Contacts of the strand formed by residues 152 - 159 (chain A) in PDB entry 3K5M


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 TRP 152 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  LEU*     4.0    20.5    +      -       -      +
    151A  LYS*     1.3    82.4    -      -       -      +
    153A  VAL*     1.3    63.6    -      -       -      +
    154A  SER      4.2     0.7    -      -       -      +
    171A  GLU      5.5     0.2    -      -       -      +
    172A  GLY*     3.2     5.9    -      -       -      -
    173A  CYS*     3.1    32.0    +      -       -      +
    217A  PRO*     4.2     0.9    -      -       -      -
    219A  VAL*     3.3    25.9    -      -       +      +
    221A  ILE*     3.9    24.0    -      -       +      -
    340A  THR*     4.0     9.6    -      -       -      -
    343A  PHE*     3.7    26.9    -      +       +      -
    344A  HIS*     3.0    52.3    -      +       -      -
    349A  MET*     3.7    33.2    -      -       +      +
    350A  PRO*     5.9     1.3    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
    152A  TRP*     1.3    74.7    -      -       -      +
    154A  SER*     1.3    64.0    +      -       -      +
    155A  ILE*     3.8     2.9    +      -       +      -
    170A  LEU*     4.2    15.9    -      -       +      -
    171A  GLU      3.1    19.1    -      -       -      +
    211A  TRP*     3.5    32.5    -      -       +      -
    212A  PHE*     4.0    20.0    -      -       +      -
    217A  PRO*     3.8    21.5    -      -       +      -
    219A  VAL      2.8    12.3    +      -       -      +
    220A  ILE*     4.0    10.7    -      -       +      +
    221A  ILE*     2.8    29.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 154 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  TRP*     4.2     0.6    -      -       -      +
    153A  VAL*     1.3    71.8    -      -       -      +
    155A  ILE*     1.3    61.5    +      -       -      +
    170A  LEU*     3.6     1.2    -      -       -      -
    171A  GLU*     2.6    46.7    +      -       -      -
    221A  ILE*     3.4    21.6    +      -       -      +
    222A  GLY*     4.8     0.7    -      -       -      -
    336A  CYS*     2.7    42.0    +      -       -      -
    339A  VAL*     3.5    15.8    -      -       -      +
    340A  THR*     4.5     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  VAL*     4.6     5.8    -      -       +      +
    154A  SER*     1.3    76.9    +      -       -      +
    156A  ASP*     1.3    72.7    +      -       -      +
    157A  ILE*     4.8     2.9    -      -       +      -
    168A  ILE*     4.4     7.9    -      -       +      -
    169A  GLY      3.3    11.9    -      -       -      +
    170A  LEU*     3.8    16.6    -      -       +      -
    208A  LEU*     4.5     7.0    -      -       +      -
    212A  PHE*     5.5     4.9    -      -       +      -
    220A  ILE*     3.7    24.2    -      -       +      -
    221A  ILE      3.0    17.9    +      -       -      +
    222A  GLY*     4.2     9.5    -      -       -      -
    223A  TRP      5.1     0.7    +      -       -      -
    225A  VAL*     3.9    10.3    -      -       +      +
    229A  ASP*     4.2    12.9    -      -       +      +
    230A  LEU*     5.1     7.9    -      -       +      -
    233A  LEU*     3.9    27.8    -      -       +      -
    246A  LEU*     6.0     1.8    -      -       +      -
    336A  CYS*     4.3     0.2    -      -       -      -
----------------------------------------------------------
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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  ILE*     1.3    79.3    -      -       -      +
    157A  ILE*     1.3    66.3    +      -       -      +
    158A  GLU*     2.7    28.6    -      -       -      +
    168A  ILE      3.7     0.2    -      -       -      -
    169A  GLY      2.7    34.9    +      -       -      -
    223A  TRP*     5.4     7.3    +      -       -      +
    228A  PHE*     5.6     1.4    -      -       -      -
    229A  ASP*     3.7    11.0    -      -       -      +
    293A  LEU*     6.0     0.5    -      -       -      +
    332A  ASN*     3.0    15.5    -      -       -      +
    335A  ASN*     3.4    22.6    +      -       +      +
    336A  CYS*     3.6    19.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  ILE*     4.8     2.5    -      -       +      -
    156A  ASP*     1.3    81.8    -      -       -      +
    158A  GLU*     1.3    72.9    +      -       -      +
    159A  THR*     3.9    13.7    -      -       +      -
    165A  LEU*     4.0    12.3    -      -       +      -
    167A  CYS      3.4     7.4    -      -       -      +
    168A  ILE*     3.9    27.6    -      -       +      -
    228A  PHE*     3.5    21.6    -      -       +      -
    229A  ASP*     3.0    33.3    +      -       +      +
    232A  MET*     3.5    32.5    -      -       +      -
    233A  LEU*     4.3    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  ASP*     2.7    24.3    -      -       -      +
    157A  ILE*     1.3    78.1    -      -       -      +
    159A  THR*     1.3    68.4    +      -       -      +
    165A  LEU*     3.9     1.7    -      -       -      +
    166A  TYR*     2.9    30.6    +      -       +      +
    167A  CYS*     3.2    32.8    +      -       -      +
    228A  PHE*     5.7     0.4    -      -       -      -
    317A  ILE*     4.0    13.8    -      -       +      +
    328A  LEU*     4.5    13.0    -      -       +      -
    331A  TYR*     3.7    21.9    +      -       -      -
    332A  ASN*     3.6    14.3    -      -       +      +
    335A  ASN*     3.3    14.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157A  ILE*     3.9    27.1    -      -       +      -
    158A  GLU*     1.3    81.2    +      -       -      +
    160A  THR*     1.3    74.4    +      -       -      +
    163A  GLY*     3.6    24.7    -      -       -      +
    164A  GLU      3.2    13.5    -      -       -      +
    165A  LEU*     4.3     6.5    -      -       +      -
    166A  TYR*     3.5    16.4    -      -       -      -
    228A  PHE*     4.2    18.1    -      -       +      -
    232A  MET*     5.0     2.0    -      -       +      -
    314A  MET*     4.7     6.8    -      -       -      +
    317A  ILE*     4.5     6.6    -      -       -      +
----------------------------------------------------------
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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