Contacts of the strand formed by residues 156 - 163 (chain B) in PDB entry 1P57


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 GLN 156 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  ILE*     3.8    23.8    -      -       +      +
     19B  GLY*     3.8     5.7    +      -       -      +
     20B  ARG*     3.2    24.3    +      -       -      +
     21B  ASP*     2.9    27.1    +      -       -      +
     22B  THR*     4.7     1.1    -      -       -      -
    139B  THR*     3.1     8.5    -      -       -      -
    140B  GLY      3.0    36.8    +      -       -      +
    144B  THR*     4.3    15.5    -      -       +      +
    152B  ALA*     3.6    23.4    -      -       +      +
    154B  VAL*     2.9    20.0    +      -       -      +
    155B  LEU*     1.3    78.9    +      -       -      +
    157B  GLU*     1.3    60.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 157 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  ILE*     4.5     1.1    -      -       -      -
     19B  GLY*     3.2     3.2    -      -       -      -
     20B  ARG*     3.0    43.0    +      -       +      +
     21B  ASP      5.0     1.1    -      -       -      +
     22B  THR*     2.6    30.8    +      -       -      -
     26B  ARG*     2.9    33.5    +      -       -      -
     27B  TRP*     3.0    15.3    +      -       -      +
    137B  THR*     4.2     6.4    +      -       +      +
    138B  VAL      3.4     5.8    -      -       -      -
    139B  THR*     3.7    17.0    -      -       +      -
    156B  GLN*     1.3    75.3    -      -       -      +
    158B  ALA*     1.3    60.0    +      -       -      +
    159B  ARG*     5.5     6.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 158 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  ILE*     3.7    20.0    -      -       +      -
     18B  GLY      5.2     0.2    -      -       -      -
     19B  GLY*     4.1     6.5    -      -       -      -
    137B  THR*     3.2     4.7    -      -       -      +
    138B  VAL*     2.9    43.1    +      -       +      +
    157B  GLU*     1.3    75.7    -      -       -      +
    159B  ARG*     1.3    63.8    +      -       -      +
    186B  ILE*     3.5    27.6    -      -       -      +
    189B  ASP      5.3     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 159 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135B  ILE*     3.6    34.7    -      -       +      +
    136B  CYS      3.1     7.0    -      -       -      +
    137B  THR*     3.7    21.5    -      -       +      +
    157B  GLU*     5.5     6.1    -      -       -      +
    158B  ALA*     1.3    75.5    -      -       -      +
    160B  VAL*     1.3    67.3    +      -       -      +
    184B  TYR*     3.0    22.5    +      -       -      +
    186B  ILE*     4.1     6.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 160 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134B  LYS      3.9     0.2    -      -       -      +
    135B  ILE*     4.1     3.8    -      -       -      +
    136B  CYS*     2.9    28.7    +      -       -      +
    138B  VAL*     4.1    22.0    -      -       +      -
    159B  ARG*     1.3    81.8    -      -       -      +
    161B  PRO*     1.3    69.0    -      -       +      +
    183B  ALA*     4.2     7.0    -      -       +      -
    184B  TYR*     3.8    28.0    -      -       +      +
    186B  ILE*     3.8    28.7    -      -       +      +
    189B  ASP*     4.9     2.2    -      -       -      +
    199B  PHE*     3.7    26.4    -      -       +      -
    228B  TYR*     4.7     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 161 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133B  GLY*     3.7    20.6    -      -       -      +
    134B  LYS      3.2     7.2    -      -       -      +
    135B  ILE*     3.9    11.2    -      -       +      -
    160B  VAL*     1.3    84.8    -      -       -      +
    162B  ILE*     1.3    68.3    -      -       -      +
    163B  ILE*     5.4     1.3    -      -       +      -
    183B  ALA*     3.0     5.6    -      -       -      -
    184B  GLY*     2.9    80.9    +      -       +      +
    185B  PRO*     6.2     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 162 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130B  LEU*     4.0    36.6    -      -       +      -
    131B  VAL      3.5    26.0    -      -       -      +
    132B  ASP*     3.8    21.9    -      -       -      +
    133B  GLY*     2.9    22.8    +      -       -      +
    134B  LYS*     3.0    17.0    +      -       +      +
    136B  CYS*     4.2    17.9    -      -       -      -
    161B  PRO*     1.3    77.1    -      -       -      +
    163B  ILE*     1.3    67.4    +      -       -      +
    181B  PHE*     4.3    11.9    -      -       +      -
    182B  CYS      3.7     8.1    -      -       -      +
    183B  ALA*     4.2     0.9    -      -       -      +
    199B  PHE*     3.9    21.5    -      -       +      -
    201B  CYS*     4.4     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 163 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132B  ASP*     3.9     7.5    -      -       -      +
    161B  PRO*     3.8     3.8    -      -       +      +
    162B  ILE*     1.3    82.2    -      -       -      +
    164B  SER*     1.3    77.4    +      -       -      +
    165B  ASN*     3.7     5.5    +      -       -      +
    167B  VAL*     3.7    25.1    -      -       +      -
    168B  CYS*     4.1    11.2    -      -       +      +
    173B  PHE*     4.8     8.1    -      -       +      -
    181B  PHE*     5.1     1.0    -      -       -      +
    182B  CYS*     2.9    23.6    +      -       +      +
    183B  ALA      4.1     0.4    -      -       -      -
    184B  GLY      3.3    43.5    -      -       -      +
    185B  PRO*     5.0     4.5    -      -       +      -
    225B  PRO*     3.7    25.4    -      -       +      -
----------------------------------------------------------
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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