Contacts of the strand formed by residues 159 - 164 (chain B) in PDB entry 5JLH


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 THR 159 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152B  MET*     3.3    33.7    -      -       +      -
    153B  ASP      3.2     6.5    -      -       -      +
    154B  SER*     3.1    18.2    -      -       -      +
    158B  VAL*     1.3    80.2    -      -       -      +
    160B  HIS*     1.3    71.8    +      -       -      +
    161B  THR*     4.7     2.0    -      -       -      +
    176B  ARG*     3.5     0.3    -      -       -      -
    177B  LEU*     2.8    56.9    +      -       +      +
    179B  LEU*     3.1    20.4    +      -       -      +
    180B  ALA*     4.6     1.0    +      -       -      -
    260B  LEU*     5.6     2.6    -      -       -      +
    273B  ILE*     4.7     2.9    -      -       +      +
    276B  THR*     5.7     0.4    -      -       -      +
    302B  THR*     5.0     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 160 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  HIS      5.5     0.6    +      -       -      -
     73B  GLY*     5.8     1.3    -      -       -      -
    107B  ALA*     3.2    26.9    -      -       +      +
    108B  PRO*     3.6    43.2    +      -       +      -
    136B  GLN*     4.3     2.2    +      -       -      -
    137B  ALA*     5.9     0.7    -      -       +      -
    152B  MET*     3.7     2.4    -      -       -      +
    153B  ASP*     2.5    62.5    +      -       +      +
    158B  VAL*     3.0    51.2    +      -       +      +
    159B  THR*     1.3    76.3    -      -       -      +
    161B  THR*     1.3    66.9    +      -       -      +
    162B  VAL*     5.3     0.7    -      -       +      -
    175B  LEU      3.5     7.4    -      -       -      +
    176B  ARG*     3.8    19.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 161 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150B  ILE*     3.7    26.7    -      -       +      -
    151B  VAL      3.4     7.4    -      -       -      +
    152B  MET*     3.6    18.9    -      -       -      +
    159B  THR*     4.7     2.1    -      -       -      +
    160B  HIS*     1.3    83.1    +      -       -      +
    162B  VAL*     1.3    68.1    +      -       -      +
    163B  PRO*     3.8     0.7    -      -       -      +
    174B  ILE*     3.3     3.1    -      -       -      -
    175B  LEU*     2.8    44.2    +      -       -      +
    177B  LEU*     6.0     0.7    -      -       -      +
    276B  THR*     4.5     9.1    +      -       -      -
    277B  THR*     4.7     9.4    -      -       -      +
    280B  SER*     3.4    23.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 162 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108B  PRO*     3.9    27.8    -      -       +      -
    135B  ILE*     5.3     4.3    -      -       +      -
    137B  ALA*     3.9    20.6    -      -       +      -
    138B  VAL*     5.0     5.8    -      -       +      -
    149B  GLY      4.0     0.9    -      -       -      +
    150B  ILE*     3.7     1.9    -      -       -      -
    151B  VAL*     3.0    35.1    +      -       -      +
    161B  THR*     1.3    81.9    -      -       -      +
    163B  PRO*     1.3    74.7    -      -       -      +
    164B  ILE*     3.7    19.1    +      -       +      +
    169B  ALA*     5.3     3.6    -      -       +      -
    170B  LEU      5.5     0.2    -      -       -      +
    174B  ILE*     3.8    31.2    -      -       +      -
    374B  PHE*     5.9     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 163 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149B  GLY      3.7     4.7    -      -       -      +
    150B  ILE*     3.9    15.9    -      -       +      -
    161B  THR      3.8     6.5    -      -       -      +
    162B  VAL*     1.3    95.4    -      -       +      +
    164B  ILE*     1.3    60.5    +      -       -      +
    169B  ALA      4.3     0.2    -      -       -      -
    170B  LEU*     3.8    25.4    +      -       +      +
    173B  ALA*     3.4    41.7    -      -       +      +
    174B  ILE*     4.1     3.1    -      -       +      +
    280B  SER*     4.6     4.7    -      -       -      -
    284B  CYS*     3.9    20.4    -      -       -      -
    292B  LEU*     4.0    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 164 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  VAL      4.5     2.0    -      -       -      +
     43A  MET*     4.4     3.1    -      -       -      -
    138B  VAL*     3.9    25.8    -      -       +      -
    141B  LEU*     3.2    34.5    -      -       +      -
    147B  THR      3.7     8.3    -      -       -      +
    148B  THR*     3.3     3.6    -      -       -      +
    149B  GLY      2.8    39.2    +      -       -      +
    151B  VAL*     5.7     1.3    -      -       +      -
    162B  VAL*     4.2    11.7    -      -       +      +
    163B  PRO*     1.3    75.6    -      -       -      +
    165B  TYR*     1.3    61.4    +      -       -      +
    167B  GLY      3.2     9.2    -      -       -      +
    168B  TYR      3.1    27.6    -      -       -      +
    169B  ALA*     3.6    17.7    -      -       +      +
    170B  LEU*     6.0     0.7    -      -       -      -
    288B  ILE*     5.7     0.7    -      -       -      -
    292B  LEU*     3.7     5.3    -      -       -      +
----------------------------------------------------------
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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