Contacts of the helix formed by residues 181 - 195 (chain A) in PDB entry 3PEI
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 THR 181 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ALA 3.9 0.9 - - - +
178A ASN* 3.7 21.5 - - - +
179A ILE 3.1 4.9 + - - +
180A CYS* 1.3 77.0 - - - +
182A THR* 1.3 60.6 + - - +
183A ASP* 3.6 10.5 + - - +
184A TYR* 2.9 33.0 + - - +
185A MSE 2.9 14.1 + - - +
226A MSE 3.4 35.4 - - + -
253A VAL* 4.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A THR* 1.3 72.9 - - - +
183A ASP* 1.3 65.6 + - - +
185A MSE 3.3 9.1 + - - +
186A LEU* 3.0 22.9 + - - +
226A MSE 3.6 22.9 - - + +
227A SER 2.7 31.8 + - - +
229A TYR* 3.8 12.2 - - - -
253A VAL* 4.2 9.8 - - + +
302A LEU* 3.8 13.6 - - + +
303A ALA* 3.6 38.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A THR* 3.1 9.7 + - - +
182A THR* 1.3 78.8 + - - +
184A TYR* 1.3 66.1 + - - +
186A LEU* 3.1 7.9 + - - +
187A ASN* 2.9 24.6 + - - +
190A ARG* 5.8 0.2 + - - -
226A MSE 6.4 0.9 - - - -
227A SER* 5.1 3.0 + - - -
229A TYR* 3.0 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLN* 4.4 12.1 + - - -
172A LEU* 4.2 6.0 - - + +
175A LEU* 3.4 34.7 - - + +
179A ILE* 3.4 34.3 - - + +
180A CYS* 4.2 11.4 - - - -
181A THR* 2.9 20.0 + - - +
183A ASP* 1.3 76.5 - - - +
185A MSE 1.3 60.0 + - - +
187A ASN* 3.3 9.9 + - + +
188A GLU* 2.9 60.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 4.0 24.9 - - + -
180A CYS* 3.8 22.2 - - - -
181A THR 2.9 13.9 + - - +
182A THR* 3.7 7.4 - - - +
183A ASP 3.2 0.2 - - - -
184A TYR* 1.3 76.9 - - - +
186A LEU* 1.3 66.4 + - - +
188A GLU* 3.2 8.3 + - + +
189A ALA 3.1 17.0 + - - -
274A MSE 3.7 28.0 - - + -
277A VAL* 4.5 8.5 - - + -
281A MSE 3.7 32.1 - - + -
300A MSE 3.8 29.4 - - + +
302A LEU* 3.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A THR 3.0 16.8 + - - +
183A ASP* 3.1 6.9 + - - +
185A MSE 1.3 75.5 - - - +
187A ASN* 1.3 58.5 + - - +
189A ALA* 3.1 7.7 + - - +
190A ARG* 2.9 55.4 + - - +
201A LEU* 4.9 4.7 - - + -
203A TYR* 4.1 28.5 - - + +
229A TYR* 3.9 35.0 - - + +
231A VAL* 3.6 30.7 - - + -
302A LEU* 4.4 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ASP 2.9 12.9 + - - +
184A TYR* 3.5 12.6 + - - +
186A LEU* 1.3 74.8 - - - +
188A GLU* 1.3 66.6 + - - +
190A ARG* 3.1 21.3 + - - +
191A GLU* 2.8 64.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR* 2.9 37.6 + - - +
172A LEU* 4.0 9.9 - - + +
184A TYR* 2.9 56.6 + - + +
185A MSE 3.2 14.1 + - + +
187A ASN* 1.3 81.2 + - - +
189A ALA* 1.3 59.5 + - - +
191A GLU* 3.2 19.5 + - - +
192A LEU* 2.9 31.0 + - - +
281A MSE 3.7 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A MSE 3.1 12.2 + - - +
186A LEU 3.4 8.5 - - - +
188A GLU* 1.3 77.8 - - - +
190A ARG* 1.3 56.9 + - - +
192A LEU* 3.8 0.5 - - - +
193A THR* 2.8 35.7 + - - +
201A LEU* 4.1 7.6 - - + -
231A VAL* 3.7 28.7 - - + -
233A MSE 4.0 16.4 - - - -
281A MSE 4.0 9.4 - - - +
300A MSE 4.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 2.9 37.7 + - + +
187A ASN* 3.1 26.2 + - - +
189A ALA* 1.3 77.6 - - - +
191A GLU* 1.3 58.1 + - + +
193A THR* 3.3 7.7 + - - -
194A SER* 2.9 32.3 + - - -
201A LEU* 3.5 20.2 - - + +
203A TYR* 2.9 35.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ASN* 2.8 49.6 + - - +
188A GLU* 3.8 16.6 - - - +
190A ARG* 1.3 73.6 - - + +
192A LEU* 1.3 59.0 + - - +
194A SER* 2.9 20.6 + - - -
195A LYS* 3.1 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR* 4.6 5.4 - - + +
188A GLU 2.9 16.8 + - - +
189A ALA* 3.9 2.7 - - - +
191A GLU* 1.3 75.9 - - - +
193A THR* 1.3 65.8 + - - +
195A LYS* 3.3 12.5 + - + +
196A TYR* 3.7 22.9 - - + -
199A PHE* 3.7 20.0 - - + -
233A MSE 4.2 7.2 - - - -
281A MSE 3.4 43.7 - - + +
284A MSE 4.0 18.2 - - + -
285A LYS* 4.1 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ALA 2.8 24.1 + - - +
190A ARG* 3.3 10.6 + - - -
192A LEU* 1.3 78.8 - - - +
194A SER* 1.3 60.4 + - - +
195A LYS 3.2 0.9 + - - -
196A TYR 3.5 2.6 - - - +
199A PHE* 3.5 36.9 - - + +
200A SER* 3.9 15.9 - - - +
201A LEU* 3.7 18.6 - - + +
233A MSE 3.6 26.9 - - + -
490A K 2.9 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ARG 2.9 14.9 + - - -
191A GLU* 2.9 20.3 + - - -
193A THR* 1.3 78.0 + - - +
195A LYS* 1.3 65.0 + - - +
196A TYR 3.5 2.1 + - - -
490A K 4.4 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLU* 3.1 23.1 - - - +
192A LEU* 3.3 6.0 + - + +
193A THR 3.1 1.8 - - - -
194A SER* 1.3 82.2 - - - +
196A TYR* 1.3 84.8 + - + +
----------------------------------------------------------
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