Contacts of the strand formed by residues 31 - 37 (chain D) in PDB entry 3CII


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 31 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27D  TYR*     3.4     4.3    -      -       -      -
     28D  VAL      2.8    30.8    +      -       -      -
     29D  ASP      3.6     0.6    -      -       -      -
     30D  ASP*     1.3    76.5    +      -       -      +
     32D  GLN*     1.3    77.6    +      -       -      +
     33D  PHE*     3.3     8.1    +      -       +      +
     49D  ALA*     4.1    18.8    -      -       +      -
     51D  TRP*     4.6     8.7    -      -       +      +
    179D  LEU*     4.3     9.5    -      -       +      +
    209D  TYR*     2.2    36.4    +      -       -      -
    239D  GLY*     6.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 32 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25D  VAL*     3.5    25.4    -      -       +      +
     26D  GLY      3.5     7.4    -      -       -      +
     27D  TYR*     3.6    33.4    +      -       +      +
     31D  THR*     1.3    79.2    -      -       -      +
     33D  PHE*     1.3    60.3    +      -       -      +
     34D  VAL      4.2     4.3    -      -       -      +
     35D  ARG*     3.7     2.0    -      -       -      +
     48D  ARG*     3.6    29.0    -      -       +      +
     49D  ALA*     4.3     1.9    +      -       -      +
     52E  SER*     5.0     5.2    -      -       -      -
     53E  ASP*     2.7    50.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 33 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5D  LEU*     3.8    17.0    -      -       +      -
      7D  TYR*     3.9     8.7    -      -       -      -
     26D  GLY      3.0    35.6    +      -       -      -
     27D  TYR      3.5     4.5    -      -       -      -
     28D  VAL*     3.5    23.3    -      -       +      -
     31D  THR*     3.5    10.8    -      -       +      +
     32D  GLN*     1.3    74.1    -      -       -      +
     34D  VAL*     1.3    92.8    +      -       +      +
     47D  PRO*     3.4     3.5    -      -       -      +
     48D  ARG*     2.4    36.8    +      -       -      -
     49D  ALA*     3.2    24.6    +      -       +      -
     51D  TRP*     3.8    15.9    -      +       +      -
     52D  MET*     3.8    16.1    -      -       +      +
    171D  TYR*     3.8    28.0    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 34 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7D  TYR*     4.1     6.7    -      -       -      +
     25D  VAL*     3.4     5.2    -      -       -      +
     26D  GLY*     3.1    32.9    +      -       -      +
     32D  GLN*     4.2     1.7    -      -       -      +
     33D  PHE*     1.3   102.9    -      -       +      +
     35D  ARG*     1.3    60.9    +      -       -      +
     45D  MET*     3.9    25.4    -      -       +      -
     46D  VAL      3.3     4.9    -      -       -      +
     47D  PRO*     4.3     0.2    -      -       +      -
     48D  ARG*     4.0     2.9    -      -       -      -
     52D  MET*     3.4    33.4    -      -       +      -
     59D  TYR*     4.3     3.1    -      -       -      +
     60D  TRP*     3.6    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 35 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23D  ILE*     5.8     1.3    -      -       -      -
     24D  SER      3.0    12.6    -      -       -      +
     25D  VAL*     3.8     3.1    -      -       +      -
     32D  GLN*     3.7     8.5    -      -       -      +
     34D  VAL*     1.3    75.4    -      -       -      +
     36D  PHE*     1.3    80.8    +      -       -      +
     37D  ASP*     4.0    17.9    -      -       -      +
     40D  ALA*     3.9    23.2    -      -       -      +
     42D  SER*     4.8     7.3    +      -       -      -
     44D  ARG      5.4     0.4    +      -       -      -
     45D  MET*     3.6     8.4    -      -       -      +
     46D  VAL*     3.1    57.7    +      -       +      +
     48D  ARG*     3.3    31.0    -      -       -      +
     53E  ASP*     3.2    45.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 36 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22D  PHE*     3.7    38.8    -      +       +      -
     23D  ILE*     3.2    10.7    -      -       -      +
     24D  SER*     2.8    41.1    +      -       -      -
     35D  ARG*     1.3    81.6    -      -       -      +
     37D  ASP*     1.3    66.4    +      -       -      +
     38D  ASN*     4.4    18.4    -      -       +      -
     43D  PRO*     3.4    31.4    -      -       +      -
     44D  ARG*     3.7    21.1    -      -       -      -
     45D  MET*     3.8    14.8    -      -       -      -
     64D  THR*     4.8     0.7    -      -       +      -
     67D  ALA*     3.7    31.2    -      -       +      -
     68D  ARG*     4.2    16.2    -      -       +      -
     71D  ALA*     5.1     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 37 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21D  ARG*     3.1    34.3    +      -       -      -
     22D  PHE      3.7     3.8    -      -       -      -
     23D  ILE*     3.6    16.5    -      -       +      +
     35D  ARG*     4.0    22.6    -      -       -      +
     36D  PHE*     1.3    82.5    -      -       -      +
     38D  ASN*     1.3    63.3    +      -       -      +
     39D  ASP*     2.8    30.5    +      -       -      +
     40D  ALA*     3.7    12.2    +      -       +      +
     42D  SER      3.6    18.6    +      -       -      +
     43D  PRO*     3.8     3.6    -      -       -      +
     44D  ARG      4.9     1.4    +      -       -      -
     51E  HIS*     6.2     0.3    -      -       -      -
     53E  ASP*     5.5     1.9    -      -       -      +
----------------------------------------------------------
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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