Contacts of the strand formed by residues 356 - 362 (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 MET 356 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348A  LEU*     3.2    19.8    -      -       -      +
    349A  ASN*     3.0    31.4    +      -       +      +
    354A  VAL*     3.3    11.3    +      -       -      +
    355A  ALA*     1.3    79.2    -      -       -      +
    357A  LEU*     1.3    63.5    +      -       -      +
    380A  MET*     3.7    30.5    -      -       +      -
    388A  LEU*     3.6    35.4    -      -       +      -
    389A  CYS      3.4    15.5    -      -       -      +
    390A  VAL*     4.1    13.9    -      -       +      -
    391A  VAL*     3.8     3.7    -      -       -      +
     26C  ARG*     4.9    15.5    -      -       -      -
     27C  ILE*     4.9    15.7    -      -       -      -
     30C  CYS*     6.0     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 357 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    346A  LEU*     3.9    23.8    -      -       +      -
    347A  GLN      3.1    16.2    -      -       -      +
    348A  LEU*     4.4     8.5    -      -       +      -
    349A  ASN*     4.4     1.5    -      -       -      +
    356A  MET*     1.3    81.8    -      -       -      +
    358A  GLU*     1.3    62.3    +      -       -      +
    359A  LEU*     3.7    23.8    -      -       +      -
    372A  PHE*     3.5    26.2    -      -       +      -
    388A  LEU*     3.3     6.7    -      -       -      +
    389A  CYS*     3.0    39.8    +      -       -      +
    391A  VAL*     4.3     3.6    -      -       +      -
    412A  VAL*     4.9     4.9    -      -       +      -
    428A  PHE*     3.5    33.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 358 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345A  SER      3.7     1.2    -      -       -      +
    346A  LEU*     3.6     1.2    -      -       -      -
    347A  GLN*     2.7    47.9    +      -       +      +
    349A  ASN*     3.9    18.0    +      -       -      +
    357A  LEU*     1.3    73.8    -      -       -      +
    359A  LEU*     1.3    65.3    +      -       -      +
    360A  THR*     4.1     6.9    +      -       +      +
    382A  ARG*     5.8     1.2    -      -       -      +
    386A  SER*     3.8    15.1    -      -       -      -
    387A  MET      3.2    14.4    -      -       -      +
    388A  LEU*     3.4    19.7    -      -       +      -
   1963B  ARG*     5.8     0.5    +      -       -      -
   1971B  SER*     5.2     0.7    +      -       -      -
   2002B  LEU*     4.8     1.7    -      -       -      +
   2005B  ARG*     2.9    50.7    +      -       -      +
   2006B  LEU*     3.6    18.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 359 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343A  VAL*     4.6    13.5    -      -       +      -
    345A  SER      3.6     4.5    -      -       -      +
    346A  LEU*     3.6    29.2    -      -       +      -
    357A  LEU*     3.7    20.0    -      -       +      +
    358A  GLU*     1.3    82.6    -      -       -      +
    360A  THR*     1.3    63.0    +      -       -      +
    364A  PHE*     3.5    13.6    -      -       +      -
    370A  VAL*     4.1    24.0    -      -       +      -
    386A  SER*     3.0     5.4    -      -       -      -
    387A  MET*     2.5    47.4    +      -       +      +
    389A  CYS*     4.8     1.8    -      -       -      -
    412A  VAL*     4.7     6.7    -      -       +      -
    414A  LEU*     3.9    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 360 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343A  VAL*     3.7     2.4    -      -       -      +
    344A  GLU*     3.1     7.2    +      -       -      +
    345A  SER*     2.9    50.6    +      -       -      +
    347A  GLN*     4.5     9.0    +      -       -      +
    358A  GLU*     4.3    11.2    -      -       -      +
    359A  LEU*     1.3    79.1    -      -       -      +
    361A  GLY*     1.3    59.3    +      -       -      +
    364A  PHE*     4.1     1.8    -      -       -      -
    385A  GLU      3.1    12.1    -      -       -      +
    386A  SER*     4.8     1.8    -      -       -      -
   1995B  ASP*     5.4     6.0    +      -       -      +
   2005B  ARG*     4.0    29.6    -      -       -      +
   2035B  TRP*     5.1     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 361 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342A  VAL      3.0    15.0    -      -       -      -
    344A  GLU*     3.6    18.7    -      -       -      +
    360A  THR*     1.3    75.6    -      -       -      +
    362A  GLN*     1.3    66.3    +      -       -      +
    364A  PHE*     3.6     9.8    -      -       -      -
    385A  GLU*     3.0    27.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 362 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  LYS*     5.7     8.5    -      -       -      +
    342A  VAL*     2.9    33.6    +      -       +      +
    344A  GLU*     2.6    29.0    +      -       -      +
    361A  GLY*     1.3    78.4    -      -       -      +
    363A  ASN*     1.3    82.8    +      -       -      +
    364A  PHE*     3.3    11.5    -      -       -      -
    384A  GLY      3.8     6.3    -      -       -      -
    385A  GLU*     4.3     8.5    -      -       +      +
   2061B  ARG*     4.1    22.6    +      -       -      +
----------------------------------------------------------
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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