Contacts of the strand formed by residues 146 - 151 (chain E) in PDB entry 3V56


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 CYS 146 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192D  TYR*     4.0    14.8    -      -       -      -
    250D  ILE*     3.9    17.0    -      -       +      -
    284D  LEU*     4.3    11.2    -      -       -      -
    144E  GLN      4.2     2.7    -      -       -      -
    145E  ASP*     1.3    75.7    -      -       -      +
    147E  LEU*     1.3    61.4    +      -       -      +
    172E  PHE*     4.1    12.1    -      -       -      +
    173E  LYS*     3.6     1.6    -      -       -      +
    174E  ARG*     2.8    65.0    +      -       -      +
    178E  LEU*     4.1     6.4    -      -       -      +
    281E  ALA      3.3    12.6    -      -       -      +
    282E  LEU*     4.1     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 147 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146E  CYS*     1.3    77.1    -      -       -      +
    148E  GLN*     1.3    62.9    +      -       -      +
    149E  LEU*     3.8    32.1    -      -       +      -
    170E  LEU*     3.8    19.7    -      -       +      -
    172E  PHE*     3.5     5.8    -      -       -      +
    173E  LYS*     4.0    10.5    -      -       +      -
    178E  LEU*     3.8    23.3    -      -       +      +
    179E  GLU*     3.6    36.8    -      -       -      +
    180E  GLU*     3.7     3.8    -      -       -      +
    185E  ILE*     3.8    22.2    -      -       +      -
    196E  TYR*     4.3     1.1    +      -       -      -
    280E  GLY*     3.2     2.9    -      -       -      -
    281E  ALA      3.0    31.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 148 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230D  PHE*     4.5    11.4    -      -       -      -
    249D  GLY*     3.9     1.7    -      -       -      -
    250D  ILE*     2.9    36.5    +      -       -      -
    147E  LEU*     1.3    74.3    -      -       -      +
    149E  LEU*     1.4    69.8    +      -       -      +
    150E  ILE*     4.3     9.6    -      -       +      +
    170E  LEU*     3.9     5.5    -      -       -      +
    171E  SER*     2.9    38.5    +      -       -      -
    172E  PHE*     3.0    37.1    +      -       +      +
    196E  TYR*     2.6    35.0    +      -       +      +
    278E  PHE*     4.9     5.2    -      -       +      -
    279E  PHE      3.6     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 149 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147E  LEU*     3.8    18.4    -      -       +      -
    148E  GLN*     1.4    73.5    -      -       -      +
    150E  ILE*     1.3    62.6    +      -       -      +
    168E  TRP*     3.8    40.6    -      -       +      -
    169E  LEU      3.4    13.5    -      -       -      +
    170E  LEU*     4.0    11.0    -      -       +      -
    180E  GLU*     3.8    27.4    -      -       +      -
    183E  ASN      5.1     0.7    -      -       -      +
    184E  LYS      4.9     8.5    -      -       -      -
    185E  ILE*     3.7    24.9    -      -       +      -
    278E  PHE*     3.3     6.8    -      -       -      +
    279E  PHE*     2.7    48.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 150 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148E  GLN*     4.3    10.1    +      -       -      +
    149E  LEU*     1.3    78.4    -      -       -      +
    151E  ALA*     1.3    65.8    +      -       -      +
    168E  TRP*     3.5     5.1    -      -       -      -
    169E  LEU*     2.9    52.7    +      -       +      +
    170E  LEU      5.5     0.4    -      -       -      +
    171E  SER*     4.0    28.7    -      -       -      +
    274E  GLY*     3.4    35.4    -      -       -      +
    277E  THR      3.8     3.8    -      -       -      -
    278E  PHE*     4.0     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 151 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150E  ILE*     1.3    77.4    -      -       -      +
    152E  ASP*     1.3    59.4    +      -       -      +
    153E  SER*     3.4     2.1    +      -       -      -
    166E  VAL*     3.9     7.4    -      -       +      -
    167E  PRO      3.6     6.5    -      -       -      -
    168E  TRP*     3.6     5.0    -      -       -      -
    169E  LEU*     4.6     2.9    -      -       -      +
    272E  LEU*     3.4    39.4    -      -       +      +
    273E  ASP      4.3     1.6    -      -       -      +
    274E  GLY*     4.1     8.2    +      -       -      -
    277E  THR*     3.0    37.2    +      -       +      +
----------------------------------------------------------
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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