Contacts of the strand formed by residues 134 - 144 (chain L) 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 GLY 134 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129L  GLN*     2.9    40.8    +      -       -      +
    130L  LEU*     3.5     8.5    -      -       -      +
    132L  SER*     3.2     6.3    +      -       -      -
    133L  GLY*     1.3    78.7    -      -       -      +
    135L  ALA*     1.3    63.4    +      -       -      +
    186L  LEU      4.3     2.7    -      -       -      -
    187L  THR*     5.1     1.1    -      -       -      -
    188L  LYS      4.3     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 135 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125L  PRO*     3.9     7.2    -      -       +      -
    129L  GLN*     3.8     4.7    -      -       -      +
    130L  LEU*     4.0     3.6    -      -       +      -
    134L  GLY*     1.3    75.5    -      -       -      +
    136L  SER*     1.3    60.9    +      -       -      +
    186L  LEU*     2.7    48.1    +      -       +      +
    188L  LYS*     3.7     9.9    -      -       -      -
    191L  TYR*     3.4    40.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 136 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144H  LEU*     3.4    21.4    -      -       -      +
    146H  LYS*     5.5     0.4    -      -       -      -
    124L  PRO      4.3     0.7    -      -       -      -
    125L  PRO*     3.5    18.4    -      -       -      +
    129L  GLN*     3.0    30.0    +      -       -      +
    135L  ALA*     1.3    73.0    -      -       -      +
    137L  VAL*     1.3    61.4    +      -       -      +
    138L  VAL*     4.0     3.1    +      -       -      +
    183L  THR*     3.9     6.2    -      -       -      +
    184L  LEU      3.2     4.7    -      -       -      -
    185L  THR*     3.3    32.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 137 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122L  ILE*     4.0     4.0    -      -       +      -
    123L  PHE      3.2    19.1    -      -       -      +
    125L  PRO*     4.5     8.7    -      -       +      -
    135L  ALA      4.3     0.4    +      -       -      -
    136L  SER*     1.3    73.0    -      -       -      +
    138L  VAL*     1.3    60.9    +      -       -      +
    153L  TRP*     3.3    29.9    -      -       +      -
    183L  THR*     3.4     1.0    -      -       -      -
    184L  LEU*     2.8    71.1    +      -       +      +
    186L  LEU*     6.1     0.7    -      -       +      -
    191L  TYR*     5.8     1.3    -      -       +      -
    197L  TYR*     4.7    10.3    -      -       +      -
    214L  PHE*     3.5    27.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 138 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127H  ALA*     5.7     3.4    -      -       +      -
    144H  LEU*     4.1    25.8    -      -       +      -
    181H  SER*     5.0     3.8    -      -       -      -
    122L  ILE*     3.4     0.5    -      -       -      +
    123L  PHE*     2.5    51.0    +      -       +      +
    136L  SER*     4.0     4.2    +      -       -      +
    137L  VAL*     1.3    76.6    -      -       -      +
    139L  CYS*     1.3    62.5    +      -       -      +
    140L  PHE*     3.9    32.8    -      -       +      -
    153L  TRP*     4.4     1.3    -      -       -      -
    181L  SER*     4.2     3.8    -      -       -      +
    182L  SER      3.4     4.3    -      -       -      +
    183L  THR*     3.2    34.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 139 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121L  SER      2.9    15.0    -      -       -      +
    122L  ILE*     3.4    14.6    -      -       +      -
    123L  PHE*     4.7     0.2    -      -       -      -
    138L  VAL*     1.3    77.1    -      -       -      +
    140L  PHE*     1.3    64.7    +      -       -      +
    141L  LEU*     3.6     3.6    -      -       -      +
    153L  TRP*     3.2    28.3    -      -       -      -
    182L  SER*     3.0    33.7    +      -       -      -
    199L  CYS*     2.0    48.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 140 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127H  ALA*     5.0     4.7    -      -       +      -
    140H  THR*     3.7     8.5    -      -       +      -
    142H  GLY*     4.5     9.0    -      -       -      -
