Contacts of the strand formed by residues 164 - 171 (chain A) in PDB entry 2UYC


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 GLU 164 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  LYS*     3.2    54.7    +      -       +      +
    151A  VAL*     4.4     7.4    -      -       +      -
    152A  LEU      3.6     4.3    -      -       -      -
    153A  ASN*     3.2    30.6    -      -       +      +
    162A  LYS*     2.9    40.6    +      -       -      +
    163A  ASN*     1.3    70.7    -      -       -      +
    165A  ARG*     1.3    87.3    +      -       -      +
    250A  THR*     4.7     1.4    +      -       -      -
    426D    G      6.1     0.9    -      -       -      +
    427D    C      4.6     1.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  GLU*     3.3    22.6    +      -       +      +
    120A  ASN      3.4    11.4    -      -       -      +
    121A  VAL*     3.6    14.9    -      -       -      +
    122A  LYS      4.0     2.5    -      -       -      +
    151A  VAL*     3.1     8.3    -      -       -      +
    152A  LEU      2.8    32.4    +      -       -      -
    163A  ASN*     3.3    33.1    -      -       -      +
    164A  GLU*     1.3   103.0    +      -       -      +
    166A  ILE*     1.3    59.8    +      -       -      +
    167A  TYR*     3.4    27.1    -      -       +      +
    250A  THR*     3.2    24.9    -      -       -      +
    251A  LEU      4.5     1.6    +      -       -      -
    303A  GLY      5.0     0.6    +      -       -      -
    305A  SER      5.1     0.4    +      -       -      -
    306A  VAL*     6.4     1.6    -      -       +      -
    427D    C      2.8    66.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  GLU*     3.5     5.5    -      -       -      +
    120A  ASN*     2.9    47.4    +      -       +      +
    121A  VAL      3.6    15.9    -      -       -      +
    122A  LYS*     4.5     0.2    -      -       -      +
    124A  PHE*     4.0     9.9    -      -       +      -
    125A  ALA*     4.4    15.0    -      -       +      -
    133A  LEU*     4.8     6.7    -      -       +      -
    149A  ALA*     3.9     9.6    -      -       +      -
    150A  LYS*     3.3    39.5    -      -       -      +
    151A  VAL*     3.6    16.4    -      -       +      +
    165A  ARG*     1.3    72.7    -      -       -      +
    167A  TYR*     1.3    60.6    +      -       -      +
    168A  MET*     4.1    23.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  PHE*     4.2     9.2    -      +       +      -
    118A  MET      3.6     2.2    -      -       -      +
    119A  GLU*     3.9    20.3    -      -       +      +
    148A  HIS      3.5     1.4    -      -       -      +
    149A  ALA*     3.1     4.7    -      -       -      -
    150A  LYS      2.9    32.8    +      -       -      +
    152A  LEU*     3.6    37.4    +      -       +      -
    163A  ASN*     4.1     7.6    +      -       -      -
    165A  ARG*     3.4    39.2    -      -       +      +
    166A  ILE*     1.3    72.3    -      -       -      +
    168A  MET*     1.3    61.5    +      -       -      +
    169A  ILE*     4.1     1.1    -      -       +      -
    182A  PHE*     3.6    12.0    -      -       +      -
    306A  VAL*     5.6     1.4    -      -       +      +
    307A  VAL*     5.1     6.4    +      -       -      +
    310A  VAL*     3.6    22.8    -      -       +      +
    311A  LEU*     3.6    27.3    -      -       +      +
    314A  ILE*     3.5    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  PHE*     3.9    33.0    -      -       +      -
    116A  VAL      3.4     4.7    -      -       -      +
    117A  PHE*     3.5     1.4    -      -       -      -
    118A  MET*     2.9    58.4    +      -       +      +
    119A  GLU      4.3     1.6    -      -       -      +
    120A  ASN*     4.4     2.0    -      -       +      -
    124A  PHE*     4.2     7.2    -      -       +      -
    133A  LEU*     4.0    13.7    -      -       -      -
    136A  VAL*     4.1    13.2    -      -       -      -
    147A  PHE*     3.7    38.1    -      -       +      -
    148A  HIS      3.2     3.8    -      -       -      -
    149A  ALA*     3.9     7.9    -      -       +      -
    166A  ILE*     4.1    24.2    -      -       +      +
    167A  TYR*     1.3    77.6    -      -       -      +
    169A  ILE*     1.3    63.8    +      -       -      +
    170A  CYS*     4.1     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  VAL*     4.0     6.5    -      -       +      -
    116A  VAL      3.5     1.6    -      -       -      -
    117A  PHE*     3.2    40.4    -      -       +      -
    148A  HIS*     2.8    39.2    +      -       +      +
    167A  TYR*     4.7     2.0    -      -       +      -
    168A  MET*     1.3    77.7    -      -       -      +
    170A  CYS*     1.3    63.2    +      -       -      +
    171A  PHE*     3.7    24.7    -      -       +      -
    180A  PHE*     3.4    32.1    -      -       +      -
    182A  PHE*     4.2    10.3    -      -       +      -
    314A  ILE*     3.6    11.7    -      -       +      -
    318A  ILE*     3.7    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  LYS      3.7     0.3    -      -       -      +
    115A  VAL*     3.2     9.1    -      -       -      +
    116A  VAL*     2.8    48.2    +      -       +      +
    118A  MET*     4.1    10.5    -      -       -      -
    140A  MET*     3.8    19.3    -      -       +      -
    145A  TYR*     3.9    15.6    -      -       +      -
    146A  SER      3.2    12.8    -      -       -      +
    147A  PHE*     3.6    31.9    -      -       -      -
    168A  MET      4.4     1.1    -      -       -      -
    169A  ILE*     1.3    80.6    -      -       -      +
    171A  PHE*     1.3    61.9    +      -       -      +
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Residues in contact with PHE 171 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  LYS      3.6     2.0    -      -       -      -
    115A  VAL*     3.7    28.0    -      -       +      -
    145A  TYR*     3.2     2.9    -      -       -      -
    146A  SER*     2.8    47.6    +      -       -      +
    148A  HIS*     3.9    11.9    -      +       -      -
    169A  ILE*     3.7    16.8    -      -       +      -
    170A  CYS*     1.3    74.1    -      -       -      +
    172A  ARG*     1.3    67.7    +      -       -      +
    173A  ASN*     3.1     1.0    +      -       -      +
    175A  LEU*     4.9     1.1    -      -       +      -
    177A  ILE*     3.5    43.5    -      -       +      +
    180A  PHE*     3.5    45.3    -      +       +      -
    318A  ILE*     4.1    13.9    -      -       +      -
    321A  SER*     4.4     1.8    -      -       -      -
    322A  LEU*     3.8    16.2    -      -       +      -
----------------------------------------------------------
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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