Contacts of the strand formed by residues 152 - 161 (chain A) in PDB entry 4U7B


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 ILE 152 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148A  PHE*     3.4     7.3    +      -       +      +
    149A  LEU*     3.0    36.5    +      -       +      +
    150A  HIS      4.4     1.4    -      -       -      +
    151A  ARG*     1.3    81.4    -      -       -      +
    153A  VAL*     1.3    66.5    +      -       -      +
    154A  THR*     4.6     2.5    -      -       -      +
    198A  ASP*     3.2    19.2    -      -       -      +
    237A  TYR*     4.7     0.2    +      -       -      -
    245A  ILE*     3.9    24.8    -      -       +      +
    247A  LEU*     3.6    41.5    -      -       +      +
    271A  LEU*     4.4     9.0    -      -       +      -
    282A  PRO*     6.1     0.2    -      -       +      -
    326A  ILE*     3.6    36.1    -      -       +      -
    329A  LEU*     4.8     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 153 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  ARG      3.9     4.0    -      -       -      +
    152A  ILE*     1.3    76.9    -      -       -      +
    154A  THR*     1.3    63.0    +      -       -      +
    196A  TRP*     4.7     7.2    -      -       +      -
    197A  TRP      3.4    22.9    -      -       -      +
    198A  ASP*     4.2     5.4    -      -       +      +
    203A  ILE*     4.6     7.9    -      -       +      -
    226A  LEU*     5.2     3.6    -      -       +      -
    230A  LEU*     4.5    22.7    -      -       +      -
    237A  TYR*     4.8     4.5    -      -       +      +
    244A  VAL*     3.6    22.2    -      -       +      -
    245A  ILE      3.0    20.5    +      -       -      +
    246A  PHE*     3.2    27.4    -      -       +      -
    247A  LEU      3.4     8.2    +      -       -      -
    268A  TRP*     6.2     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 154 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  ILE*     4.2     4.3    -      -       -      +
    153A  VAL*     1.3    76.0    -      -       -      +
    155A  GLY*     1.3    59.2    +      -       -      +
    196A  TRP*     3.2    11.3    -      -       -      +
    197A  TRP*     3.1    55.0    +      -       +      +
    246A  PHE*     5.0     0.4    -      -       -      -
    247A  LEU*     2.7    44.5    +      -       -      +
    281A  ALA*     5.5     0.9    -      -       -      +
    282A  PRO*     4.0    15.0    -      -       +      +
    283A  SER*     3.2    20.2    +      -       -      +
    326A  ILE*     4.5     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154A  THR*     1.3    83.9    +      -       -      +
    156A  ASP*     1.3    62.8    +      -       -      +
    157A  GLU*     5.1     0.3    -      -       -      +
    195A  VAL      3.2    16.2    -      -       -      -
    196A  TRP*     3.4    17.6    +      -       -      -
    197A  TRP*     4.8     0.4    -      -       -      -
    219A  TYR*     5.2     0.7    +      -       -      -
    247A  LEU      3.3     3.4    +      -       -      +
    248A  HIS*     3.9    23.4    -      -       -      +
    249A  ALA      4.5     1.0    +      -       -      -
    254A  HIS*     5.5     0.9    -      -       -      -
    283A  SER*     3.4     7.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  GLY*     1.3    74.9    -      -       -      +
    157A  GLU*     1.3   101.3    +      -       -      +
    194A  CYS*     3.8     1.2    -      -       -      +
    195A  VAL*     3.2    28.6    +      -       -      +
    196A  TRP*     5.3     2.7    -      -       -      -
    249A  ALA*     3.6    27.5    +      -       -      +
    281A  ALA*     5.2     6.9    -      -       -      +
    283A  SER*     3.6    23.7    +      -       -      -
    284A  ASP*     4.1    18.7    -      -       -      +
    288A  PHE*     3.9     9.2    -      -       +      -
     57F    T      4.2    12.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  GLY      5.1     0.2    -      -       -      +
    156A  ASP*     1.3   103.6    +      -       -      +
    158A  LYS*     1.3    63.7    +      -       -      +
    192A  MET*     3.7    24.9    -      -       +      -
    193A  LEU      3.1    13.0    -      -       -      +
    194A  CYS*     3.5    26.2    -      -       -      +
    196A  TRP*     5.2     1.7    -      -       -      -
    214A  VAL*     3.8    13.7    -      -       -      +
    219A  TYR*     4.4    10.1    -      -       -      -
    254A  HIS*     3.1    37.3    +      -       -      -
    284A  ASP*     5.2     0.7    -      -       -      +
    288A  PHE*     4.0     4.8    -      -       -      -
     56F    A      4.6     3.1    +      -       -      -
     57F    T      4.6     6.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157A  GLU*     1.3    76.0    -      -       -      +
    159A  TRP*     1.3    83.2    +      -       -      +
    160A  ILE*     4.0     1.8    -      -       +      +
    192A  MET*     4.5     4.4    -      -       -      +
    193A  LEU*     2.9    39.6    +      -       +      +
    288A  PHE*     3.4    47.1    -      -       +      -
    291A  MET*     4.1    13.5    -      -       +      -
    295A  LEU*     3.8    29.1    -      -       -      +
     55F    G      4.3    13.1    +      -       -      -
     56F    A      2.6    41.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158A  LYS*     1.3   102.9    +      -       -      +
    160A  ILE*     1.3    58.0    +      -       -      +
    161A  PHE*     4.0    23.0    +      +       +      -
    190A  LYS*     3.3    48.4    -      -       +      +
    191A  THR      3.9     2.5    -      -       -      -
    192A  MET*     3.6    49.4    -      -       +      +
    211A  GLY*     5.2     8.7    -      -       -      -
    212A  GLU      4.1    17.7    -      -       -      -
    213A  THR*     5.5     5.6    -      -       -      -
     56F    A      5.1     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158A  LYS*     4.0    11.4    -      -       -      +
    159A  TRP*     1.3    77.2    -      -       -      +
    161A  PHE*     1.3    71.5    -      -       -      +
    162A  PHE*     3.6     2.1    +      -       -      -
    164A  ASN*     5.3     1.6    -      -       -      +
    190A  LYS*     3.7     1.1    -      -       -      -
    191A  THR*     3.0    38.1    +      -       -      +
    193A  LEU*     3.9    19.7    -      -       +      -
    207A  LEU*     4.4     5.6    -      -       +      -
    291A  MET*     3.8    24.5    -      -       +      -
    295A  LEU*     4.1    16.2    -      -       +      -
    300A  PHE*     4.1    19.7    -      -       +      -
    306A  VAL*     4.2     8.7    -      -       +      +
    310A  LEU*     3.8    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 161 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  TRP*     4.3    23.6    -      +       +      -
    160A  ILE*     1.3    83.7    -      -       -      +
    162A  PHE*     1.3    63.0    +      -       -      +
    163A  VAL*     3.3    23.1    -      -       +      +
    164A  ASN*     3.6    23.3    +      -       -      +
    184A  PRO*     6.0     5.4    -      -       +      -
    185A  ASN      4.3    11.0    -      -       -      -
    186A  ARG*     3.7    35.0    -      -       -      -
    188A  GLY      5.2     2.5    -      -       -      -
    189A  LYS      3.8    11.2    -      -       -      -
    190A  LYS*     4.2    23.6    -      -       +      -
    300A  PHE*     3.9     3.6    -      -       -      -
----------------------------------------------------------
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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