Contacts of the helix formed by residues 173 - 195 (chain A) in PDB entry 3QN3
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 SER 173 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 3.5 5.6 - - - +
172A THR* 1.3 85.0 + - - +
174A PHE* 1.3 64.2 + - - +
175A LYS* 3.6 4.6 + - - +
176A GLU* 3.1 31.9 + - - +
177A ALA* 3.1 22.5 + - - +
403A GLU* 4.0 9.0 - - - -
407A ASP* 5.2 3.6 - - - -
409A TYR* 3.9 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.6 26.4 - - + +
142A PRO 3.8 24.7 - - - -
144A PRO* 4.5 13.7 - - + -
173A SER* 1.3 71.1 - - - +
175A LYS* 1.3 58.6 + - - +
177A ALA* 3.1 3.0 + - + +
178A LEU* 2.8 54.8 + - + +
396A TYR* 4.2 6.5 - + - -
399A LEU* 3.6 46.2 - - + -
400A LEU* 3.9 19.5 - - + -
403A GLU* 3.3 21.1 + - - +
407A ASP 5.1 0.4 + - - -
409A TYR* 3.7 24.0 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A SER* 3.4 4.9 - - - +
174A PHE* 1.3 75.1 - - - +
176A GLU* 1.3 63.4 + - + +
178A LEU* 3.5 2.1 + - - +
179A ARG* 3.0 27.0 + - - +
400A LEU* 3.9 23.3 - - + -
403A GLU* 3.0 25.8 + - - +
404A PHE* 5.9 7.5 - - + -
10B TYR* 6.0 0.2 - - - +
11B GLU* 3.0 45.2 + - - +
57B ARG* 3.6 13.7 - - - +
58B PHE* 5.4 4.0 - - + -
64B LEU* 3.8 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 3.8 20.1 - - + -
172A THR 5.8 0.2 - - - +
173A SER* 3.1 25.5 + - - +
175A LYS* 1.3 81.4 - - + +
177A ALA* 1.3 65.0 + - - +
179A ARG* 2.9 46.8 + - - +
180A SER* 3.1 22.5 + - - -
230A TYR* 5.1 1.2 + - - -
57B ARG* 5.0 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PRO* 5.3 1.6 - - + -
168A PRO* 3.6 21.9 - - + +
171A PHE* 3.8 15.1 - - + -
173A SER 3.1 14.7 + - - +
174A PHE* 3.4 9.4 - - + +
176A GLU* 1.3 76.5 - - - +
178A LEU* 1.3 60.3 + - - +
180A SER* 2.7 21.9 + - - -
181A VAL* 3.3 3.6 + - - +
409A TYR* 3.5 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PRO* 5.4 3.6 - - + -
168A PRO* 5.5 0.2 - - - -
174A PHE* 2.8 34.0 + - + +
175A LYS 3.8 4.3 - - - +
177A ALA* 1.3 71.8 - - - +
179A ARG* 1.3 66.9 + - - +
181A VAL* 3.2 12.2 + - + +
182A CYS* 3.0 28.5 + - - -
387A LEU* 3.9 17.5 - - + -
396A TYR* 3.5 39.3 - - + -
400A LEU* 3.7 40.2 - - + -
13B LEU* 4.2 15.7 - - + -
58B PHE* 6.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LYS 3.0 18.8 + - - +
176A GLU* 2.9 43.5 + - - +
178A LEU* 1.3 76.2 - - - +
180A SER* 1.3 56.5 + - - +
182A CYS* 3.1 2.8 + - - +
183A GLU* 2.8 69.8 + - - +
230A TYR* 3.5 12.0 + - - -
56B GLU* 4.5 5.3 + - - +
57B ARG* 4.0 30.2 - - - +
58B PHE* 3.6 43.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PRO* 3.5 9.0 - - - +
171A PHE* 3.3 32.6 - - - -
176A GLU 3.1 7.9 + - - -
177A ALA 2.7 18.9 + - - -
179A ARG* 1.3 75.2 - - - +
181A VAL* 1.3 60.1 + - - +
183A GLU* 3.4 1.6 + - - +
184A ILE* 2.9 35.0 + - - +
230A TYR* 3.6 31.6 + - - -
234A VAL* 4.0 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PRO* 5.2 0.9 - - + -
146A CYS* 4.0 11.0 - - - -
166A ILE* 3.7 34.5 - - + +
168A PRO* 3.7 35.9 - - + -
177A ALA 4.0 4.5 - - - +
178A LEU* 3.2 21.7 + - + +
180A SER* 1.3 85.3 + - - +
182A CYS* 1.3 57.5 - - - +
184A ILE* 3.8 1.3 - - - +
185A TYR* 2.9 29.8 + - - +
234A VAL* 5.0 3.8 - - + -
387A LEU* 3.7 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 3.0 20.2 + - - +
179A ARG 3.5 7.0 - - - +
181A VAL* 1.3 76.3 - - - +
183A GLU* 1.3 56.9 + - - +
185A TYR* 3.4 5.8 + - - +
186A ALA* 3.1 27.5 + - - +
387A LEU* 3.9 22.0 - - - -
13B LEU* 3.6 41.3 - - - -
17B GLY 4.2 10.0 - - - +
58B PHE* 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 2.8 43.5 + - + +
180A SER 3.8 3.4 - - - +
182A CYS* 1.3 73.1 - - - +
184A ILE* 1.3 63.3 + - - +
186A ALA* 3.3 7.5 + - - +
187A ILE* 3.1 31.4 + - + +
228A ALA* 4.8 5.5 - - + +
230A TYR* 2.5 37.7 + - + -
56B GLU 4.0 4.8 - - - +
57B ARG* 3.6 0.9 - - - -
58B PHE* 2.8 39.8 + - + +
