Contacts of the strand formed by residues 128 - 134 (chain B) in PDB entry 1UMZ


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 HIS 128 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59B  GLN*     3.2     7.2    -      -       -      -
     60B  MET      2.9    30.2    +      -       -      -
    121B  PHE*     3.2    51.2    -      +       +      +
    122B  ASP      4.6     2.2    +      -       -      -
    123B  PRO*     4.8     1.8    -      -       +      -
    126B  GLU*     3.4    30.1    +      -       +      +
    127B  PHE*     1.3    77.3    +      -       -      +
    129B  TYR*     1.3    62.1    +      -       -      +
    130B  TYR*     3.4    25.3    -      -       +      +
    144B  ASP*     2.8    29.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 129 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57B  SER*     3.4    22.2    -      -       -      +
     58B  MET      3.6     3.4    -      -       -      -
     59B  GLN*     3.4    41.6    +      -       +      -
    128B  HIS*     1.3    73.2    -      -       -      +
    130B  TYR*     1.3    63.6    +      -       -      +
    131B  SER*     4.2     3.1    -      -       -      -
    143B  VAL*     3.4     5.2    -      -       -      +
    144B  ASP*     2.7    54.2    +      -       -      +
    201B  SER*     3.9    19.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 130 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57B  SER*     3.4     1.6    -      -       -      -
     58B  MET      2.8    33.6    +      -       -      +
     60B  MET*     3.8    32.0    +      -       +      -
     62B  LEU*     4.5     2.1    -      -       +      +
     74B  PHE*     3.4    19.7    -      -       +      -
     88B  PHE*     4.2    15.7    -      +       +      -
     90B  PHE*     3.5    41.3    -      +       +      -
    101B  LEU*     4.3     2.2    -      -       +      -
    119B  LEU*     3.9     1.8    -      -       +      +
    121B  PHE*     3.5    25.2    -      +       -      -
    123B  PRO*     3.9    10.0    -      -       -      +
    128B  HIS*     3.4    28.2    -      -       +      +
    129B  TYR*     1.3    74.9    -      -       -      +
    131B  SER*     1.3    60.7    +      -       -      +
    142B  LEU      3.4     2.9    -      -       -      -
    143B  VAL*     3.8    34.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 131 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  HIS*     4.2    13.3    +      -       -      -
     56B  PHE      3.1    12.3    -      -       -      -
     57B  SER*     3.5    16.8    -      -       -      -
     74B  PHE*     4.6     0.4    -      -       -      -
     88B  PHE*     3.4     9.2    -      -       -      -
    129B  TYR*     5.3     2.7    -      -       -      -
    130B  TYR*     1.3    76.7    -      -       -      +
    132B  VAL*     1.3    63.2    +      -       -      +
    133B  LEU      4.3     0.2    -      -       -      -
    140B  VAL      3.7     0.2    -      -       -      +
    141B  PHE*     3.5     0.9    -      -       -      -
    142B  LEU*     2.8    59.0    +      -       -      +
    144B  ASP      4.7     3.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 132 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  GLY      3.7     0.9    -      -       -      +
     55B  HIS*     3.4     8.1    -      -       -      -
     56B  PHE*     2.9    47.2    +      -       +      +
     74B  PHE*     4.8     4.0    -      -       +      -
     76B  LEU*     4.3    13.0    -      -       +      -
     86B  ILE*     4.0    33.7    -      -       +      +
     88B  PHE*     3.6    22.2    -      -       +      -
    131B  SER*     1.3    77.4    -      -       -      +
    133B  LEU*     1.3    72.2    -      -       -      +
    134B  TRP*     4.2    12.6    -      -       +      -
    139B  ILE*     4.3     4.7    -      -       +      -
    140B  VAL      3.3     6.7    -      -       -      +
    141B  PHE*     4.8     2.5    -      -       +      -
    142B  LEU*     5.0     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 133 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  GLY      3.5    12.1    -      -       -      +
     55B  HIS*     4.0    12.8    -      -       +      -
    131B  SER      4.3     0.2    -      -       -      -
    132B  VAL*     1.3    73.5    -      -       -      +
    134B  TRP*     1.3    60.5    +      -       -      +
    135B  ASN*     4.2     7.0    -      -       -      +
    138B  MET*     3.7     9.7    -      -       +      +
    139B  ILE*     3.2     5.2    -      -       -      -
    140B  VAL*     2.8    54.2    +      -       +      +
    142B  LEU*     4.5     7.9    -      -       +      +
    223B  TRP*     3.9    27.6    -      -       +      -
    224B  TRP*     3.9    16.8    -      -       +      -
    229B  PHE*     3.7    33.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  TYR      3.5    22.7    -      -       -      -
     52B  LEU*     3.8    20.9    -      -       +      -
     53B  PHE*     3.3    40.2    -      +       -      +
     54B  GLY*     2.8    39.7    +      -       -      +
     56B  PHE*     4.1    14.8    -      +       +      -
     76B  LEU*     4.1    11.4    -      -       +      -
     86B  ILE*     4.2     2.0    -      -       +      -
    132B  VAL*     4.2    13.2    -      -       +      -
    133B  LEU*     1.3    75.7    -      -       -      +
    135B  ASN*     1.3    70.7    +      -       -      +
    138B  MET      3.7     2.0    -      -       -      -
    139B  ILE*     3.6    22.7    -      -       +      -
    161B  PHE*     4.3     0.2    -      +       -      -
    162B  PRO*     2.8    35.0    +      -       +      +
    165B  GLN      4.2     1.3    -      -       -      -
    167B  MET*     3.4    42.6    -      -       +      -
    224B  TRP*     4.2     1.7    -      -       -      -
----------------------------------------------------------
 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