Contacts of the strand formed by residues 150 - 158 (chain D) in PDB entry 6B0Z


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 150 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156B  TYR*     3.6    12.3    -      -       -      -
    157B  THR      3.2    13.5    -      -       -      -
    159B  SER*     3.2    11.5    +      -       -      -
    148D  GLY      3.4     1.8    +      -       -      -
    149D  PRO*     1.3    74.1    -      -       -      +
    151D  LYS*     1.3    59.0    +      -       -      -
    171D  ASN*     3.6     5.5    -      -       -      +
    172D  PHE*     2.8    39.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 151 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155B  THR      3.5     1.0    -      -       -      +
    156B  TYR*     3.2     4.9    -      -       -      -
    157B  THR*     2.8    48.8    +      -       +      +
    150D  GLY*     1.3    73.2    -      -       -      -
    152D  VAL*     1.3    63.6    +      -       -      +
    153D  GLU*     3.5    34.2    +      -       +      +
    168D  LEU*     3.6    24.7    -      -       +      +
    170D  HIS      3.9     2.5    -      -       -      -
    171D  ASN*     2.8    33.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 152 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154B  ILE*     3.9    23.6    -      -       +      -
    155B  THR      3.2    10.3    -      -       -      +
    156B  TYR*     4.3    11.0    -      -       +      -
    144D  PHE*     4.4     2.2    -      -       +      -
    146D  VAL*     4.0    15.9    -      -       +      -
    151D  LYS*     1.3    75.3    -      -       -      +
    153D  GLU*     1.3    57.9    +      -       -      +
    168D  LEU*     3.6     4.9    -      -       -      +
    169D  VAL*     2.8    49.0    +      -       +      -
    170D  HIS      2.9    18.2    +      -       -      +
    172D  PHE*     3.5    27.8    -      -       +      -
    179D  ALA*     4.0    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 153 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154B  ILE*     3.2     7.0    -      -       -      +
    155B  THR*     2.8    48.3    +      -       -      +
    157B  THR*     4.8     7.3    +      -       -      -
    164B  LYS*     5.1     4.2    +      -       -      -
    151D  LYS*     3.5    31.0    -      -       +      +
    152D  VAL*     1.3    78.4    -      -       -      +
    154D  ILE*     1.3    60.3    +      -       -      +
    155D  THR*     4.3     3.1    +      -       -      +
    166D  THR*     3.6    26.1    -      -       +      +
    167D  TYR      3.2    13.0    -      -       -      +
    168D  LEU*     4.2     8.6    -      -       -      +
    169D  VAL*     4.1     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 154 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142B  THR*     4.7     4.3    -      -       +      -
    144B  PHE*     3.8    29.4    -      -       +      -
    152B  VAL*     4.0    14.6    -      -       +      -
    153B  GLU      3.2    15.5    -      -       -      +
    154B  ILE*     4.6     5.2    -      -       +      -
    169B  VAL*     4.6     9.2    -      -       +      -
    179B  ALA*     4.8     0.2    -      -       +      -
    180B  MET*     3.6    32.8    -      -       -      +
    181B  GLY*     4.0     4.0    -      -       -      +
    153D  GLU*     1.3    74.3    -      -       -      +
    155D  THR*     1.3    59.6    +      -       -      +
    167D  TYR*     2.7    64.2    +      -       +      +
    169D  VAL*     3.7    18.6    -      -       +      +
    181D  GLY*     4.8     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 155 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144B  PHE*     5.3     1.1    -      -       -      -
    151B  LYS      3.5     1.9    -      -       -      +
    152B  VAL*     3.3     5.8    -      -       -      +
    153B  GLU*     2.8    47.4    +      -       -      +
    155B  THR*     5.5     7.3    +      -       -      +
    153D  GLU*     4.9     3.1    -      -       -      +
    154D  ILE*     1.3    78.2    +      -       -      +
    156D  TYR*     1.3    62.0    +      -       -      +
    157D  THR*     3.7     9.9    -      -       -      +
    164D  LYS*     3.5    34.9    +      -       +      +
    165D  VAL      3.2     9.4    -      -       -      +
    166D  THR*     3.0    23.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 156 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144B  PHE*     4.2    23.5    -      +       +      -
    145B  VAL      5.4     1.3    -      -       -      -
    146B  VAL*     3.5    19.5    -      -       +      -
    147B  PRO*     3.5    28.9    -      -       +      +
    148B  GLY*     2.9    29.8    +      -       -      -
    149B  PRO      3.3     9.4    +      -       -      -
    150B  GLY*     4.1    17.7    -      -       -      -
    151B  LYS      3.4     4.0    -      -       -      -
    152B  VAL*     3.8    18.4    -      -       +      +
    155D  THR*     1.3    72.3    -      -       -      +
    157D  THR*     1.3    64.0    +      -       -      +
    158D  PRO*     3.7    27.8    -      -       +      +
    163D  GLN      4.4     5.8    -      -       -      -
    164D  LYS*     3.4     5.9    -      -       -      +
    165D  VAL*     2.7    48.5    +      -       +      +
    167D  TYR*     5.1     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 157 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150B  GLY*     3.2     0.6    -      -       -      -
    151B  LYS*     2.8    42.8    +      -       -      +
    153B  GLU*     4.8     7.3    +      -       -      -
    155D  THR*     3.7     5.7    -      -       -      +
    156D  TYR*     1.3    76.1    -      -       -      +
    158D  PRO*     1.3    74.7    -      -       +      +
    159D  SER*     4.6     0.2    -      -       -      -
    161D  GLY*     5.6     4.5    -      -       -      -
    164D  LYS*     3.6    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 158 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147B  PRO*     6.2     0.2    -      -       +      -
    149B  PRO      3.4     8.3    -      -       -      +
    150B  GLY*     3.9     0.2    -      -       -      -
    156D  TYR*     3.7    28.0    -      -       +      +
    157D  THR*     1.3    95.3    -      -       +      +
    159D  SER*     1.3    65.9    +      -       -      +
    160D  ASP*     3.3    18.8    -      -       -      +
    161D  GLY*     3.1    14.6    +      -       -      -
    162D  THR*     3.9     5.2    -      -       -      +
    163D  GLN*     3.1    46.9    -      -       +      +
    164D  LYS*     4.1     1.1    -      -       -      -
----------------------------------------------------------
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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