59B GLY 4.8 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ILE* 4.7 6.5 - - + -
166A ILE* 3.9 22.7 - - + -
180A SER 2.9 26.4 + - - +
181A VAL* 3.9 3.8 - - - +
183A GLU* 1.3 74.6 - - - +
185A TYR* 1.3 57.7 + - - +
187A ILE* 3.1 4.7 + - - +
188A LEU* 2.9 28.6 + - - +
221A LEU* 4.9 1.6 - - - +
224A CYS* 3.9 26.1 - - + +
225A ILE* 4.0 19.7 - - + +
228A ALA* 3.4 25.6 - - + -
230A TYR* 4.1 7.4 - - + -
234A VAL* 3.9 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ILE* 3.7 28.2 - - + +
181A VAL 2.9 19.6 + - - +
182A CYS* 3.5 6.7 - - - +
183A GLU 3.4 0.2 - - - -
184A ILE* 1.3 76.2 - - - +
186A ALA* 1.3 58.8 + - + +
188A LEU* 3.5 6.2 + - - +
189A LYS* 2.9 35.4 + - + +
201A LEU* 3.4 16.6 - - - +
205A GLY 2.7 29.2 + - - -
207A PHE* 3.5 31.1 - + - -
386A ALA* 3.8 11.9 - - + -
387A LEU* 4.1 21.3 - - + -
388A ALA* 3.4 25.5 - - + +
16B ARG 4.3 10.5 - - - -
17B GLY* 5.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A CYS 3.1 16.1 + - - +
183A GLU* 3.7 8.3 - - - +
184A ILE 3.3 0.2 - - - -
185A TYR* 1.3 77.2 - - + +
187A ILE* 1.3 66.7 + - + +
189A LYS* 3.4 10.1 + - - +
190A LYS* 3.1 23.2 + - - +
18B ASN* 5.9 5.4 - - - +
58B PHE 6.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLU* 3.1 12.7 + - + +
184A ILE* 3.1 7.6 + - - +
186A ALA* 1.3 76.6 - - + +
188A LEU* 1.3 59.7 + - - +
190A LYS* 3.1 10.0 + - + +
191A GLU* 2.8 35.0 + - + +
224A CYS* 4.0 24.5 - - + -
227A LYS* 4.1 19.3 - - + +
228A ALA* 3.5 41.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ILE* 3.8 31.4 - - + -
149A ILE* 3.9 13.7 - - + -
184A ILE 2.9 17.2 + - - +
185A TYR* 3.6 4.3 - - - +
187A ILE* 1.3 76.9 - - - +
189A LYS* 1.3 63.2 + - - +
191A GLU* 3.1 2.3 + - + +
192A LEU* 2.9 30.3 + - + +
207A PHE* 3.7 28.5 - - + -
220A LEU* 3.4 42.6 - - + +
221A LEU* 4.6 2.0 - - + -
224A CYS* 3.6 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A TYR* 2.9 26.8 + - + +
186A ALA* 3.5 10.5 - - - +
187A ILE 3.3 0.2 - - - -
188A LEU* 1.3 75.4 - - - +
190A LYS* 1.3 58.4 + - - +
192A LEU* 3.5 2.0 + - - +
193A ALA* 3.1 27.8 + - + +
199A THR* 3.6 29.6 + - + +
207A PHE* 3.7 26.4 - - + -
16B ARG* 5.1 16.5 + - - +
203B ASP* 4.2 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ALA 3.1 13.6 + - - +
187A ILE* 3.5 11.7 - - + +
189A LYS* 1.3 75.0 - - - +
191A GLU* 1.3 68.7 + - - +
193A ALA* 3.3 6.1 + - + +
194A ASN* 3.0 44.9 + - - +
----------------------------------------------------------
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 ILE* 2.8 28.0 + - + +
188A LEU* 3.1 8.0 + - - +
190A LYS* 1.3 77.4 - - - +
192A LEU* 1.3 64.3 + - + +
194A ASN* 3.3 9.8 + - - +
195A SER* 2.9 31.5 + - - +
220A LEU* 4.6 15.6 - - + +
223A THR* 4.5 6.6 - - - +
224A CYS* 4.1 16.8 - - - -
227A LYS* 3.0 37.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
149A ILE* 5.8 1.1 - - + -
188A LEU* 2.9 27.0 + - + +
189A LYS 3.7 4.0 - - - +
191A GLU* 1.3 77.2 - - - +
193A ALA* 1.3 63.1 + - - +
195A SER* 3.2 8.4 + - - -
197A HIS* 3.0 58.2 + - + +
198A SER 4.3 9.4 - - - +
199A THR* 4.4 2.7 - - + -
207A PHE* 3.3 52.7 - - + -
209A PRO* 4.1 14.1 - - + -
211A LEU* 5.9 0.2 - - + -
220A LEU* 4.1 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LYS* 3.1 17.8 + - + +
190A LYS* 3.8 7.4 - - + +
191A GLU 3.3 0.2 - - - -
192A LEU* 1.3 75.6 - - - +
194A ASN* 1.3 66.2 + - - +
196A GLY* 3.3 12.8 + - - -
197A HIS 4.0 9.9 - - - +
199A THR* 3.8 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LYS* 3.0 46.2 + - - +
191A GLU* 4.0 10.4 + - - +
193A ALA* 1.3 79.0 - - - +
195A SER* 1.3 58.1 + - - +
196A GLY 3.3 2.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLU* 2.9 21.8 + - - +
192A LEU 3.2 2.6 + - - -
194A ASN* 1.3 77.2 - - - +
196A GLY* 1.3 62.1 + - - +
197A HIS* 3.3 23.9 + - - -
----------------------------------------------------------
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