Contacts of the helix formed by residues 211 - 227 (chain D) in PDB entry 2R7I
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 TYR 211 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D ALA* 3.9 16.4 - - + -
11D VAL* 3.2 33.7 - - + -
12D TYR* 2.7 25.1 + + + -
15D VAL* 3.8 1.0 - - - +
148D HIS* 3.4 64.4 + + + +
151D GLY* 3.6 13.9 - - - -
152D ILE 3.7 17.0 - - - -
153D MET* 4.0 10.1 - - + -
182D TYR* 3.5 30.6 + + + +
210D ASP* 1.3 77.4 + - + +
212D SER* 1.3 65.7 + - - +
213D LEU 3.0 0.2 - - - -
214D ASP* 2.9 23.4 + - - +
215D MET* 3.9 2.8 + - - +
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Residues in contact with SER 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D GLU* 4.3 0.5 + - - -
210D ASP* 2.7 28.9 + - - -
211D TYR* 1.3 77.8 - - - +
213D LEU* 1.3 64.7 + - - +
215D MET* 2.9 24.1 + - - +
216D TRP 3.3 3.5 + - - -
309D HIS* 3.3 44.6 - - - +
312D ARG* 3.1 19.5 + - - -
313D LEU 5.6 0.7 - - - -
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Residues in contact with LEU 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D MET* 5.6 0.4 - - + -
155D ARG* 4.3 18.2 - - + +
192D VAL* 4.2 8.1 - - + -
193D ALA* 5.8 1.8 - - + -
197D PHE 5.2 0.4 - - - +
199D GLY* 4.0 14.8 - - - +
201D GLU* 3.7 21.3 - - - +
202D LEU* 3.8 34.5 - - + -
209D TYR* 3.5 34.8 - - + -
210D ASP 3.1 16.1 + - - +
211D TYR 3.0 0.2 + - - -
212D SER* 1.3 81.6 + - - +
214D ASP* 1.3 67.8 + - - +
216D TRP* 3.3 10.0 + - - +
217D SER* 3.4 15.2 + - - +
312D ARG* 3.9 1.1 - - - +
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Residues in contact with ASP 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D LEU* 4.3 10.2 - - + +
148D HIS* 3.0 31.5 - - + +
153D MET* 3.8 5.2 - - - -
154D HIS* 2.3 40.2 + - - +
155D ARG* 3.8 6.2 - - - -
157D VAL* 3.4 22.5 - - + +
211D TYR 2.9 10.2 + - - +
213D LEU* 1.3 78.4 - - - +
215D MET* 1.3 60.7 + - - +
217D SER* 3.3 8.2 + - - -
218D LEU* 2.9 26.5 + - - +
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Residues in contact with MET 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D LEU* 3.5 29.6 - - + -
144D LEU* 4.5 9.0 - - - -
148D HIS* 4.5 11.2 - - + +
211D TYR 4.3 7.0 - - - +
212D SER* 2.9 14.8 + - - +
214D ASP* 1.3 75.6 - - - +
216D TRP* 1.3 60.7 + - - +
218D LEU* 3.6 13.1 - - + +
219D GLY* 2.9 24.6 + - - -
304D LEU* 3.9 31.6 - - + +
312D ARG* 4.6 7.4 - - + -
313D LEU 3.3 23.3 - - - +
314D THR* 3.9 4.3 - - - +
315D ALA* 3.7 29.4 - - - +
318D ALA* 4.0 1.3 - - + -
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Residues in contact with TRP 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D TYR 5.2 0.2 + - - -
197D PHE 3.5 14.6 - - - -
198D LYS 3.3 12.9 + - - -
199D GLY* 3.4 18.6 - - - -
200D PRO* 3.5 25.6 - - + -
212D SER 3.3 6.1 + - - -
213D LEU 3.5 9.6 - - - +
215D MET* 1.3 76.1 - - - +
217D SER* 1.3 62.2 + - - +
219D GLY* 3.0 4.5 + - - -
220D CYS* 2.9 38.1 + - - -
233D PHE* 4.0 14.1 - + - -
241D GLN* 6.2 0.2 - - - +
245D ILE* 3.8 31.3 - - + +
249D LEU* 3.7 20.6 - - + -
304D LEU 4.5 4.9 - - - -
305D LEU* 3.6 43.5 - - + +
306D ARG 3.6 20.2 - - - -
312D ARG* 3.6 18.4 - - - +
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Residues in contact with SER 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ARG 5.4 1.0 + - - -
157D VAL* 3.4 36.7 + - - +
193D ALA* 5.0 5.2 - - - +
197D PHE* 3.2 30.0 + - - +
213D LEU* 3.4 13.6 + - - +
214D ASP* 3.3 11.4 + - - -
216D TRP* 1.3 75.6 - - - +
218D LEU* 1.3 69.2 + - - +
220D CYS* 2.9 17.8 + - - +
221D MET* 3.1 10.4 + - - +
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Residues in contact with LEU 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D MET* 3.5 37.2 - - + -
140D ILE* 3.8 33.7 - - + -
141D LEU* 3.3 34.8 - - + -
144D LEU* 4.4 8.1 - - + -
157D VAL* 4.4 8.1 - - + +
214D ASP 2.9 16.2 + - - +
215D MET* 3.6 18.4 - - + +
217D SER* 1.3 73.9 - - - +
219D GLY* 1.3 64.9 + - - +
221D MET* 2.8 20.7 + - - +
222D LEU* 2.9 13.0 + - - +
300D PHE* 5.0 0.9 - - + -
304D LEU* 4.3 7.6 - - + -
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Residues in contact with GLY 219 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215D MET 2.9 14.2 + - - -
216D TRP 3.0 5.1 + - - -
218D LEU* 1.3 74.3 - - - +
