Contacts of the strand formed by residues 146 - 152 (chain A) 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 VAL 146 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  TRP*     3.6    32.5    -      -       +      +
    142A  LEU*     3.2     2.9    -      -       -      -
    143A  VAL      2.8    39.6    +      -       -      +
    144A  ASP*     3.4     1.3    -      -       +      -
    145A  ASP*     1.3    91.3    -      -       -      +
    147A  PRO*     1.4    79.3    -      -       +      +
    148A  ILE*     3.5     1.6    +      -       -      +
    239A  ARG*     4.2    17.9    -      -       +      +
    243A  VAL*     3.9    20.2    -      -       +      -
     19B  TRP*     4.1    18.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140A  VAL*     4.1    18.4    -      -       +      -
    141A  PHE      3.4     7.6    -      -       -      +
    142A  LEU*     4.2    10.8    -      -       +      -
    145A  ASP      3.4    10.1    -      -       -      +
    146A  VAL*     1.4    97.0    -      -       +      +
    148A  ILE*     1.3    59.1    +      -       -      +
    149A  ARG      3.6     2.2    -      -       -      +
    232A  LEU*     4.2    16.4    -      -       +      -
    236A  GLN*     3.7    42.8    -      -       +      +
    239A  ARG*     4.3     7.0    -      -       +      +
    240A  LEU*     3.6    21.0    -      -       +      -
    243A  VAL*     3.9     1.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  PHE*     4.1    12.8    -      -       +      -
    101A  LEU*     3.8    18.8    -      -       +      -
    103A  THR*     4.1    12.6    -      -       +      -
    115A  GLN*     4.0     0.3    -      -       -      +
    117A  ILE*     3.9    21.1    -      -       +      +
    120A  TRP*     3.7    22.2    -      -       +      -
    141A  PHE*     2.8    23.2    +      -       +      +
    143A  VAL*     3.7    34.3    -      -       +      -
    146A  VAL      3.9     2.9    -      -       -      +
    147A  PRO*     1.3    77.8    -      -       -      +
    149A  ARG*     1.3    66.8    +      -       +      +
    240A  LEU*     3.4     6.7    -      -       -      +
    243A  VAL*     4.2     9.8    -      -       +      +
    244A  ARG*     2.8    27.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  THR*     3.1    38.5    +      -       -      +
    104A  ASN      3.5     2.2    -      -       -      +
    105A  VAL*     3.9    18.9    -      -       -      +
    113A  ARG*     2.9    40.5    +      -       -      +
    115A  GLN*     3.2    30.7    +      -       -      +
    140A  VAL*     3.6     3.1    -      -       -      +
    141A  PHE*     3.0    58.2    +      -       +      +
    147A  PRO      3.6     1.2    -      -       -      -
    148A  ILE*     1.3    88.0    -      -       +      +
    150A  VAL*     1.3    77.8    +      -       -      +
    151A  PHE*     4.6     5.5    -      -       -      +
    240A  LEU*     3.6     6.6    -      -       -      +
    244A  ARG*     4.2     2.2    -      -       -      +
    252A  TYR*     3.4    20.2    +      -       -      -
    271A  ASP*     4.8     3.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138A  MET*     3.9    32.1    -      -       +      -
    139A  ILE      3.3    11.0    -      -       -      +
    140A  VAL*     4.3     5.4    -      -       +      -
    147A  PRO*     5.2     0.4    -      -       +      -
    149A  ARG*     1.3    86.3    +      -       -      +
    151A  PHE*     1.3    63.6    +      -       -      +
    152A  LYS*     4.1    14.1    -      -       +      -
    232A  LEU*     3.3    32.8    -      -       +      -
    237A  TYR*     4.9     4.5    -      -       +      +
    240A  LEU*     3.8    16.5    -      -       +      +
    269A  ASP*     3.0    37.9    +      -       -      +
    271A  ASP*     4.1     5.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  VAL*     4.0    37.9    -      -       +      -
    107A  THR*     4.2     4.5    -      -       +      -
    113A  ARG*     3.5    43.1    -      -       -      -
    138A  MET*     3.4     0.7    -      -       -      -
    139A  ILE*     2.8    47.0    +      -       +      +
    141A  PHE*     5.0     2.9    -      -       +      -
    149A  ARG*     4.6     5.1    -      -       -      +
    150A  VAL*     1.3    74.1    -      -       -      +
    152A  LYS*     1.3    67.2    +      -       -      +
    159A  VAL*     4.4     0.7    -      -       +      -
    160A  LYS      3.8    24.2    -      -       -      -
    161A  PHE*     3.5    26.0    -      +       -      -
    162A  PRO*     4.3     0.7    -      -       +      -
    252A  TYR*     4.4     4.7    -      -       -      -
    265A  GLU*     3.8    22.4    -      -       +      -
    269A  ASP*     3.7    10.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  TYR      3.8     5.8    +      -       -      +
    138A  MET*     3.8    17.9    -      -       +      -
    150A  VAL*     4.1    10.5    -      -       +      -
    151A  PHE*     1.3    85.2    -      -       -      +
    153A  ASN*     1.3    61.9    +      -       -      +
    154A  CYS*     3.1    27.2    +      -       -      +
    159A  VAL*     6.0     0.2    -      -       -      +
    161A  PHE*     3.7     6.7    -      -       -      -
    230A  GLN      3.3    16.8    +      -       -      -
    231A  ASP*     2.7    37.3    +      -       -      +
    237A  TYR*     3.9     9.0    -      -       -      -
    265A  GLU*     5.1     0.5    -      -       -      +
    268A  ARG*     4.3    26.2    -      -       +      +
    269A  ASP*     2.9    25.1    +      -       -      +
----------------------------------------------------------
 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