Contacts of the strand formed by residues 139 - 148 (chain H) in PDB entry 1UB6


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 139 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129H  PRO*     4.3    16.2    -      -       +      -
    134H  THR      5.3     2.2    -      -       -      +
    135H  THR*     4.2    32.1    -      -       +      +
    136H  GLY      4.0     7.6    +      -       -      +
    138H  SER*     1.3    74.5    -      -       -      +
    140H  THR*     1.3    74.1    +      -       -      +
    141H  LEU*     3.8     7.0    +      -       +      +
    185H  THR*     3.1    25.1    -      -       -      -
    186H  VAL*     2.7    25.8    +      -       +      +
    188H  SER*     5.1     1.3    -      -       -      +
    191H  TRP*     3.5    34.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 140 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129H  PRO*     4.6     0.7    -      -       -      +
    139H  VAL*     1.3    83.7    -      -       -      +
    141H  LEU*     1.3    63.1    +      -       -      +
    183H  SER*     4.2     7.4    -      -       -      -
    184H  VAL      3.4     9.9    -      -       -      +
    185H  THR*     3.5    15.4    -      -       +      +
    119L  THR*     4.6    11.5    +      -       -      +
    121L  SER*     2.8    37.6    +      -       -      +
    123L  PHE*     2.8    25.2    -      -       +      -
    140L  PHE*     3.7    23.6    -      -       +      -
    142L  ASN*     4.3     6.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 141 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127H  ALA      3.7     1.6    -      -       -      -
    128H  ALA*     3.9     4.0    -      -       +      -
    129H  PRO*     3.4    24.0    -      -       +      -
    139H  VAL*     3.8     7.8    +      -       +      +
    140H  THR*     1.3    76.3    -      -       -      +
    142H  GLY*     1.3    56.8    +      -       -      +
    157H  TRP*     4.7     0.2    -      -       +      -
    183H  SER*     3.2     3.6    -      -       -      -
    184H  VAL*     2.6    53.4    +      -       +      +
    186H  VAL*     5.0     4.3    -      -       +      -
    191H  TRP*     3.2    42.0    -      -       +      -
    196H  VAL*     3.7    38.1    -      -       +      -
    213H  LEU*     3.3    22.4    -      -       +      -
    123L  PHE*     4.6     3.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 142 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127H  ALA*     2.6    50.6    +      -       -      +
    141H  LEU*     1.3    77.4    -      -       -      +
    143H  CYS*     1.3    61.6    +      -       -      -
    157H  TRP*     3.4    10.5    -      -       -      -
    182H  SER      3.0    13.2    -      -       -      -
    183H  SER*     4.0     2.0    -      -       -      -
    213H  LEU*     3.6     4.1    -      -       -      +
    140L  PHE*     4.5     4.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 143 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124H  VAL*     4.3    10.5    -      -       +      -
    125H  TYR      3.4     5.4    -      -       -      +
    126H  PRO*     4.5     8.7    -      -       -      -
    127H  ALA*     5.2     0.9    -      -       -      -
    142H  GLY*     1.3    80.6    -      -       -      -
    144H  LEU*     1.3    60.6    +      -       -      +
    145H  VAL*     3.9     7.5    +      -       +      +
    155H  VAL*     5.3     3.8    -      -       +      -
    157H  TRP*     3.7     6.5    -      -       +      -
    181H  SER*     3.6     3.5    -      -       -      -
    182H  SER*     2.9    31.9    +      -       -      +
    198H  CYS*     2.0    52.3    -      -       +      -
    200H  VAL*     5.2     1.8    -      -       +      -
    211H  LYS*     4.5     2.0    -      -       -      -
    213H  LEU*     4.1    10.5    -      -       -      -
    140L  PHE*     5.4     1.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 144 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123H  SER      3.4     1.7    -      -       -      +
    124H  VAL*     3.4     3.5    -      -       -      -
    125H  TYR*     2.7    60.0    +      -       +      +
    127H  ALA*     5.0     5.7    -      -       +      +
    142H  GLY      4.4     0.2    -      -       -      -
    143H  CYS*     1.3    72.7    -      -       -      +
    145H  VAL*     1.3    63.6    +      -       -      +
    146H  LYS*     4.2    17.7    -      -       +      -
    179H  THR*     3.9    19.1    -      -       +      -
    180H  MET      3.8    11.4    -      -       -      +
    181H  SER*     4.1    13.7    -      -       -      +
    129L  GLN*     4.9     1.3    -      -       -      +
    136L  SER*     3.4    26.5    -      -       -      +
    138L  VAL*     4.1    22.0    -      -       +      -
    183L  THR*     4.8     7.6    -      -       +      +
    185L  THR*     6.2     0.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 145 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122H  PRO*     3.4    32.1    -      -       +      -
    123H  SER      3.4     4.3    -      -       -      +
    124H  VAL*     4.4     4.9    -      -       +      -
    143H  CYS*     4.3     8.3    -      -       +      +
    144H  LEU*     1.3    76.5    -      -       -      +
    146H  LYS*     1.3    59.1    +      -       -      +
    148H  TYR*     3.5    13.3    -      -       +      -
    153H  VAL*     4.7     4.5    -      -       +      -
    155H  VAL*     4.4     4.0    -      -       +      -
    179H  THR*     3.3     2.9    -      -       -      +
    180H  MET*     2.9    58.0    +      -       -      +
    200H  VAL*     3.7    38.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 146 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122H  PRO      3.8     0.2    -      -       -      -
    123H  SER*     2.8    39.2    +      -       -      -
    125H  TYR*     3.6    34.5    -      -       +      -
    144H  LEU*     4.1    11.0    -      -       +      -
    145H  VAL*     1.3    74.1    -      -       -      +
    147H  GLY*     1.3    61.3    +      -       -      +
    148H  TYR*     3.5     3.4    -      -       -      -
    174H  GLN*     4.5    12.1    -      -       -      +
    178H  TYR      3.6     5.8    -      -       -      -
    179H  THR*     3.2    28.9    +      -       +      +
    129L  GLN*     3.9    18.6    -      -       -      +
    136L  SER*     4.9     0.2    -      -       -      +
    185L  THR*     4.6    13.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 147 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120H  THR*     2.7    23.2    +      -       -      -
    121H  PRO      3.1    10.8    -      -       -      +
    123H  SER*     5.0     3.7    +      -       -      -
    146H  LYS*     1.3    80.9    -      -       -      +
    148H  TYR*     1.3    53.6    +      -       -      +
    177H  LEU*     3.6    30.3    -      -       -      +
    178H  TYR      3.2     6.1    +      -       -      -
    179H  THR*     4.1     1.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 148 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120H  THR*     3.3    17.5    -      -       -      +
    122H  PRO*     3.7    19.7    -      -       +      -
    145H  VAL*     3.5    36.8    -      -       +      -
    146H  LYS      4.1     1.8    -      -       -      -
    147H  GLY*     1.3    80.2    -      -       -      +
    149H  PHE*     1.3    58.2    +      -       -      +
    150H  PRO      3.8     4.0    -      -       -      -
    151H  GLU*     3.3    23.6    -      -       -      -
    153H  VAL*     3.2    16.6    -      -       +      +
    171H  ALA*     3.3    16.6    -      -       -      +
    177H  LEU*     3.6     4.4    -      -       -      -
    178H  TYR*     2.7    72.9    +      -       +      +
    179H  THR      4.0     0.2    -      -       -      -
    180H  MET*     3.1    22.2    -      -       -      +
    202H  HIS*     3.6    22.2    -      +       -      +
----------------------------------------------------------
 Back to top of page


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