Contacts of the helix formed by residues 213 - 233 (chain A) in PDB entry 1IR1
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 ARG 213 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A SER* 3.5 19.0 + - - +
209A GLN* 3.4 31.0 + - - +
210A PRO* 3.7 29.6 + - - +
212A MET* 1.3 74.5 - - - +
214A TRP* 1.3 67.1 + - + +
215A ARG* 3.4 3.8 - - + +
216A ASP* 3.3 25.2 + - - +
217A ARG* 3.2 19.7 + - - +
146D LYS* 5.1 4.8 - - - +
149D GLN 5.5 3.8 + - - -
285D ARG* 3.8 45.8 - - - +
372D PRO* 6.2 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASN 3.6 16.6 - - - +
208A SER* 3.2 22.3 + - - +
212A MET 3.9 0.4 + - - -
213A ARG* 1.3 73.6 - - + +
215A ARG* 1.3 95.4 + - + +
217A ARG* 3.2 17.6 + - - +
218A PHE* 2.9 44.5 + + + -
252A LYS* 3.8 29.4 - - + -
253A ARG* 3.6 59.8 - - + +
256A PHE* 3.8 30.7 - + + -
286D ASP* 5.0 14.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ARG* 3.4 2.5 - - + +
214A TRP* 1.3 105.1 - - + +
216A ASP* 1.3 67.0 + - - +
218A PHE* 3.4 2.7 + - - +
219A LEU* 3.0 42.0 + - - +
256A PHE* 3.3 49.0 - - + -
161D LYS* 5.6 1.0 - - - +
258D ARG* 3.7 21.0 - - - +
285D ARG* 3.7 21.5 - - - +
286D ASP* 3.1 25.5 + - - +
287D ASN* 3.6 17.6 + - - +
288D GLY* 3.6 17.1 - - - +
58V SER* 4.8 7.9 + - - -
59V PRO 4.6 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ALA* 3.6 20.2 - - + -
213A ARG* 3.3 24.3 + - - +
214A TRP 3.3 0.4 - - - -
215A ARG* 1.3 78.9 + - - +
217A ARG* 1.3 64.2 + - - +
219A LEU* 3.3 5.9 + - - +
220A PHE* 3.0 28.9 + - + -
152D PRO 5.2 1.9 - - - +
153D HIS* 3.6 13.2 + - - -
157D VAL* 3.6 29.2 - - + +
161D LYS* 3.0 29.7 + - - +
285D ARG* 6.1 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ALA* 3.8 11.1 - - - +
185A TYR* 3.8 11.7 - - + -
202A ASP* 2.9 40.1 + - - +
206A VAL* 3.4 24.5 + - - +
207A ASN 2.9 30.5 + - - -
209A GLN* 5.5 0.2 + - - -
212A MET* 3.6 37.2 + - - +
213A ARG 3.2 4.0 + - - +
214A TRP* 3.2 13.9 + - - +
216A ASP* 1.3 79.5 - - - +
218A PHE* 1.3 85.0 + - + +
219A LEU 3.2 0.2 + - - -
220A PHE* 3.3 0.7 + - - +
221A CYS* 2.8 43.4 + - - +
240A LEU* 5.1 0.9 - - + +
241A ASN 4.0 6.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A TRP* 2.9 52.6 + + + +
215A ARG 3.7 4.5 - - - +
217A ARG* 1.3 101.3 - - - +
219A LEU* 1.3 64.6 + - - +
221A CYS* 3.5 1.4 + - - +
222A ALA* 3.0 24.4 + - - +
240A LEU* 3.7 50.8 - - + +
241A ASN 3.6 19.5 - - - -
242A ALA* 4.9 0.9 - - + -
253A ARG* 3.4 30.5 - - + -
256A PHE* 3.8 18.8 - + + -
257A ALA* 4.5 7.6 - - + -
260A LEU* 3.7 8.0 - - + +
265A VAL* 5.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ARG* 3.0 34.2 + - - +
216A ASP* 3.5 4.9 - - - +
218A PHE* 1.3 79.2 - - - +
220A PHE* 1.3 69.2 + - + +
