Contacts of the strand formed by residues 173 - 182 (chain O) in PDB entry 3KYM


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 TYR 173 (chain O).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10O  THR*     5.4     0.2    -      -       -      +
    103O  LYS*     4.0    20.3    +      -       -      -
    105O  GLU*     2.9    39.2    +      -       -      +
    138O  ASN*     3.2     2.3    +      -       -      -
    139O  PHE*     2.7    58.1    +      -       +      +
    140O  TYR*     3.3    27.1    -      +       -      -
    141O  PRO      4.3     7.6    -      -       -      -
    142O  ARG*     4.0    34.5    -      -       +      +
    163O  VAL*     4.3    11.2    -      -       +      -
    164O  THR*     3.8    21.8    -      -       -      +
    165O  GLU*     4.6     0.4    -      -       -      -
    166O  GLN*     3.9    23.8    -      -       +      -
    172O  THR*     1.3    76.3    -      -       -      +
    174O  SER*     1.3    66.0    +      -       -      +
    170P  HIS*     5.9     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 174 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136O  LEU      3.5     8.5    -      -       -      -
    137O  ASN*     3.5     3.8    +      -       -      -
    138O  ASN*     2.9    24.1    +      -       -      -
    139O  PHE*     3.9     1.1    -      -       -      -
    163O  VAL*     3.5     4.1    -      -       -      +
    164O  THR*     3.0    37.0    +      -       -      -
    173O  TYR*     1.3    73.4    +      -       -      +
    175O  LEU*     1.3    60.3    +      -       -      +
    170P  HIS*     3.2    37.6    +      -       -      -
    172P  PHE*     3.3    15.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 175 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134O  CYS      3.5     1.0    -      -       -      +
    135O  LEU*     3.6     4.3    -      -       -      +
    136O  LEU*     2.7    52.1    +      -       +      +
    139O  PHE*     3.9    23.1    -      -       +      -
    142O  ARG*     5.3     3.8    -      -       -      +
    144O  ALA*     4.6    18.4    -      -       +      +
    146O  VAL*     4.8     4.3    -      -       +      -
    161O  GLU*     3.8    28.5    -      -       +      +
    162O  SER      3.3     9.4    -      -       -      +
    163O  VAL*     4.4    19.3    -      -       +      -
    174O  SER*     1.3    76.2    -      -       -      +
    176O  SER*     1.3    92.2    +      -       -      +
    177O  SER*     3.9     6.7    -      -       -      +
    172P  PHE*     3.7     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 176 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133O  VAL*     5.1     5.2    -      -       -      -
    134O  CYS      3.2     7.0    -      -       -      -
    135O  LEU*     4.8     3.6    -      -       -      +
    160O  GLN      5.1     0.2    +      -       -      -
    161O  GLU*     2.9     7.1    -      -       -      +
    162O  SER*     2.8    41.4    +      -       -      -
    175O  LEU*     1.3    77.6    -      -       -      +
    177O  SER*     1.3    57.4    +      -       -      +
    178O  THR*     4.2    10.1    +      -       -      -
    172P  PHE*     3.5    27.1    -      -       -      +
    185P  SER*     4.5    12.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 177 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132O  VAL      3.6     0.9    -      -       -      +
    133O  VAL*     3.3     5.0    -      -       -      +
    134O  CYS*     2.8    44.0    +      -       -      -
    146O  VAL*     3.7    28.4    -      -       -      +
    148O  TRP*     3.0    29.0    +      -       -      -
    159O  SER*     4.1     7.8    +      -       -      -
    160O  GLN      3.6     3.5    +      -       -      -
    161O  GLU*     4.2     3.6    -      -       -      +
    175O  LEU*     3.9     3.5    -      -       -      +
    176O  SER*     1.3    72.8    -      -       -      +
    178O  THR*     1.3    65.2    +      -       -      +
    179O  LEU      4.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 178 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131O  SER*     3.8    23.1    -      -       -      +
    132O  VAL      3.4     6.5    -      -       -      +
    133O  VAL*     3.8    18.1    -      -       +      +
    158O  ASN      3.9     0.7    -      -       -      +
    159O  SER*     3.0    24.6    -      -       -      -
    160O  GLN*     2.7    23.3    +      -       -      +
    176O  SER*     4.2     9.7    +      -       -      -
    177O  SER*     1.3    79.0    +      -       -      +
    179O  LEU*     1.3    62.5    +      -       -      +
    180O  THR*     4.0     7.9    +      -       -      +
    147P  LEU*     5.3     7.3    -      -       +      +
    149P  LYS*     6.4     0.2    -      -       -      -
    185P  SER*     4.7     4.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 179 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130O  ALA      3.7     0.9    -      -       -      +
    131O  SER*     3.3    10.2    +      -       -      -
    132O  VAL*     2.8    60.7    +      -       +      +
    148O  TRP*     4.1    43.0    -      -       +      -
    150O  VAL*     4.2    20.4    -      -       +      -
    155O  GLN*     4.4     6.1    -      -       +      -
    158O  ASN*     3.6    37.2    -      -       -      +
    159O  SER*     4.3     2.5    -      -       -      +
    177O  SER      4.1     0.4    +      -       -      -
    178O  THR*     1.3    71.4    -      -       -      +
    180O  THR*     1.3    60.9    +      -       -      +
    181O  LEU*     4.1    17.0    -      -       +      -
    192O  TYR*     4.6     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 180 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129O  THR*     4.6    18.6    -      -       +      -
    130O  ALA      3.8     1.8    -      -       -      -
    131O  SER*     4.4     9.1    +      -       -      +
    158O  ASN*     3.0    33.2    +      -       -      +
    160O  GLN*     5.6     4.2    -      -       -      +
    178O  THR*     4.1     9.5    +      -       -      +
    179O  LEU*     1.3    76.9    +      -       -      +
    181O  LEU*     1.3    65.2    +      -       -      +
    149P  LYS*     4.9     9.5    -      -       -      +
    177P  GLN*     6.1     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 181 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129O  THR*     3.6     6.9    -      -       -      +
    130O  ALA*     2.7    42.2    +      -       +      +
    132O  VAL*     5.1     3.1    -      -       +      -
    150O  VAL*     5.2     5.6    -      -       +      -
    155O  GLN*     5.4     4.3    -      -       -      +
    158O  ASN*     4.4    13.5    -      -       -      +
    179O  LEU*     4.1    17.5    -      -       +      -
    180O  THR*     1.3    79.5    -      -       -      +
    182O  SER*     1.3    60.3    +      -       -      +
    185O  ASP*     3.3    23.1    -      -       -      +
    186O  TYR*     3.9    20.2    -      -       +      -
    189O  HIS*     6.3     0.4    -      -       +      -
    192O  TYR*     3.7    38.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 182 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128O  GLY      3.7    12.1    -      -       -      -
    129O  THR*     4.4     1.1    -      -       -      +
    130O  ALA      4.5     0.7    -      -       -      -
    181O  LEU*     1.3    75.6    -      -       -      +
    183O  LYS*     1.3    55.5    +      -       -      +
    184O  ALA      4.5     1.0    +      -       -      -
    185O  ASP*     2.6    35.9    +      -       -      +
    186O  TYR*     2.8    36.0    +      -       -      +
----------------------------------------------------------
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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