS*     1.3    61.1    +      -       -      -
     36R  VAL      3.5     0.5    +      -       -      -
     48R  VAL*     2.8    24.9    -      -       -      +
     49R  GLU*     4.7     9.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 35 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19R  GLY*     4.1    14.4    -      -       -      +
     20R  ASP      3.3     8.5    -      -       -      +
     21R  THR*     3.9    10.9    +      -       -      +
     34R  GLY*     1.3    70.9    -      -       -      -
     36R  VAL*     1.3    75.5    +      -       -      +
     37R  LEU*     3.5    27.8    -      -       +      +
     48R  VAL*     4.4     0.4    -      -       -      -
     49R  GLU*     3.6    39.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 36 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16R  PHE*     4.0    20.6    -      -       +      -
     17R  LYS      3.2    19.3    -      -       -      +
     18R  LYS*     2.7    38.9    -      -       -      +
     20R  ASP      2.7    16.7    +      -       -      +
     22R  VAL*     3.8    22.2    -      -       +      -
     34R  GLY      3.5     0.4    +      -       -      +
     35R  LYS*     1.3    83.4    -      -       -      +
     37R  LEU*     1.3    67.4    +      -       -      +
     38R  LEU      4.0    14.6    -      -       -      +
     46R  VAL*     4.5     2.9    -      -       +      -
     47R  VAL      3.8     4.7    -      -       -      +
     48R  VAL*     3.7    20.4    -      -       +      -
     80R  LYS*     4.8     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 37 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18R  LYS*     3.7    16.4    -      -       -      +
     35R  LYS*     3.5    29.8    -      -       +      +
     36R  VAL*     1.3    86.6    -      -       -      +
     38R  LEU*     1.3    64.6    -      -       +      +
     39R  ALA      4.0     0.4    -      -       -      -
     47R  VAL*     2.5    37.3    +      -       +      +
     49R  GLU*     3.5    28.5    -      -       +      +
     73R  GLU*     5.0     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 38 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16R  PHE*     5.3     0.3    -      -       -      -
     18R  LYS*     4.4     1.1    -      -       -      -
     36R  VAL*     4.0     6.6    -      -       -      +
     37R  LEU*     1.3    83.7    -      -       +      +
     39R  ALA*     1.3    61.1    +      -       -      +
     40R  LEU*     3.6    30.7    -      -       +      -
     45R  LYS      3.4     8.8    -      -       -      +
     46R  VAL*     3.6     2.3    -      -       -      +
     47R  VAL*     3.0    50.9    +      -       +      +
     75R  ALA*     5.8     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 39 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14R  LEU*     3.5    15.9    -      -       +      -
     16R  PHE*     5.5     0.2    -      -       -      -
     17R  LYS      5.2     0.2    -      -       -      -
     18R  LYS*     3.3    29.3    -      -       +      +
     36R  VAL*     5.2     1.1    -      -       +      -
     38R  LEU*     1.3    74.8    -      -       -      +
     40R  LEU*     1.3    66.9    +      -       -      +
     41R  PRO*     2.8    14.0    -      -       -      +
     84X    G      2.9    39.7    -      -       -      +
     85X    C      3.9     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 40 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14R  LEU*     3.7     3.1    -      -       -      +
     38R  LEU*     4.2    33.2    -      -       +      -
     39R  ALA*     1.3    76.2    -      -       -      +
     41R  PRO*     1.3    59.3    -      -       +      +
     42R  ARG*     3.7     1.8    -      -       -      -
     43R  ASP*     4.4    11.2    -      -       -      +
     44R  GLN*     3.0    11.1    +      -       -      -
     45R  LYS*     2.6    72.2    +      -       +      +
     85X    C      3.7    16.4    -      -       -      +
----------------------------------------------------------
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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