222A ALA* 3.3 6.1 + - - +
223A GLU* 3.3 17.0 + - - +
256A PHE* 4.3 8.4 - - + -
260A LEU* 4.7 5.8 - - + -
161D LYS* 4.1 23.6 - - + +
288D GLY* 5.9 0.2 - - - -
58V SER* 5.1 2.2 - - - +
59V PRO 3.9 20.9 - - - +
60V GLY 3.7 13.9 - - - +
61V TYR* 4.0 20.5 - - + +
65V ARG* 3.4 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ALA* 3.6 32.8 - - + +
183A LYS* 4.1 13.2 - - + -
186A GLY* 4.4 1.8 - - - +
216A ASP* 3.0 27.2 + - + +
217A ARG 4.0 0.9 - - - +
219A LEU* 1.3 77.7 - - + +
221A CYS* 1.3 61.9 + - - +
223A GLU* 3.3 3.9 + - - +
224A ALA* 3.1 18.7 + - - +
157D VAL* 5.3 3.6 - - + -
160D ASP* 3.7 41.7 - - + -
161D LYS* 3.9 28.9 - - + -
65V ARG* 3.9 27.1 - - + -
66V TYR* 3.4 41.0 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A TYR* 4.0 13.5 - - - -
186A GLY* 4.5 6.7 - - - -
189A VAL* 4.1 13.9 - - + +
217A ARG* 2.8 35.0 + - - +
218A PHE 4.0 2.9 - - - +
220A PHE* 1.3 74.6 - - - +
222A ALA* 1.3 61.3 + - - +
224A ALA* 3.7 7.1 - - - +
225A LEU* 2.9 35.1 + - + +
238A HIS* 3.8 37.9 - - + -
240A LEU* 4.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A PHE 3.0 14.3 + - - +
219A LEU 3.5 9.6 - - - +
220A PHE 3.2 0.2 - - - -
221A CYS* 1.3 75.6 - - - +
223A GLU* 1.3 65.9 + - - +
225A LEU* 3.3 11.5 + - - +
226A TYR* 3.0 44.3 + - + -
240A LEU* 6.1 0.4 - - - +
260A LEU* 4.1 21.3 - - + -
262A VAL* 4.5 6.3 - - + -
61V TYR* 4.3 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A LEU 3.3 9.4 + - - +
220A PHE* 3.6 10.4 - - - +
222A ALA* 1.3 79.7 - - - +
224A ALA* 1.3 61.4 + - - +
226A TYR* 3.5 2.1 + - - +
227A LYS* 3.1 25.2 + - + +
61V TYR* 3.5 16.5 - - + +
62V TYR 3.2 18.2 - - - +
63V ASP* 4.0 14.7 - - - +
64V GLY 3.5 5.0 + - - +
65V ARG* 2.9 58.3 + - - +
66V TYR* 3.2 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLY* 3.1 31.9 - - - +
189A VAL* 4.1 4.3 - - + -
190A TYR* 3.7 22.3 - - + +
220A PHE 3.1 15.7 + - - +
221A CYS 3.7 4.3 - - - +
223A GLU* 1.3 75.7 - - - +
225A LEU* 1.3 63.4 + - - +
227A LYS* 3.3 5.2 + - - +
228A ALA* 3.0 24.8 + - - +
66V TYR* 4.0 9.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A VAL* 4.9 2.0 - - + -
193A LEU* 3.8 26.2 - - + +
221A CYS* 2.9 24.6 + - + +
222A ALA* 3.6 8.1 - - - +
224A ALA* 1.3 74.8 - - - +
226A TYR* 1.3 84.7 + - + +
228A ALA* 3.5 1.6 + - - +
229A GLN* 3.0 32.6 + - - +
236A LYS* 4.1 22.6 - - + +
237A GLY* 4.7 1.6 - - - -
238A HIS* 4.2 26.9 - - + +
240A LEU* 6.0 2.5 - - + -
262A VAL* 3.9 26.2 - - + -
263A PRO* 4.9 4.3 - - + -
62S TYR* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ALA* 3.0 37.7 + - + +
223A GLU 4.0 2.9 - - - +
225A LEU* 1.3 89.9 - - + +
227A LYS* 1.3 65.0 + - - +
229A GLN* 3.8 19.8 - - - +
230A ALA* 3.1 24.4 + - - +
