Contacts of the helix formed by residues 173 - 185 (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.
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 ALA 173 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K LYS* 4.7 1.6 - - - +
36K THR* 4.4 10.3 - - + +
172K SER* 1.3 80.2 + - - +
174K SER* 1.3 49.6 + - - +
175K GLU 3.1 3.8 - - - -
176K GLY* 2.7 11.7 + - - +
177K ALA* 2.5 37.1 + - + +
205K VAL* 3.7 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 174 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K THR* 4.5 0.4 + - - -
168K ARG* 5.1 3.8 + - - -
169K ALA* 2.5 42.1 + - - +
170K ILE* 3.3 24.5 + - - -
171K GLY 4.2 4.9 - - - -
172K SER 3.1 2.8 + - - -
173K ALA* 1.3 77.3 - - - +
175K GLU* 1.3 57.2 + - - +
177K ALA* 3.9 0.9 - - - -
178K GLN* 2.9 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 175 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K LYS* 6.1 0.4 - - - +
172K SER 4.2 5.4 + - - +
173K ALA 3.1 1.3 - - - -
174K SER* 1.3 80.4 - - - +
176K GLY* 1.3 72.6 + - - +
178K GLN* 4.2 4.2 - - - +
179K SER* 3.5 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 176 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173K ALA* 2.7 16.8 + - - +
175K GLU* 1.3 86.3 + - - +
177K ALA* 1.3 56.0 + - - -
179K SER* 3.1 23.4 - - - -
180K SER* 3.5 10.0 + - - -
201K ILE* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 177 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K THR* 5.1 1.8 - - - +
38K ILE* 3.7 29.6 - - + +
169K ALA* 3.8 15.3 - - + -
173K ALA* 2.5 23.5 + - + +
174K SER* 3.8 1.6 - - - +
175K GLU 3.2 0.2 - - - -
176K GLY* 1.3 69.5 - - - +
178K GLN* 1.3 62.7 + - - +
179K SER 3.1 1.3 - - - -
180K SER* 3.6 3.1 + - - -
181K LEU* 2.9 30.1 + - - +
201K ILE* 4.2 16.2 - - + +
205K VAL* 5.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 178 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167K ALA 3.3 12.8 + - - -
168K ARG* 3.0 42.7 - - - +
169K ALA* 2.7 33.3 + - - +
174K SER* 2.9 28.3 + - - +
175K GLU* 4.2 4.5 - - - +
177K ALA* 1.3 74.8 - - - +
179K SER* 1.3 66.7 + - - +
181K LEU* 3.1 17.7 - - - +
182K GLN* 3.0 41.4 + - - +
54L SER* 4.5 0.2 + - - -
56L LEU* 3.9 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 179 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175K GLU* 3.5 10.3 + - - -
176K GLY* 3.1 19.7 + - - -
178K GLN* 1.3 81.1 - - - +
180K SER* 1.3 62.0 + - - +
181K LEU 3.0 0.2 + - - -
182K GLN* 3.5 12.5 + - - +
183K GLU* 3.6 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 180 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176K GLY 3.5 10.9 + - - -
177K ALA 3.6 3.5 + - - -
179K SER* 1.3 79.2 - - - +
181K LEU* 1.3 63.4 + - - +
183K GLU* 3.7 10.1 - - - +
184K VAL* 3.2 23.8 + - - +
201K ILE* 3.2 34.4 - - - +
204K GLN* 4.6 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K ILE* 3.9 25.1 - - + -
40K ILE* 5.5 3.4 - - + -
167K ALA* 3.5 36.1 - - + +
177K ALA 2.9 18.9 + - - +
178K GLN* 3.1 29.6 - - - +
179K SER 3.0 1.6 - - - -
180K SER* 1.3 71.9 - - - +
182K GLN* 1.3 66.7 + - - +
183K GLU 2.8 5.7 + - - -
184K VAL* 2.9 9.8 + - - +
185K TYR* 2.9 32.9 + - + +
201K ILE* 5.0 4.0 - - + +
56L LEU* 3.6 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 182 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178K GLN* 3.0 38.7 + - - +
179K SER* 4.2 6.1 + - - +
181K LEU* 1.3 75.7 - - - +
183K GLU* 1.3 61.7 + - - +
184K VAL 3.4 0.2 - - - -
185K TYR* 3.7 22.0 + - + +
54L SER* 3.8 14.6 - - - -
55L GLU* 3.6 28.8 + - + +
56L LEU* 3.4 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 183 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179K SER 3.6 11.0 + - - +
180K SER* 3.7 14.4 - - - +
181K LEU 2.8 0.6 + - - -
182K GLN* 1.3 82.1 - - - +
184K VAL* 1.3 66.7 + - + +
185K TYR 3.8 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 184 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180K SER 3.2 19.5 - - - +
181K LEU* 2.9 12.4 + - + +
183K GLU* 1.3 83.9 - - + +
185K TYR* 1.3 61.8 + - - +
186K HIS* 3.5 8.4 - - - -
189K MET* 3.1 27.6 - - + +
197K SER* 5.3 13.0 - - - +
201K ILE* 5.4 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 185 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40K ILE* 5.1 7.2 - - + -
41K GLN 4.5 15.2 + - - -
166K ASP* 3.2 43.1 + - + +
167K ALA* 4.5 15.9 - - + -
181K LEU* 2.9 25.4 + - + +
182K GLN* 3.7 20.9 + - + +
183K GLU 3.4 2.9 - - - +
184K VAL* 1.3 80.5 - - - +
186K HIS* 1.3 87.4 + - - +
187K LYS* 4.7 7.8 - - + +
189K MET* 4.6 13.0 - - + -
56L LEU* 4.7 13.9 - - + -
----------------------------------------------------------
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