Contacts of the strand formed by residues 152 - 166 (chain B) in PDB entry 2IDW


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 152 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ILE      3.5     5.8    +      -       -      +
     51A  GLY*     3.6     7.1    -      -       -      -
    147B  ILE      4.1     0.2    -      -       -      +
    148B  GLY*     3.3     0.3    -      -       -      -
    149B  GLY      2.9    30.5    +      -       -      -
    150B  ILE      3.6     0.4    +      -       -      -
    151B  GLY*     1.3    77.5    -      -       -      +
    153B  PHE*     1.3    70.7    +      -       -      -
    602B  ACY      4.3     8.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 153 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  GLY*     4.2     3.0    -      -       -      +
    146B  MET*     3.8    31.9    -      -       +      -
    147B  ILE*     3.3    13.2    -      -       -      -
    148B  GLY*     3.4    28.9    -      -       -      -
    152B  GLY*     1.3    79.2    -      -       -      -
    154B  ILE*     1.3    66.6    +      -       -      +
    602B  ACY      4.2    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 154 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ILE*     3.8    16.2    -      -       +      -
     51A  GLY*     3.7    23.3    -      -       -      +
    132B  VAL*     4.8     3.4    -      -       +      -
    146B  MET*     3.2     8.9    -      -       -      +
    147B  ILE*     2.9    49.2    +      -       +      +
    153B  PHE*     1.3    80.2    -      -       -      +
    155B  LYS*     1.3    64.0    +      -       -      +
    156B  VAL*     3.8    20.2    -      -       +      -
    178B  GLY      4.7     0.7    -      -       -      -
    179B  PRO*     4.0    43.1    -      -       +      +
    180B  THR*     4.3     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 155 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144B  PRO*     6.3     3.1    -      -       -      -
    145B  LYS      3.5     6.7    -      -       -      +
    146B  MET*     4.2    17.5    -      -       +      -
    154B  ILE*     1.3    73.7    -      -       -      +
    156B  VAL*     1.3    60.9    +      -       -      +
    178B  GLY*     4.2     0.3    -      -       -      -
    179B  PRO*     3.4    26.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 156 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132B  VAL*     4.6     3.6    -      -       +      -
    142B  TRP*     5.2     0.2    -      -       -      -
    144B  PRO*     3.7     4.2    -      -       -      +
    145B  LYS*     2.9    55.5    +      -       +      +
    146B  MET      4.4     2.5    -      -       -      +
    147B  ILE*     3.9    16.4    -      -       +      -
    154B  ILE*     3.8    22.7    -      -       +      -
    155B  LYS*     1.3    79.7    -      -       -      +
    157B  ARG*     1.3    62.1    +      -       -      +
    176B  LEU*     4.0    36.3    -      -       +      -
    177B  VAL      3.3    14.8    -      -       -      +
    178B  GLY*     4.1     5.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 157 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135B  GLU*     3.1    21.7    +      -       -      +
    136B  MET      2.8    29.1    +      -       -      -
    137B  SER*     4.7     1.6    -      -       -      +
    138B  LEU*     4.4     3.4    -      -       -      +
    142B  TRP*     3.4    49.1    -      -       +      +
    143B  LYS      3.8     4.3    -      -       -      -
    156B  VAL*     1.3    75.2    -      -       -      +
    158B  GLN*     1.3    59.6    +      -       -      +
    159B  TYR*     2.8    43.0    +      -       +      -
    175B  VAL      3.5     1.7    -      -       -      +
    176B  LEU*     3.4     2.4    -      -       -      -
    177B  VAL*     2.9    44.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 158 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142B  TRP*     3.2     4.7    -      -       -      -
    143B  LYS*     2.8    69.2    +      -       +      +
    145B  LYS*     3.2    28.5    -      -       +      +
    156B  VAL      3.9     0.8    +      -       -      -
    157B  ARG*     1.3    70.0    -      -       -      +
    159B  TYR*     1.3    61.3    +      -       -      +
    160B  ASP*     2.9    27.7    +      -       -      +
    174B  THR*     3.7    13.0    +      -       +      +
    175B  VAL      3.8     2.7    -      -       -      -
    176B  LEU*     3.6    23.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 159 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138B  LEU*     3.5    30.0    +      -       +      -
    139B  PRO      4.5     0.4    -      -       -      -
    140B  GLY*     3.3    28.7    -      -       -      -
    141B  ARG      3.5    15.9    -      -       -      +
    142B  TRP*     3.5    16.2    -      +       +      -
    157B  ARG*     2.8    67.4    +      -       +      -
    158B  GLN*     1.3    74.4    -      -       -      +
    160B  ASP*     1.3    63.2    +      -       -      +