260A LEU* 2.7 28.8 + - + -
261A GLY 3.4 10.2 - - - -
262A VAL* 3.6 8.3 + - + -
263A PRO* 6.0 0.2 - - + -
53S ARG* 3.1 29.3 + - - -
62S TYR* 5.6 4.7 - + - -
55V HIS* 3.6 63.2 + + + +
56V HIS* 6.1 0.7 - - + -
61V TYR* 3.9 5.4 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A TYR* 3.6 41.1 - - + -
223A GLU* 3.1 20.2 + - + +
224A ALA* 3.6 5.8 - - - +
226A TYR* 1.3 76.2 - - - +
228A ALA* 1.3 63.6 + - - +
230A ALA* 3.4 6.0 + - - +
231A GLU* 3.0 25.7 + - + +
45V GLU* 3.0 31.5 + - - -
48V HIS* 5.9 3.2 + - - +
52V TYR* 5.9 2.8 + - - +
64V GLY* 5.5 5.8 - - - +
66V TYR* 3.0 37.5 + - + +
67V TRP* 4.4 2.2 - - - +
68V THR* 4.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A TYR* 3.9 16.1 - - + +
193A LEU* 3.5 33.0 - - + -
194A ARG* 3.9 11.2 - - - +
224A ALA 3.0 16.4 + - - +
225A LEU 3.8 4.0 - - - +
227A LYS* 1.3 78.6 - - - +
229A GLN* 1.3 62.2 - - - +
231A GLU* 3.3 2.9 + - - +
232A THR* 3.0 30.8 + - - +
236A LYS* 4.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 3.0 22.2 + - - +
226A TYR* 3.8 17.3 - - - +
227A LYS 3.3 0.2 - - - -
228A ALA* 1.3 78.7 - - - +
230A ALA* 1.3 57.2 + - - +
233A GLY* 2.8 30.1 + - - -
234A GLU 3.5 22.7 - - - +
235A ILE* 3.6 14.4 - - - +
236A LYS* 3.2 28.8 + - + +
51S VAL* 4.3 17.1 + - + +
52S TYR* 6.1 1.2 - - - +
53S ARG* 5.6 3.8 - - - +
62S TYR* 3.7 28.2 + - - -
55V HIS* 6.3 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A TYR 3.1 18.1 + - - +
227A LYS* 3.7 6.3 - - - +
229A GLN* 1.3 77.1 - - - +
231A GLU* 1.3 62.1 + - - +
233A GLY* 4.9 0.6 - - - -
10S LYS* 3.2 22.9 + - - -
55V HIS* 5.3 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A TYR* 2.5 30.2 + - - -
194A ARG* 2.9 44.1 + - - +
227A LYS* 3.0 18.6 + - + +
228A ALA* 3.6 5.6 - - - +
229A GLN 3.2 0.2 - - - -
230A ALA* 1.3 78.8 - - - +
232A THR* 1.3 60.2 + - + +
4S TRP* 5.2 0.3 - - - -
5S PRO 4.1 1.6 - - - +
6S THR* 4.0 33.2 - - - +
9S MET* 4.3 12.3 + - + +
10S LYS* 3.4 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU 4.4 0.4 - - - +
194A ARG* 3.6 35.2 - - + +
228A ALA 3.0 17.6 + - - +
231A GLU* 1.3 84.7 - - + +
233A GLY* 1.3 61.5 + - - +
234A GLU* 3.2 16.4 + - - -
236A LYS* 3.3 22.1 - - - +
9S MET 4.6 6.7 - - - +
10S LYS* 3.5 3.5 - - - -
11S ARG* 2.8 36.8 + - + +
17S TYR* 4.9 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLN 2.8 18.4 + - - -
230A ALA* 4.2 0.6 + - - -
231A GLU 3.7 1.2 - - - -
232A THR* 1.3 74.4 - - - +
234A GLU* 1.3 61.9 + - - +
235A ILE 4.4 0.3 + - - -
10S LYS* 4.0 15.3 - - - +
11S ARG 4.4 2.4 - - - +
50S PHE* 4.0 25.8 - - - +
51S VAL* 4.4 15.8 + - - +
----------------------------------------------------------
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