Contacts of the strand formed by residues 177 - 186 (chain H) in PDB entry 1UB5


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 LEU 177 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118H  LYS      5.4     0.9    -      -       -      +
    120H  THR*     4.2    15.5    -      -       +      +
    147H  GLY*     3.6    36.8    -      -       -      +
    148H  TYR      3.5    11.2    -      -       -      +
    149H  PHE*     4.1    10.3    -      -       +      -
    173H  LEU*     3.6     4.3    -      -       -      -
    174H  GLN*     2.6    45.3    +      -       -      +
    175H  SER*     4.7     4.3    -      -       -      +
    176H  GLY*     1.3    91.0    -      -       -      +
    178H  TYR*     1.3    59.9    +      -       -      +
    179H  THR*     4.4     0.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 178 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147H  GLY      3.1    14.7    +      -       -      -
    148H  TYR*     2.8    54.3    +      -       +      +
    149H  PHE*     3.7    23.5    -      +       -      -
    150H  PRO      3.9     3.8    -      -       -      -
    151H  GLU*     3.5    60.8    +      -       +      +
    171H  ALA*     4.4     6.1    -      -       +      -
    172H  LEU      3.4     3.6    -      -       -      -
    173H  LEU*     3.5    47.5    -      -       +      +
    177H  LEU*     1.3    70.3    -      -       -      +
    179H  THR*     1.3    63.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 179 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144H  LEU*     3.9    16.8    -      -       +      -
    145H  VAL      3.2    12.8    -      -       -      +
    146H  LYS*     3.3    34.9    +      -       +      +
    147H  GLY      4.0     1.6    +      -       -      -
    148H  TYR*     4.0     0.4    -      -       -      -
    170H  PRO      4.3     0.7    -      -       -      +
    171H  ALA*     3.3     1.2    -      -       -      -
    172H  LEU*     2.8    43.3    +      -       -      +
    174H  GLN*     3.8    13.2    +      -       -      +
    177H  LEU*     4.4     3.8    +      -       -      +
    178H  TYR*     1.3    79.8    +      -       -      +
    180H  MET*     1.3    65.8    +      -       -      +
    165L  LEU*     6.1     2.9    -      -       +      -
    183L  THR*     6.1     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 180 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144H  LEU*     4.0     3.5    -      -       -      +
    145H  VAL*     2.7    52.9    +      -       +      +
    148H  TYR*     3.3    25.6    -      -       +      +
    151H  GLU*     5.3     1.6    -      -       +      +
    153H  VAL*     3.5    25.4    -      -       +      +
    155H  VAL*     4.5    13.2    -      -       -      -
    168H  THR*     3.8    27.6    -      -       +      -
    169H  PHE*     3.6    16.2    -      -       -      +
    170H  PRO*     4.8     2.0    -      -       +      -
    171H  ALA*     3.6    22.7    -      -       +      +
    179H  THR*     1.3    78.2    -      -       -      +
    181H  SER*     1.3    57.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 181 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143H  CYS      3.3    11.9    -      -       -      -
    144H  LEU*     4.3    16.2    -      -       -      -
    145H  VAL*     5.5     0.4    -      -       -      -
    155H  VAL*     6.0     0.2    -      -       -      -
    168H  THR*     3.9     2.4    -      -       -      +
    169H  PHE*     3.2    32.0    +      -       -      +
    180H  MET*     1.3    78.3    -      -       -      +
    182H  SER*     1.3    62.5    +      -       -      +
    138L  VAL*     4.8     6.3    -      -       -      +
    140L  PHE*     3.5    27.4    -      -       -      -
    181L  SER*     3.7    16.3    +      -       -      -
    183L  THR*     5.2     2.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 182 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142H  GLY*     3.0     4.0    -      -       -      -
    143H  CYS      2.9    34.1    +      -       -      -
    155H  VAL*     3.8    25.0    -      -       -      +
    157H  TRP*     3.2    23.1    +      -       -      -
    166H  VAL*     4.9     0.7    -      -       -      +
    167H  HIS      3.4     8.6    +      -       -      -
    168H  THR*     3.0    24.6    +      -       -      -
    181H  SER*     1.3    76.6    -      -       -      +
    183H  SER*     1.3    63.0    +      -       -      +
    140L  PHE*     4.3     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 183 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140H  THR*     4.2     3.4    -      -       -      -
    141H  LEU      3.2     6.7    -      -       -      -
    157H  TRP*     4.7     0.4    -      -       -      -
    165H  SER      3.8     1.0    -      -       -      +
    166H  VAL*     3.3     5.0    -      -       -      +
    167H  HIS*     2.8    47.4    +      -       -      +
    169H  PHE*     3.9     3.0    -      -       -      -
    182H  SER*     1.3    75.3    +      -       -      +
    184H  VAL*     1.3    61.3    +      -       -      +
    185H  THR*     5.8     0.2    +      -       -      -
    140L  PHE*     3.2    37.4    -      -       -      -
    142L  ASN*     3.0    21.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 184 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139H  VAL      3.6     0.3    -      -       -      +
    140H  THR*     3.4     5.0    -      -       -      +
    141H  LEU*     2.8    50.4    +      -       +      +
    157H  TRP*     3.5    48.0    -      -       +      -
    161H  GLY*     5.7     2.7    -      -       -      -
    165H  SER*     3.6     9.4    -      -       -      +
    166H  VAL*     4.3    17.0    -      -       +      -
    183H  SER*     1.3    75.2    -      -       -      +
    185H  THR*     1.3    74.6    +      -       -      +
    186H  VAL*     4.5     9.4    -      -       +      -
    196H  VAL*     4.4     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 185 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138H  SER*     4.4    21.3    -      -       -      +
    139H  VAL      3.4    10.1    -      -       -      +
    140H  THR*     4.1    14.4    +      -       -      +
    165H  SER*     3.0    37.9    +      -       -      +
    167H  HIS*     5.6     2.8    -      -       -      -
    183H  SER*     5.8     0.2    +      -       -      -
    184H  VAL*     1.3    82.4    +      -       -      +
    186H  VAL*     1.3    76.1    +      -       -      +
    142L  ASN*     5.1     5.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 186 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138H  SER*     3.9     3.1    -      -       -      -
    139H  VAL*     2.7    50.2    +      -       +      +
    141H  LEU*     4.6    13.5    -      -       +      -
    184H  VAL*     4.5    14.4    -      -       +      +
    185H  THR*     1.3    87.8    -      -       -      +
    187H  PRO*     1.3    75.7    -      -       +      +
    190H  THR*     4.2    10.8    -      -       +      +
    191H  TRP*     4.7     7.6    -      -       +      -
    196H  VAL*     4.7    13.5    -      -       +      -
----------------------------------------------------------
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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