Contacts of the strand formed by residues 174 - 180 (chain B) in PDB entry 5NJ8


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 GLY 174 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165B  LYS      5.0     0.5    -      -       -      +
    168B  ILE*     3.8    23.3    +      -       -      +
    169B  LEU*     3.9    17.9    +      -       -      +
    172B  ALA      3.3     1.8    -      -       -      -
    173B  ASP*     1.3    79.8    -      -       -      +
    175B  PHE*     1.3    60.7    +      -       -      +
    192B  SER*     3.9     9.0    -      -       -      -
    196B  VAL*     4.3     1.8    -      -       -      -
    340B  ILE*     4.6     4.9    -      -       -      -
    341B  GLY      3.2     9.0    -      -       -      -
    342B  ARG*     3.7    11.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 175 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174B  GLY*     1.3    73.4    -      -       -      -
    176B  LEU*     1.3    67.2    +      -       -      +
    177B  PHE*     3.6    23.6    -      +       +      -
    190B  SER*     3.9     0.4    -      -       -      +
    192B  SER*     3.7    31.6    -      -       -      +
    193B  VAL*     3.6    25.1    -      -       +      -
    196B  VAL*     3.9    23.3    -      -       +      -
    197B  LEU*     4.0    21.1    -      -       +      -
    204B  TRP*     4.3    14.1    -      +       -      -
    267B  MET*     3.9    28.5    -      -       +      -
    306B  VAL*     4.8     3.1    -      -       +      -
    340B  ILE*     3.1     6.1    -      -       -      -
    341B  GLY*     2.9    57.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 176 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  GLU*     3.5    29.4    -      -       +      -
    117A  PHE*     3.9    26.5    -      -       +      +
    118A  LEU*     3.7    20.1    -      -       +      +
    121A  ALA*     4.6     0.2    -      -       +      -
    175B  PHE*     1.3    79.3    -      -       -      +
    177B  PHE*     1.3    68.7    +      -       -      +
    178B  ILE*     3.6    24.0    -      -       +      -
    188B  TYR*     4.1     7.4    -      -       +      -
    189B  VAL*     3.5     2.3    -      -       -      -
    190B  SER*     3.2    34.6    +      -       -      +
    338B  VAL*     4.3     5.2    -      -       +      -
    339B  ALA      3.3    20.4    -      -       -      +
    340B  ILE*     3.5    16.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 177 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175B  PHE*     3.6    26.5    -      +       +      -
    176B  LEU*     1.3    77.9    -      -       -      +
    178B  ILE*     1.3    64.2    +      -       -      +
    179B  VAL*     3.7    24.2    -      -       +      -
    188B  TYR      3.1    13.2    -      -       -      +
    189B  VAL*     3.8    13.0    -      -       +      -
    204B  TRP*     4.6     8.5    -      +       +      -
    209B  LEU*     4.1    24.7    -      -       +      -
    263B  PHE*     5.5     2.9    -      +       -      -
    267B  MET*     4.6     6.1    -      -       +      -
    308B  CYS*     4.1    20.2    -      -       +      -
    337B  LEU*     3.7     5.6    -      -       +      +
    339B  ALA*     2.7    58.9    +      -       +      +
    340B  ILE      3.9     2.2    -      -       -      -
    341B  GLY*     3.7    25.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 178 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  LEU*     5.6     0.9    -      -       +      -
    117A  PHE*     3.8    17.5    -      -       +      -
    176B  LEU*     3.6    29.4    -      -       +      -
    177B  PHE*     1.3    77.7    -      -       -      +
    179B  VAL*     1.3    58.9    +      -       -      +
    186B  VAL*     4.0     0.2    -      -       -      -
    187B  VAL*     2.6    46.5    +      -       +      -
    188B  TYR*     2.9    34.6    +      -       +      +
    315B  TRP*     3.7    30.1    -      -       +      +
    336B  CYS*     3.9    11.0    -      -       +      -
    337B  LEU      3.3     3.6    -      -       -      +
    338B  VAL*     3.6    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 179 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177B  PHE*     3.7    23.6    -      -       +      -
    178B  ILE*     1.3    80.8    -      -       -      +
    180B  SER*     1.3    66.1    +      -       -      +
    184B  GLY*     6.3     0.2    -      -       -      -
    185B  ARG      3.3     9.9    -      -       -      +
    186B  VAL*     3.9    19.3    -      -       +      -
    187B  VAL*     3.9     4.7    -      -       -      +
    204B  TRP*     5.6     0.2    -      -       +      -
    209B  LEU*     3.8    38.4    -      -       +      -
    225B  LEU*     5.4     6.3    -      -       +      -
    336B  CYS*     3.1     4.9    -      -       -      +
    337B  LEU*     2.8    48.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 180 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179B  VAL*     1.3    74.7    -      -       -      +
    181B  CYS*     1.3    60.7    +      -       -      +
    182B  GLU      2.9    10.5    +      -       -      -
    183B  THR*     3.1    26.0    -      -       -      +
    184B  GLY*     4.8     1.0    -      -       -      -
    185B  ARG*     2.6    43.6    +      -       -      -
    187B  VAL*     3.8     3.2    -      -       -      +
    225B  LEU*     4.0     7.8    -      -       -      +
    334B  LYS*     5.5     4.5    -      -       -      +
    335B  PHE      4.0     2.4    +      -       -      -
    336B  CYS*     3.7    17.5    -      -       -      -
----------------------------------------------------------
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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