220D CYS* 1.3 56.2 + - - +
222D LEU* 3.4 1.0 + - - -
223D ALA* 2.9 30.8 + - - +
301D LEU* 3.5 7.6 - - - +
304D LEU* 3.6 22.0 - - - +
305D LEU* 3.8 17.9 - - - -
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Residues in contact with CYS 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D TYR 3.9 16.6 - - - +
197D PHE* 3.7 21.5 - - + -
216D TRP* 2.9 47.1 + - - -
217D SER* 2.9 10.1 + - - +
219D GLY* 1.3 74.6 - - - +
221D MET* 1.3 62.0 + - - +
223D ALA* 3.7 6.6 + - - +
224D SER* 3.2 22.0 + - - -
232D PHE* 4.3 6.2 + - + +
233D PHE* 4.1 19.5 - - + -
305D LEU* 4.3 1.8 - - - -
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Residues in contact with MET 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D PHE* 3.8 33.0 - - + -
125D TYR* 5.5 0.4 - - + -
137D MET* 5.2 1.3 - - - -
140D ILE* 3.9 18.4 - - + -
157D VAL* 4.5 12.3 - - - -
158D LYS* 3.8 12.8 - - - +
159D PRO* 3.6 42.4 - - + -
162D VAL* 4.7 2.7 - - + -
197D PHE* 3.7 10.1 - - + -
217D SER 3.1 8.0 + - - +
218D LEU* 2.8 12.9 + - - +
220D CYS* 1.3 73.2 - - - +
222D LEU* 1.3 65.6 + - - +
223D ALA 3.0 1.6 - - - -
224D SER* 3.0 10.7 + - - -
225D MET* 2.8 43.2 + - + +
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Residues in contact with LEU 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ILE* 4.2 2.9 - - + -
137D MET* 4.0 23.5 - - + -
218D LEU 2.9 10.4 + - - +
219D GLY* 3.7 7.4 - - - +
221D MET* 1.3 75.6 - - - +
223D ALA* 1.3 63.0 + - - +
225D MET* 3.3 9.2 + - - +
226D ILE* 3.1 43.9 + - + +
297D ALA* 4.3 3.6 - - + +
300D PHE* 3.4 32.1 - - + -
301D LEU* 3.8 30.5 - - + +
304D LEU* 4.4 3.4 - - + -
323D TYR* 3.7 32.1 - - + +
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Residues in contact with ALA 223 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219D GLY 2.9 18.3 + - - +
220D CYS* 3.8 5.6 - - - +
222D LEU* 1.3 76.7 - - - +
224D SER* 1.3 63.5 + - - +
226D ILE* 4.4 2.0 - - - -
227D PHE* 3.0 39.0 + - + +
232D PHE* 3.7 34.5 - - + -
301D LEU* 3.9 16.4 - - + +
305D LEU* 4.7 2.5 - - + -
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Residues in contact with SER 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D TYR* 3.6 25.8 + - - -
159D PRO* 5.5 1.6 - - - +
197D PHE* 5.8 2.9 - - - -
220D CYS 3.2 11.5 + - - -
221D MET* 3.0 13.4 + - - -
223D ALA* 1.3 79.0 - - - +
225D MET* 1.3 58.6 + - - +
228D ARG* 3.2 7.7 - - - -
229D LYS* 3.0 50.8 + - - +
230D GLU* 4.1 7.2 + - - -
231D PRO 4.4 2.0 - - - -
232D PHE* 4.1 9.6 - - - -
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Residues in contact with MET 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D PHE* 3.4 36.3 - - + -
125D TYR* 3.6 39.6 - - + +
133D ILE* 3.9 27.0 - - + +
137D MET* 3.5 38.1 - - + -
221D MET* 2.8 34.8 + - + +
222D LEU* 3.7 9.9 - - - +
223D ALA 3.0 0.2 - - - -
224D SER* 1.3 79.8 + - - +
226D ILE* 1.3 62.0 + - - +
228D ARG* 3.6 9.5 + - - +
292D LEU* 3.7 12.5 - - - +
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Residues in contact with ILE 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ILE* 4.3 10.3 - - + -
222D LEU* 3.1 40.1 + - + +
223D ALA 3.7 4.0 - - - +
225D MET* 1.3 74.0 - - - +
227D PHE* 1.3 79.8 + - + +
228D ARG 3.1 4.9 - - - -
289D ASN* 3.1 28.9 - - - +
292D LEU* 3.6 29.4 - - + +
293D VAL* 3.9 5.5 - - + +
297D ALA* 4.5 21.3 - - + +
298D LEU* 4.6 6.1 - - + -
301D LEU* 4.1 24.5 - - + -
323D TYR* 4.2 10.1 - - - +
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Residues in contact with PHE 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D ALA* 3.0 22.5 + - - +
226D ILE* 1.3 80.6 - - + +
228D ARG* 1.3 72.4 + - - +
229D LYS* 3.4 14.5 - - + +
232D PHE* 3.3 24.9 - + + -
281D TRP* 3.8 27.8 - + - -
284D PHE* 3.7 32.5 - - + +
285D VAL* 4.1 3.6 - - + -
286D HIS* 4.4 5.2 - - - -
289D ASN* 2.9 22.2 + - - +
293D VAL* 4.0 22.0 - - + -
298D LEU* 3.7 25.8 - - + -
301D LEU* 3.6 22.9 - - + -
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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
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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) + - + + + + + -
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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