Contacts of the helix formed by residues 182 - 191 (chain M) in PDB entry 5X6E
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 HIS 182 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172M GLN* 6.0 0.9 - - - -
180M ILE* 3.5 3.0 + - - +
181M ALA* 1.3 92.1 + - + +
183M SER* 1.3 64.3 + - - +
184M SER* 3.3 7.4 + - - +
185M ALA* 3.4 7.4 + - + +
186M VAL* 3.3 20.9 + - - +
18O G 3.6 20.9 - - + -
19O T 2.7 66.3 + + + -
20O T 4.0 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 183 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171M MET* 3.2 28.8 - - - +
172M GLN* 3.8 41.9 + - - +
182M HIS* 1.3 72.9 - - - +
184M SER* 1.3 62.4 + - - +
186M VAL* 3.6 3.9 + - - -
187M SER 3.3 2.3 + - - -
7P C 6.5 0.7 - - - -
8P A 5.6 7.0 - - - -
9P T 3.6 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182M HIS* 3.8 1.2 - - - +
183M SER* 1.3 77.3 - - - +
185M ALA* 1.3 64.3 + - - -
187M SER* 3.0 5.5 + - - -
188M ARG* 2.9 28.4 + - - +
19O T 3.3 18.2 - - - +
20O T 3.0 36.1 + - - +
21O A 4.0 4.5 - - - -
9P T 4.2 8.0 + - - +
10P T 3.5 24.9 - - - +
11P A 4.3 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180M ILE* 3.6 23.8 - - + -
182M HIS* 3.4 4.3 + - + +
184M SER* 1.3 80.5 + - - +
186M VAL* 1.3 60.6 + - - +
188M ARG* 3.5 29.0 + - - +
189M ILE* 3.3 27.1 + - + +
17O T 4.4 9.2 - - + +
18O G 4.8 1.8 - - + +
19O T 3.5 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M ILE* 4.5 10.8 - - + -
171M MET* 3.6 32.1 - - + +
172M GLN* 5.7 0.4 - - - -
174M LEU* 4.7 4.0 - - + -
175M GLY* 3.7 24.0 - - - +
180M ILE* 3.5 23.3 - - + -
182M HIS 3.3 16.8 - - - +
183M SER* 3.9 1.3 - - - +
184M SER 3.2 1.0 - - - -
185M ALA* 1.3 75.6 - - - +
187M SER* 1.3 52.4 + - - +
189M ILE* 2.9 7.2 + - - +
190M ILE* 2.7 52.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 187 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171M MET* 3.3 21.0 - - - +
183M SER 3.3 3.5 + - - -
184M SER 3.0 8.6 + - - -
186M VAL* 1.3 75.1 - - - +
188M ARG* 1.3 65.8 + - - +
189M ILE 3.2 0.5 + - - -
190M ILE* 3.3 13.6 + - - +
191M SER* 3.4 17.7 + - - -
9P T 3.7 40.7 + - - +
10P T 3.7 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 188 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184M SER 2.9 10.9 + - - +
185M ALA* 3.5 34.6 + - - +
187M SER* 1.3 76.6 - - - +
189M ILE* 1.3 61.3 + - - +
191M SER* 5.0 0.3 + - - -
192M LYS* 3.0 22.5 + - + +
17O T 3.3 57.4 - - - +
18O G 2.7 41.4 + - - -
19O T 3.2 13.1 + - - +
10P T 4.7 5.0 - - + +
12P A 4.3 6.5 - - - +
13P C 5.9 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 189 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M LYS* 4.3 12.6 - - + +
140M LEU* 4.6 20.6 - - + +
143M ILE* 4.3 13.0 - - + -
180M ILE* 3.7 28.3 - - + -
185M ALA 3.3 17.7 - - - +
186M VAL* 2.9 7.2 + - - +
188M ARG* 1.3 88.6 - - + +
190M ILE* 1.3 53.3 + - + +
191M SER 3.4 1.1 - - - -
192M LYS* 2.9 14.1 - - + -
193M LEU* 2.6 48.5 + - + +
17O T 4.5 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 190 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M ILE* 4.2 25.6 - - + -
147M LEU* 5.4 3.6 - - + -
171M MET* 4.1 11.4 - - + -
174M LEU* 4.6 11.4 - - + -
186M VAL* 2.7 42.0 + - + +
187M SER* 3.3 8.0 + - - +
189M ILE* 1.3 70.3 - - + +
191M SER* 1.3 61.5 + - - +
193M LEU* 2.9 30.5 - - + +
194M LYS 3.3 0.3 + - - -
199M ILE* 5.0 2.4 - - - +
206M PHE* 4.4 27.0 - - + -
9P T 3.8 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 191 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187M SER* 3.4 10.3 + - - -
188M ARG 5.0 0.2 + - - -
190M ILE* 1.3 81.2 - - - +
192M LYS* 1.3 59.4 + - - +
193M LEU 2.7 4.3 - - - +
194M LYS* 3.2 15.4 + - - +
195M GLN 3.6 9.9 + - - -
9P T 6.1 1.6 - - - -
10P T 3.4 21.8 + - - -
----------------------------------------------------------
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