Contacts of the strand formed by residues 355 - 358 (chain B) in PDB entry 3N9Z


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 LEU 355 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71B  LEU*     6.3     0.2    -      -       -      -
     72B  PHE*     3.8    34.3    -      -       +      -
    352B  SER*     4.7     1.6    -      -       -      +
    354B  THR*     1.3    78.2    -      -       -      +
    356B  GLN*     1.3    63.5    +      -       -      +
    357B  ARG*     5.3     2.2    -      -       -      +
    377B  GLN*     3.1     4.5    -      -       -      +
    378B  VAL*     2.7    41.1    +      -       +      -
    380B  ILE*     3.6    23.6    -      -       +      -
    414B  LEU*     4.0    17.0    -      -       +      +
    417B  GLY*     3.6    32.5    -      -       -      -
    601B  HEM      3.8    31.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 356 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71B  LEU*     5.7     0.9    -      -       -      -
     72B  PHE*     6.2     0.2    -      -       -      -
     81B  ARG*     3.3    23.8    -      -       -      +
     82B  PHE*     3.0    27.0    +      -       +      +
    354B  THR*     3.1    39.8    +      -       -      +
    355B  LEU*     1.3    78.1    -      -       -      +
    357B  ARG*     1.3    86.1    +      -       -      +
    375B  LEU*     3.8    17.5    -      -       +      -
    376B  VAL      3.2    10.3    -      -       -      +
    377B  GLN*     3.7    17.3    -      -       +      +
    601B  HEM      5.4     0.4    +      -       -      -
    602B  HC9      3.3    37.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 357 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71B  LEU*     4.4    22.2    -      -       +      +
     72B  PHE*     3.9    23.6    -      -       +      -
     75B  GLU*     2.8    27.9    +      -       +      +
     79B  PRO*     3.6    20.1    -      -       -      +
     80B  GLU      3.3    13.0    -      -       -      +
     81B  ARG*     4.0     6.2    -      -       -      +
    355B  LEU*     5.3     0.8    -      -       -      +
    356B  GLN*     1.3    94.3    +      -       -      +
    358B  TYR*     1.3    65.3    +      -       -      +
    359B  LEU*     3.7     0.6    +      -       +      -
    374B  THR      3.7     0.7    -      -       -      +
    375B  LEU*     3.9     4.7    -      -       -      -
    376B  VAL*     2.9    34.4    +      -       -      +
    418B  TRP      3.2    20.2    +      -       -      -
    421B  ARG*     4.0    14.8    +      -       -      +
    601B  HEM      2.8    43.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 358 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57B  VAL*     5.0     3.8    -      -       +      +
     80B  GLU*     3.0    44.1    +      -       +      +
     81B  ARG      3.4    21.1    -      -       -      -
     82B  PHE*     3.7    23.1    -      -       -      -
     83B  LEU*     5.1     1.4    +      -       +      -
    357B  ARG*     1.3    75.9    -      -       -      +
    359B  LEU*     1.3    67.6    +      -       -      +
    360B  VAL*     3.5     9.0    +      -       -      +
    373B  LYS*     3.5    24.9    -      -       +      +
    374B  THR      3.5     1.8    -      -       -      -
    375B  LEU*     3.8    35.2    -      -       +      +
----------------------------------------------------------
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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