    143H  CYS      5.4     0.7    -      -       -      -
    169H  PHE*     3.7    24.2    -      +       -      -
    181H  SER*     3.8    14.4    -      -       -      -
    182H  SER      4.4     3.8    -      -       -      -
    183H  SER*     3.3    34.3    -      -       -      -
    119L  THR      4.2     0.7    -      -       -      +
    120L  VAL*     3.1    10.9    -      -       -      +
    121L  SER*     2.7    34.6    +      -       -      +
    123L  PHE*     3.7    31.9    -      +       -      -
    138L  VAL*     3.9    15.0    -      -       +      -
    139L  CYS*     1.3    72.0    -      -       -      +
    141L  LEU*     1.3    65.3    +      -       -      +
    142L  ASN*     3.2    20.0    -      -       -      +
    180L  MET      3.6     2.5    -      -       -      -
    181L  SER*     3.6    24.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 141 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118L  PRO*     4.1    13.7    -      -       +      -
    119L  THR      4.0     3.4    -      -       -      -
    120L  VAL*     4.3     5.4    -      -       +      +
    139L  CYS      3.6    15.5    -      -       -      +
    140L  PHE*     1.3    80.5    -      -       -      +
    142L  ASN*     1.3    61.1    +      -       -      +
    144L  PHE*     3.0    18.3    -      -       +      -
    149L  ILE*     3.7    12.6    -      -       +      -
    151L  VAL*     3.3    28.9    -      -       +      -
    180L  MET*     3.0    47.5    +      -       +      +
    182L  SER*     4.6     1.3    -      -       -      -
    199L  CYS*     4.4    12.1    -      -       -      -
    200L  GLU      5.0     0.2    -      -       -      +
    201L  ALA*     3.4    32.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 142 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140H  THR*     4.3     8.9    +      -       -      +
    167H  HIS*     3.3    14.5    +      -       -      +
    169H  PHE*     3.6    18.6    -      -       -      -
    183H  SER*     3.0    22.2    +      -       -      -
    185H  THR*     5.1     5.5    -      -       +      +
    118L  PRO*     3.6     1.0    -      -       -      +
    119L  THR*     2.9    49.3    +      -       +      +
    140L  PHE*     3.2    24.8    -      -       -      +
    141L  LEU*     1.3    81.2    +      -       -      +
    143L  ASN*     1.3    82.5    +      -       -      +
    144L  PHE*     3.5     1.8    -      -       -      -
    179L  SER*     3.5     3.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 143 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167H  HIS*     2.8    30.5    +      -       -      -
    185H  THR*     6.1     1.0    -      -       -      +
    116L  ALA*     3.8    10.6    -      -       -      +
    117L  ALA      3.3    12.3    -      -       -      +
    119L  THR*     4.0     6.7    -      -       +      +
    142L  ASN*     1.3    80.8    -      -       -      +
    144L  PHE*     1.3    60.3    +      -       -      +
    172L  ASP*     4.6     1.6    +      -       -      -
    175L  ASP*     3.2    25.6    +      -       -      +
    177L  THR*     3.3    17.8    +      -       -      +
    178L  TYR      3.1     4.8    +      -       -      -
    179L  SER*     3.0     9.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 144 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116L  ALA*     3.6    13.7    -      -       -      +
    117L  ALA      4.1     0.4    -      -       -      -
    118L  PRO*     3.8    23.6    -      -       +      -
    141L  LEU*     3.0    34.1    -      -       +      -
    143L  ASN*     1.3    75.5    -      -       -      +
    145L  TYR*     1.3    64.6    +      -       -      +
    146L  PRO      3.2    26.5    -      -       -      -
    147L  LYS*     3.7    22.9    -      -       -      -
    149L  ILE*     4.1    17.9    -      -       +      -
    168L  TRP*     4.7     4.7    -      +       -      -
    177L  THR*     3.4     2.8    -      -       -      -
    178L  TYR*     2.8    62.3    +      -       +      +
    179L  SER*     3.5     7.4    -      -       -      -
    180L  MET*     3.6    18.4    -      -       +      -
    203L  HIS*     3.7    13.2    -      +       +      -
----------------------------------------------------------
 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