Contacts of the strand formed by residues 379 - 383 (chain A) in PDB entry 3NBN


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 379 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366A  PRO      5.7     0.2    -      -       -      +
    368A  LEU      4.0     7.0    -      -       -      +
    369A  ARG*     3.7    32.1    -      -       -      +
    370A  VAL*     2.9    30.1    +      -       +      +
    377A  ALA      3.1     8.7    +      -       -      -
    378A  GLU*     1.3    80.3    +      -       -      +
    380A  MET*     1.3    61.7    +      -       -      +
    381A  TYR*     4.7     1.1    -      -       +      +
    387A  MET*     4.0    26.7    -      -       +      -
    388A  LEU      3.6     7.0    -      -       -      +
    389A  CYS*     3.7     0.2    -      -       -      +
     34C  HIS*     2.5    34.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 380 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356A  MET*     3.7    35.4    -      -       +      -
    378A  GLU*     4.2    25.6    -      -       -      +
    379A  THR*     1.3    77.3    -      -       -      +
    381A  TYR*     1.3    61.9    +      -       -      +
    382A  ARG*     3.7     0.8    +      -       -      -
    387A  MET*     3.6     1.7    -      -       -      +
    388A  LEU*     2.6    53.3    +      -       +      +
    390A  VAL*     4.2    11.7    -      -       +      -
     27C  ILE*     5.0    10.1    -      -       +      +
     30C  CYS*     3.3    47.3    -      -       +      +
     31C  ARG*     3.8    13.2    -      -       -      +
     34C  HIS*     3.3     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 381 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    364A  PHE*     4.0     4.2    +      -       +      -
    365A  THR*     3.8    30.4    -      -       -      +
    366A  PRO*     3.8    24.1    -      -       +      +
    379A  THR*     5.5     1.6    -      -       +      -
    380A  MET*     1.3    72.4    -      -       -      +
    382A  ARG*     1.3    63.3    +      -       -      +
    383A  CYS*     3.3    28.3    -      -       -      -
    384A  GLY*     3.1     9.8    +      -       -      -
    387A  MET*     3.7    19.3    -      -       +      -
   2072B  GLU*     2.9    23.6    +      -       -      -
     30C  CYS      4.9     0.3    -      -       -      +
     33C  HIS*     3.5    14.4    -      -       -      -
     34C  HIS*     3.0    29.2    +      -       +      +
     37C  CYS*     3.6    39.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 382 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358A  GLU*     5.8     1.6    -      -       -      +
    380A  MET*     3.7     2.2    +      -       -      -
    381A  TYR*     1.3    81.2    -      -       -      +
    383A  CYS*     1.3    66.2    +      -       -      +
    386A  SER*     3.2    25.6    +      -       -      +
    387A  MET*     4.1     0.2    -      -       -      +
    388A  LEU*     3.5    35.3    -      -       +      +
   2005B  ARG*     2.9    31.6    +      -       +      +
   2006B  LEU*     4.8     1.7    -      -       +      -
   2007B  ALA*     3.1    25.4    -      -       -      +
   2038B  ALA      4.4     0.2    -      -       -      +
   2039B  VAL*     3.8    40.6    +      -       +      +
   2041B  ASN*     4.7     4.6    -      -       -      +
   2072B  GLU*     5.1     0.2    -      -       -      +
     29C  LEU*     5.0     5.3    +      -       -      +
     30C  CYS*     4.6    19.3    -      -       -      +
     33C  HIS*     3.1    62.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 383 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    364A  PHE*     4.1     1.0    -      -       -      +
    381A  TYR*     3.3    18.4    -      -       -      -
    382A  ARG*     1.3    79.4    -      -       -      +
    384A  GLY*     1.3    56.8    +      -       -      +
    385A  GLU*     2.6    29.8    +      -       -      -
    386A  SER*     2.8    42.6    +      -       -      +
   2035B  TRP*     4.3    10.5    -      -       -      -
   2038B  ALA*     3.6    32.5    -      -       -      +
   2039B  VAL*     3.8     8.3    -      -       +      -
   2072B  GLU*     3.1    18.4    -      -       -      +
----------------------------------------------------------
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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