Contacts of the strand formed by residues 173 - 182 (chain E) 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 E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103E  LYS*     5.8     0.2    +      -       -      -
    105E  GLU*     2.8    42.9    +      -       -      +
    138E  ASN*     3.3     2.0    -      -       -      -
    139E  PHE*     2.8    59.3    +      -       +      +
    140E  TYR*     3.9    21.1    -      +       -      -
    142E  ARG*     3.5    59.9    -      -       +      -
    163E  VAL*     4.3     7.6    -      -       +      -
    164E  THR*     3.6    19.3    -      -       -      -
    166E  GLN*     3.2    31.0    -      -       +      +
    172E  THR*     1.3    73.6    -      -       -      +
    174E  SER*     1.3    65.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 174 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136E  LEU      3.3    13.0    -      -       -      -
    137E  ASN*     3.6     3.9    +      -       -      -
    138E  ASN*     3.0    23.6    +      -       -      -
    139E  PHE*     3.4     2.0    -      -       -      -
    163E  VAL*     3.3     5.3    -      -       -      +
    164E  THR*     3.1    36.7    +      -       -      -
    173E  TYR*     1.3    71.6    +      -       -      +
    175E  LEU*     1.3    61.9    +      -       -      +
    170F  HIS*     3.5    31.1    +      -       -      -
    172F  PHE*     3.6    15.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 175 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135E  LEU*     3.6     3.1    -      -       -      +
    136E  LEU*     2.9    58.6    +      -       +      +
    139E  PHE*     3.4    18.1    -      -       +      -
    142E  ARG      6.0     1.1    -      -       -      +
    144E  ALA*     5.2    10.1    -      -       +      +
    146E  VAL*     4.7     6.7    -      -       +      -
    161E  GLU*     3.4    33.9    -      -       +      +
    162E  SER      3.1    10.5    -      -       -      +
    163E  VAL*     3.8    15.3    -      -       +      -
    174E  SER*     1.3    75.6    -      -       -      +
    176E  SER*     1.3    76.3    +      -       -      +
    177E  SER*     4.0     9.9    -      -       -      +
    172F  PHE*     3.6     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 176 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133E  VAL*     4.8    13.2    -      -       -      -
    134E  CYS      3.3     7.9    -      -       -      -
    135E  LEU*     5.2     1.8    -      -       -      -
    160E  GLN      4.0     0.5    -      -       -      +
    161E  GLU*     3.3     2.9    -      -       -      -
    162E  SER*     2.8    41.4    +      -       -      +
    175E  LEU*     1.3    78.0    -      -       -      +
    177E  SER*     1.3    60.0    +      -       -      +
    178E  THR*     4.3     5.8    +      -       -      -
    172F  PHE*     3.4    37.9    -      -       -      +
    185F  SER*     4.8     6.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 177 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132E  VAL      3.7     1.0    -      -       -      +
    133E  VAL*     3.6     3.2    -      -       -      -
    134E  CYS*     2.9    37.5    +      -       -      -
    146E  VAL*     3.8    33.7    -      -       -      +
    148E  TRP*     3.3    27.5    +      -       -      -
    159E  SER*     4.3     6.6    +      -       -      -
    160E  GLN      3.5    11.3    +      -       -      -
    161E  GLU*     4.5     4.0    -      -       -      +
    175E  LEU*     4.0     4.8    -      -       -      +
    176E  SER*     1.3    72.4    -      -       -      +
    178E  THR*     1.3    61.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 178 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131E  SER*     4.1    24.7    -      -       -      +
    132E  VAL      3.2    10.5    -      -       -      +
    133E  VAL*     4.2    15.1    -      -       +      +
    148E  TRP*     4.3     0.2    -      -       -      -
    159E  SER*     3.0    26.5    -      -       -      -
    160E  GLN*     3.0    17.0    +      -       -      -
    176E  SER*     4.7     7.1    +      -       -      -
    177E  SER*     1.3    74.4    +      -       -      +
    179E  LEU*     1.3    64.6    -      -       -      +
    180E  THR*     3.7     7.4    +      -       -      +
    147F  LEU*     5.1    10.2    -      -       +      +
    185F  SER*     5.7     2.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 179 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130E  ALA      3.4     2.9    -      -       -      +
    131E  SER*     3.3     3.6    -      -       -      -
    132E  VAL*     2.7    51.5    +      -       +      +
    148E  TRP*     3.8    54.6    -      -       +      +
    150E  VAL*     4.6     4.7    -      -       +      -
    155E  GLN*     4.5     7.0    -      -       +      +
    158E  ASN*     3.4    33.9    -      -       -      +
    159E  SER*     4.1     2.0    -      -       -      -
    178E  THR*     1.3    70.8    -      -       -      +
    180E  THR*     1.3    59.5    +      -       -      +
    181E  LEU*     3.6    30.3    -      -       +      -
    192E  TYR*     4.2    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 180 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129E  THR*     4.2    21.1    -      -       +      -
    130E  ALA      3.6     2.7    -      -       -      -
    131E  SER*     3.7    14.6    +      -       -      +
    158E  ASN*     2.9    26.2    +      -       -      +
    178E  THR*     3.7     9.7    +      -       -      +
    179E  LEU*     1.3    71.4    -      -       -      +
    181E  LEU*     1.3    76.7    +      -       -      +
    149F  LYS*     4.7     2.6    -      -       -      -
    177F  GLN*     4.6    13.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 181 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129E  THR*     3.5     4.2    -      -       -      +
    130E  ALA*     2.5    51.4    +      -       +      +
    132E  VAL*     5.7     2.0    -      -       +      -
    150E  VAL*     5.0     6.1    -      -       +      -
    155E  GLN*     5.3     1.3    -      -       -      +
    158E  ASN*     3.2    26.9    -      -       +      +
    179E  LEU*     3.6    30.3    -      -       +      +
    180E  THR*     1.3    81.7    -      -       -      +
    182E  SER*     1.3    63.3    +      -       -      +
    185E  ASP*     4.5    26.5    -      -       +      +
    186E  TYR*     5.0     3.4    -      -       +      +
    189E  HIS*     6.0     2.0    -      -       +      -
    192E  TYR*     4.1    21.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 182 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128E  GLY      4.2    10.1    -      -       -      -
    129E  THR*     4.4     2.0    -      -       -      +
    130E  ALA*     4.2     1.3    -      -       -      +
    181E  LEU*     1.3    79.9    -      -       -      +
    183E  LYS*     1.3    64.3    +      -       -      +
    184E  ALA*     3.3    11.4    +      -       -      +
    185E  ASP*     3.2    28.9    +      -       -      -
    186E  TYR*     3.4    18.2    +      -       -      +
----------------------------------------------------------
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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