Contacts of the strand formed by residues 171 - 181 (chain A) in PDB entry 5UHA


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 VAL 171 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  LEU*     3.3    37.2    -      -       +      +
     43A  LEU*     4.4     9.7    -      -       +      +
     46A  ILE*     3.9    23.1    -      -       +      -
    169A  SER*     3.1    13.1    +      -       -      +
    170A  PRO*     1.3    82.5    -      -       +      +
    172A  LEU*     1.3    65.9    +      -       -      +
    174A  VAL*     3.7    30.5    -      -       +      -
    196A  VAL*     4.7     8.3    -      -       +      -
    197A  GLU      3.9     7.4    -      -       -      +
    198A  THR*     4.8     2.9    -      -       +      +
    199A  LYS*     3.6    15.0    -      -       -      -
    202A  ILE*     5.7     0.2    -      -       +      -
    207A  ALA*     5.1     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 172 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  ASN*     5.0     3.8    -      -       -      +
     43A  LEU*     4.3     8.6    -      -       -      +
    170A  PRO      4.1     0.2    +      -       -      -
    171A  VAL*     1.3    77.0    -      -       -      +
    173A  LYS*     1.3    74.3    +      -       +      +
    197A  GLU*     3.0    48.5    +      -       -      +
    198A  THR      3.2    22.2    -      -       -      +
    199A  LYS*     4.5    13.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 173 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  ARG*     6.0     0.9    -      -       -      +
     43A  LEU*     4.8     2.2    -      -       -      -
    171A  VAL*     4.5     0.8    -      -       -      +
    172A  LEU*     1.3    96.9    -      -       +      +
    174A  VAL*     1.3    66.3    +      -       -      +
    175A  THR*     5.5     0.9    -      -       +      +
    195A  ASP*     3.9     3.1    -      -       -      +
    197A  GLU*     3.1    31.2    +      -       -      +
    909C  ASP*     3.2    32.9    +      -       +      +
    910C  GLY      4.1    11.2    -      -       -      +
    911C  THR*     3.3    30.3    -      -       +      +
    996C  ARG*     3.9    29.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 174 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  ARG*     3.4    36.9    +      -       +      -
     42A  LEU*     3.6    35.4    -      -       +      -
     43A  LEU*     4.1    14.8    -      -       +      +
    171A  VAL*     3.7    22.4    -      -       +      -
    173A  LYS*     1.3    81.5    -      -       -      +
    175A  THR*     1.3    67.0    +      -       -      +
    194A  LEU*     4.0    14.8    -      -       +      -
    195A  ASP      3.2    14.1    -      -       -      +
    196A  VAL*     4.5     4.7    -      -       +      -
    910C  GLY*     3.2    19.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 175 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  ARG*     5.1     2.7    -      -       -      +
     39A  ARG*     4.7     2.9    -      -       -      +
    173A  LYS*     5.5     1.1    -      -       +      +
    174A  VAL*     1.3    76.7    -      -       -      +
    176A  TYR*     1.3    90.5    +      -       -      +
    194A  LEU*     3.5     5.7    -      -       -      +
    195A  ASP*     2.9    50.0    +      -       +      +
    906C  PHE*     4.8     5.3    -      -       -      -
    908C  ALA      2.3    28.3    +      -       -      +
    909C  ASP*     3.3    22.2    -      -       -      +
    910C  GLY*     3.5     9.0    -      -       -      -
    997C  ASP*     6.1     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 176 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  TYR*     3.4    40.9    +      +       -      -
     35A  GLY*     3.8    14.6    -      -       -      -
     36A  ASN*     3.1    44.0    +      -       +      +
     39A  ARG*     4.2    13.5    -      -       +      -
    175A  THR*     1.3    98.7    +      -       -      +
    177A  LYS*     1.3    63.0    +      -       -      +
    192A  LEU*     4.2    18.6    -      -       +      -
    193A  ILE      3.2    14.8    -      -       -      +
    194A  LEU*     4.2     7.6    -      -       +      -
    195A  ASP*     4.6     1.1    -      -       -      +
    906C  PHE*     4.2     7.4    -      +       -      -
    908C  ALA*     4.7     1.2    -      -       -      +
   1011C  PHE*     4.0    29.2    -      +       -      -
   1016C  GLY*     3.1    19.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 177 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  GLN*     4.9    11.4    +      -       -      +
     32A  TYR*     5.1     2.9    -      -       -      -
    176A  TYR*     1.3    75.6    -      -       -      +
    178A  VAL*     1.3    66.6    +      -       -      +
    179A  ASP*     6.0     2.2    -      -       -      +
    191A  LYS      3.8     0.5    -      -       -      +
    192A  LEU*     4.2     0.2    -      -       -      +
    193A  ILE*     3.0    65.1    +      -       +      +
    999C  ASP*     5.6     3.6    +      -       -      -
   1011C  PHE*     5.9     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 178 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  GLY*     3.8    10.5    -      -       -      -
     32A  TYR*     3.5    47.3    +      -       +      +
    176A  TYR*     4.9     0.7    -      -       +      -
    177A  LYS*     1.3    78.8    -      -       -      +
    179A  ASP*     1.3    67.6    +      -       -      +
    180A  ALA*     3.6    13.9    +      -       +      +
    190A  ASP*     3.7    29.6    -      -       +      +
    191A  LYS      3.3     8.5    -      -       -      +
    192A  LEU*     3.7    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 179 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177A  LYS*     4.3     3.0    +      -       -      +
    178A  VAL*     1.3    73.4    -      -       -      +
    180A  ALA*     1.3    62.5    +      -       -      +
    181A  THR*     3.7     5.8    +      -       -      -
    189A  PHE*     4.0     1.6    -      -       -      +
    190A  ASP*     3.8     0.2    -      -       -      -
    191A  LYS*     2.8    67.0    +      -       +      +
    193A  ILE*     4.4    10.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 180 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178A  VAL*     3.6     8.3    +      -       +      +
    179A  ASP*     1.3    72.0    -      -       -      +
    181A  THR*     1.3    60.7    +      -       -      +
    182A  ARG*     3.2    23.6    +      -       -      +
    189A  PHE      3.4     4.7    -      -       -      -
    190A  ASP*     3.3    30.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 181 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  ASP      3.7     2.7    +      -       -      -
    180A  ALA*     1.3    68.4    -      -       -      +
    182A  ARG*     1.3    62.7    +      -       -      +
    183A  VAL*     3.8    26.5    -      -       +      +
    187A  THR*     3.3    20.9    -      -       -      +
    188A  ASP*     3.1    24.8    -      -       -      +
    189A  PHE*     2.8    44.1    +      -       +      +
----------------------------------------------------------
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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