Contacts of the strand formed by residues 150 - 156 (chain K) in PDB entry 5T0G


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 150 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146K  VAL*     3.6    11.0    -      -       -      -
    147K  ASP*     2.7    40.4    +      -       -      +
    148K  GLU      3.4     1.6    -      -       -      -
    149K  LYS*     1.3    80.3    -      -       -      +
    151K  PRO*     1.3    75.7    -      -       -      +
    152K  GLN*     3.3     0.6    +      -       -      -
    222K  PRO*     5.2     1.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 151 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41K  GLN*     2.8    26.0    +      -       -      +
     42K  THR      3.0    27.5    -      -       -      +
     43K  SER*     3.2    22.2    -      -       -      +
     44K  GLU      4.1     1.1    -      -       -      -
     45K  GLY*     3.6    15.0    -      -       -      +
     46K  VAL*     3.6    17.3    -      -       +      -
    145K  GLY      3.7     6.1    -      -       -      +
    146K  VAL*     3.8    11.0    -      -       +      -
    149K  LYS      4.8     0.2    -      -       -      +
    150K  GLY*     1.3    82.3    -      -       -      +
    152K  GLN*     1.3    58.8    +      -       -      +
    222K  PRO*     4.4    14.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 152 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41K  GLN*     2.5    25.3    +      -       -      +
     46K  VAL*     3.4     9.0    -      -       -      +
    109K  VAL*     4.3     9.7    -      -       +      +
    143K  PHE      3.9     1.0    -      -       -      +
    144K  GLY*     3.6     1.4    -      -       -      -
    145K  GLY      2.8    38.1    +      -       -      +
    147K  ASP*     3.1    31.4    +      -       -      +
    149K  LYS*     3.9    31.9    +      -       -      +
    151K  PRO*     1.3    81.3    +      -       -      +
    153K  LEU*     1.3    59.3    +      -       -      +
    154K  PHE*     4.2    20.8    -      -       +      -
    164K  GLN*     3.4    22.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 153 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39K  GLY*     3.4    32.5    -      -       -      +
     40K  ILE      3.4     7.6    -      -       -      +
     41K  GLN*     3.1    27.0    +      -       +      +
     46K  VAL*     4.2    10.3    -      -       +      -
     48K  LEU*     4.4    15.7    -      -       +      -
    142K  LEU*     4.7     4.5    -      -       +      -
    143K  PHE      3.2    24.0    -      -       -      +
    144K  GLY*     4.0     7.0    -      -       -      -
    152K  GLN*     1.3    73.8    -      -       -      +
    154K  PHE*     1.3    77.0    +      -       -      +
    164K  GLN*     4.1     0.9    -      -       -      +
    165K  CYS      2.8    28.3    +      -       -      +
    166K  ASP      3.4    18.6    -      -       -      +
    168K  ARG*     4.5     8.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 154 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109K  VAL*     3.6    27.6    -      -       +      -
    110K  GLU*     3.5    39.5    -      -       +      -
    113K  THR*     3.9    11.0    -      -       -      +
    142K  LEU*     3.4     5.7    -      -       -      +
    143K  PHE*     2.6    50.5    +      -       +      +
    147K  ASP*     5.3     3.1    -      -       -      -
    149K  LYS*     5.8     4.9    -      -       -      -
    152K  GLN*     4.2    20.0    -      -       +      -
    153K  LEU*     1.3    91.0    -      -       -      +
    155K  HIS*     1.3    59.8    +      -       -      +
    162K  PHE*     3.5    27.4    -      +       +      -
    163K  VAL      4.5     1.6    -      -       -      -
    164K  GLN*     3.6    36.3    -      -       +      -
    165K  CYS*     4.9     1.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 155 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140K  ALA*     4.3     7.0    -      -       +      -
    141K  LEU      3.5     2.9    +      -       -      -
    142K  LEU*     3.4    16.6    -      -       +      +
    143K  PHE*     6.0     0.7    -      -       -      -
    154K  PHE*     1.3    75.9    -      -       -      +
    156K  MET*     1.3    91.8    +      -       -      +
    157K  ASP*     4.5     7.7    +      -       +      +
    161K  THR      6.0     0.2    -      -       -      -
    162K  PHE*     3.4     5.5    -      -       -      -
    163K  VAL*     2.9    54.8    +      -       +      +
    165K  CYS*     4.0     9.3    -      -       +      +
    168K  ARG*     3.7    44.1    +      -       +      -
    170K  ILE*     4.0    22.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 156 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113K  THR*     5.1     4.7    -      -       +      +
    116K  VAL*     3.5    45.5    -      -       +      +
    117K  SER*     4.8     5.2    -      -       -      +
    120K  ALA*     4.8     5.2    -      -       +      -
    139K  VAL      6.0     0.4    -      -       -      +
    140K  ALA*     3.7     0.7    -      -       -      +
    141K  LEU*     2.9    55.8    +      -       +      +
    143K  PHE*     4.2    14.8    -      -       +      -
    155K  HIS*     1.3    90.4    +      -       -      +
    157K  ASP*     1.3    81.5    +      -       -      +
    158K  PRO*     5.4     1.6    -      -       +      -
    160K  GLY*     4.2    15.0    -      -       -      -
    161K  THR      4.0     9.9    -      -       -      +
    162K  PHE*     4.7    11.4    -      -       +      -
----------------------------------------------------------
 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