Contacts of the strand formed by residues 172 - 180 (chain A) in PDB entry 3SMZ


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 SER 172 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  ARG*     4.3     3.7    -      -       -      +
    139A  LEU*     5.6     0.2    -      -       -      +
    140A  PRO      5.0     0.7    +      -       -      -
    141A  PRO*     3.2    41.9    +      -       -      +
    143A  LEU      4.5     2.3    +      -       -      -
    163A  LEU*     3.9    24.2    -      -       -      +
    164A  VAL      3.8     4.6    +      -       -      -
    165A  TYR*     3.7    23.7    -      -       -      -
    171A  GLN*     1.3    78.3    +      -       -      +
    173A  LYS*     1.3    58.1    +      -       -      +
    174A  GLY*     3.1    20.7    +      -       -      -
    175A  TYR      4.4     0.2    +      -       -      -
    296A  PHE*     5.5     0.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 173 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  PRO*     5.4     2.2    -      -       -      -
    164A  VAL*     3.0    23.4    +      -       +      +
    166A  SER*     3.8    22.2    -      -       -      +
    171A  GLN      4.4     0.4    -      -       -      +
    172A  SER*     1.3    72.1    -      -       -      +
    174A  GLY*     1.3    59.4    +      -       -      +
    175A  TYR*     3.3    30.7    +      -       +      +
    219A  HIS*     3.0    40.6    +      -       -      +
    220A  SER      5.2     0.4    +      -       -      -
    272A  ALA      4.8     3.6    +      -       -      -
    276A  GLU*     3.0    34.5    +      -       -      +
    295A  SER*     5.8     0.7    -      -       -      -
    296A  PHE*     3.5    67.5    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 174 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138A  ASN*     3.3     9.6    +      -       -      -
    139A  LEU*     2.8    55.1    +      -       -      +
    141A  PRO*     4.6     8.0    -      -       -      +
    172A  SER*     3.1    15.5    +      -       -      -
    173A  LYS*     1.3    78.3    -      -       -      +
    175A  TYR*     1.3    57.4    +      -       -      +
    296A  PHE      5.6     0.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 175 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  CYS*     4.1     6.7    -      -       -      -
    136A  VAL      3.2    14.1    -      -       -      +
    137A  ALA*     3.7    15.7    -      -       +      -
    138A  ASN      4.9     0.2    -      -       -      +
    139A  LEU*     4.0     5.2    -      -       -      -
    163A  LEU*     3.6     4.8    -      -       -      +
    164A  VAL*     3.1    49.2    +      -       +      +
    172A  SER*     4.4     1.0    +      -       -      -
    173A  LYS*     3.3    23.1    -      -       +      +
    174A  GLY*     1.3    79.1    -      -       -      +
    176A  GLY*     1.3    59.8    -      -       -      +
    177A  PHE*     4.3     3.4    -      +       -      -
    218A  LEU      2.6    29.6    +      -       -      -
    219A  HIS*     3.3     4.2    -      -       -      -
    220A  SER*     2.9    19.3    +      -       -      -
    296A  PHE*     3.6    28.9    -      +       +      -
    297A  CYS      3.8    13.5    -      -       -      -
    299A  PRO*     3.5    24.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 176 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  CYS*     3.4     6.2    -      -       -      -
    136A  VAL      2.9    32.2    +      -       -      -
    139A  LEU*     4.1     2.8    -      -       -      +
    148A  PHE*     3.6    16.9    -      -       -      -
    162A  PHE      3.0    13.9    -      -       -      -
    163A  LEU*     3.9     3.4    -      -       -      -
    164A  VAL      4.5     0.7    -      -       -      -
    175A  TYR*     1.3    74.4    -      -       -      +
    177A  PHE*     1.3    68.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 177 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  LEU*     3.9    19.1    -      -       +      -
    134A  LEU      3.3    15.9    -      -       -      +
    135A  CYS*     3.5    22.4    -      -       +      -
    148A  PHE*     3.6     5.1    -      -       -      -
    160A  ARG      4.5     0.4    -      -       -      -
    161A  CYS*     3.3     5.0    +      -       -      -
    162A  PHE*     2.8    69.5    +      +       +      -
    164A  VAL*     4.1    14.1    -      -       +      -
    175A  TYR*     4.3     6.3    -      +       -      -
    176A  GLY*     1.3    75.5    -      -       -      -
    178A  ALA*     1.3    61.2    +      -       -      +
    179A  GLU      4.1     0.4    -      -       -      -
    208A  THR*     3.8    13.2    -      -       +      -
    213A  LEU*     3.8    24.9    -      -       +      -
    218A  LEU*     3.9    14.8    -      -       +      -
    299A  PRO*     3.7    30.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 178 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  ALA      3.6     3.6    -      -       -      +
    133A  LEU*     3.9     2.0    -      -       -      -
    134A  LEU*     3.0    37.2    +      -       +      +
    136A  VAL*     5.0     2.2    -      -       +      -
    148A  PHE*     4.5     3.4    -      -       +      -
    152A  VAL*     4.0    27.1    -      -       +      -
    158A  LEU*     4.0    16.4    -      -       +      -
    160A  ARG      3.7     4.7    -      -       -      -
    161A  CYS*     4.6     0.7    -      -       -      +
    176A  GLY      4.3     0.2    +      -       -      -
    177A  PHE*     1.3    73.6    -      -       -      +
    179A  GLU*     1.3    59.6    +      -       -      +
    180A  TYR*     3.9    15.9    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 179 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  ARG*     4.2     7.3    +      -       -      +
    130A  THR*     3.8    32.0    +      -       +      +
    132A  ALA      3.4     8.1    -      -       -      +
    133A  LEU*     3.8    14.5    -      -       +      +
    158A  LEU*     3.5     5.0    -      -       -      +
    159A  GLU*     2.7    48.7    +      -       +      +
    160A  ARG*     2.8    64.1    +      -       +      +
    177A  PHE      4.1     0.2    -      -       -      -
    178A  ALA*     1.3    72.5    -      -       -      +
    180A  TYR*     1.3    67.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 180 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  THR*     4.5     1.9    +      -       -      -
    132A  ALA*     2.9    27.4    +      -       -      +
    134A  LEU*     4.1     6.5    -      -       +      -
    152A  VAL*     2.6    42.3    +      -       +      +
    155A  PHE*     4.1     3.1    -      -       +      -
    156A  GLY      3.5    28.7    -      -       -      -
    157A  SER      3.6     6.1    -      -       -      +
    158A  LEU*     3.6    13.9    -      -       +      -
    159A  GLU*     4.0     4.0    -      -       -      +
    178A  ALA*     4.0    17.9    -      -       +      -
    179A  GLU*     1.3    83.4    -      -       -      +
    181A  MET*     1.4    64.2    +      -       -      +
    182A  LYS      3.6    18.6    -      -       -      +
    185A  SER*     3.7    14.4    -      -       -      -
    186A  ALA*     3.6    20.0    -      -       +      +
    189A  ALA*     3.2    33.1    -      -       +      +
----------------------------------------------------------
 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