    162B  ILE*     3.5    25.6    -      -       +      +
    174B  THR*     3.3     2.6    -      -       -      +
    175B  VAL      2.9    36.6    +      -       -      +
    177B  VAL*     3.8    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 160 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141B  ARG      4.5     5.4    +      -       -      +
    143B  LYS*     3.6    23.2    +      -       -      -
    158B  GLN*     2.9    28.7    +      -       -      +
    159B  TYR*     1.3    74.8    -      -       -      +
    161B  GLN*     1.3    76.7    +      -       +      +
    162B  ILE*     3.3     8.0    +      -       -      +
    174B  THR*     3.1    19.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 161 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160B  ASP*     1.3    81.6    -      -       +      +
    162B  ILE*     1.3    62.6    +      -       -      +
    163B  ILE*     3.9     2.9    +      -       -      +
    172B  ILE*     3.7    23.7    -      -       +      +
    173B  GLY*     3.4    15.4    +      -       -      +
    174B  THR*     4.7     0.8    +      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
    115B  ILE*     4.0    21.8    -      -       +      -
    116B  GLY      5.4     1.8    -      -       -      +
    138B  LEU*     4.6     7.9    -      -       +      -
    139B  PRO      3.7    23.3    -      -       -      +
    140B  GLY*     5.0     3.6    -      -       -      -
    159B  TYR*     3.5    42.2    -      -       +      +
    160B  ASP      3.8     6.5    -      -       -      +
    161B  GLN*     1.3    77.3    -      -       -      +
    163B  ILE*     1.3    77.0    +      -       -      +
    164B  ILE*     3.5     5.8    +      -       +      +
    172B  ILE*     3.2     4.4    -      -       -      -
    173B  GLY      2.9    29.8    +      -       -      +
    175B  VAL*     4.1    15.0    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
    114B  LYS      4.1     4.5    -      -       -      +
    115B  ILE*     4.3     6.9    -      -       -      -
    116B  GLY      4.5     2.9    +      -       -      -
    161B  GLN      3.9     2.4    +      -       -      +
    162B  ILE*     1.3    82.0    -      -       -      +
    164B  ILE*     1.3    62.6    +      -       -      +
    165B  GLU*     4.1    11.4    -      -       -      +
    170B  LYS*     3.7    32.5    -      -       +      +
    171B  ALA      3.6     6.3    -      -       -      +
    172B  ILE*     4.0    24.2    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
    113B  ILE*     4.0    24.0    -      -       +      -
    114B  LYS      3.3    11.7    -      -       -      +
    115B  ILE*     4.4    18.6    -      -       +      -
    131B  THR*     4.9     2.2    -      -       +      -
    133B  ILE*     5.2     1.3    -      -       +      -
    162B  ILE*     3.9     9.9    -      -       +      +
    163B  ILE*     1.3    78.8    -      -       -      +
    165B  GLU*     1.3    71.8    +      -       -      +
    166B  ILE*     4.0     7.0    +      -       +      +
    169B  HIS      3.8     0.3    -      -       -      +
    170B  LYS*     3.8     0.7    -      -       -      -
    171B  ALA*     2.9    45.3    +      -       +      +
    175B  VAL*     4.7     6.5    -      -       +      -
    185B  ILE*     4.2    12.3    -      -       +      -
    189B  LEU*     3.7    35.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 165 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113B  ILE*     3.0    10.9    -      -       -      +
    114B  LYS*     2.7    64.9    +      -       +      +
    163B  ILE*     4.1    10.4    -      -       -      +
    164B  ILE*     1.3    75.6    -      -       -      +
    166B  ILE*     1.3    59.7    +      -       -      +
    167B  ALA      4.1     0.4    -      -       -      -
    168B  GLY*     4.7     7.4    -      -       -      +
    169B  HIS      3.4    12.8    -      -       -      +
    170B  LYS*     3.9    27.1    -      -       +      -
    606B  ACY      2.4    34.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 166 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  PHE*     4.6     1.9    -      -       +      -
    111B  VAL*     4.1     9.2    -      -       +      -
    112B  THR      4.1     1.6    -      -       -      -
    113B  ILE*     4.2     8.5    -      -       +      -
    124B  LEU*     4.0    22.9    -      -       +      -
    164B  ILE*     4.0    12.8    -      -       +      +
    165B  GLU*     1.3    76.5    -      -       -      +
    167B  ALA*     1.3    73.2    +      -       +      +
    169B  HIS*     2.8    29.7    +      -       -      +
    171B  ALA*     4.1    17.5    -      -       +      -
    185B  ILE*     3.9    23.3    -      -       +      -
    189B  LEU*     3.9    24.2    -      -       +      +
    193B  ILE*     3.9    28.7    -      -       +      -
----------------------------------------------------------
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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