Contacts of the strand formed by residues 372 - 376 (chain A) in PDB entry 3CB4


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 372 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    369A  THR*     4.7     4.8    -      -       -      -
    370A  VAL*     3.5    31.9    +      -       +      +
    371A  VAL*     1.3    74.1    -      -       -      +
    373A  GLU*     1.3    60.5    +      -       -      +
    374A  VAL*     4.0     4.9    -      -       +      -
    383A  TYR*     3.3    12.4    -      -       -      +
    384A  VAL*     3.1    36.8    +      -       +      +
    385A  ASP      5.9     0.4    -      -       -      -
    399A  LEU*     3.9    23.1    -      -       +      -
    400A  ARG      3.7     9.9    -      -       -      +
    401A  GLU*     4.1    10.3    -      -       +      -
    402A  PRO*     3.8    21.1    -      -       +      -
    448A  ALA*     3.3    18.4    -      -       +      +
    475A  PHE*     4.2     2.0    -      -       -      -
    480A  MET*     4.1    12.9    -      -       +      +
    498A  ILE*     3.2    62.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 373 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372A  TYR*     1.3    72.3    -      -       -      +
    374A  VAL*     1.3    57.1    +      -       -      +
    375A  GLU      4.2     0.2    +      -       -      -
    381A  VAL*     3.5    24.9    -      -       +      +
    382A  ILE      3.7     2.7    -      -       -      -
    383A  TYR*     2.8    30.8    +      -       +      -
    398A  GLU      4.0     0.9    -      -       -      +
    400A  ARG*     2.7    71.1    +      -       +      +
    475A  PHE*     3.6    47.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 374 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372A  TYR*     4.5     1.1    -      -       +      -
    373A  GLU*     1.3    79.2    -      -       -      +
    375A  GLU*     1.3    66.4    +      -       -      +
    376A  THR      5.0     0.2    -      -       -      +
    380A  GLU      3.1     4.0    -      -       -      +
    381A  VAL*     3.5     2.8    -      -       -      -
    382A  ILE*     2.9    45.8    +      -       +      +
    384A  VAL*     3.7    30.1    -      -       +      -
    390A  LEU*     3.7     6.3    -      -       +      -
    391A  PRO*     4.2    10.8    -      -       +      -
    396A  ILE*     3.8    37.9    -      -       +      -
    398A  GLU      3.8     2.9    -      -       -      +
    399A  LEU*     3.7    22.0    -      -       +      -
    400A  ARG*     5.2     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 375 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    373A  GLU      4.2     0.4    +      -       -      -
    374A  VAL*     1.3    73.6    -      -       -      +
    376A  THR*     1.3    62.2    +      -       -      +
    379A  ARG*     3.2    51.2    +      -       -      +
    380A  GLU      3.4     6.5    -      -       -      +
    381A  VAL*     4.2    12.7    -      -       +      +
    396A  ILE*     3.7     3.6    -      -       -      -
    397A  TYR*     2.7    50.3    +      -       +      -
    398A  GLU      3.0    14.2    +      -       -      +
    400A  ARG*     2.7    35.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 376 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374A  VAL*     3.8     2.3    +      -       -      +
    375A  GLU*     1.3    76.6    -      -       -      +
    377A  THR*     1.3    87.6    +      -       +      +
    378A  SER*     3.2    20.3    +      -       -      +
    379A  ARG*     3.4    14.0    -      -       -      +
    380A  GLU*     3.1    31.2    +      -       -      +
    382A  ILE*     4.3    16.6    -      -       -      +
    391A  PRO*     5.2     7.4    -      -       +      +
    395A  ASN*     3.2    18.8    -      -       +      +
    396A  ILE*     4.7     0.4    -      -       -      +
    397A  TYR*     3.6     8.3    -      -       -      +
----------------------------------------------------------
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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