Contacts of the helix formed by residues 211 - 227 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ALA* 3.9 16.8 - - + -
11C VAL* 3.3 32.8 - - + -
12C TYR* 2.8 25.4 + + + -
15C VAL* 3.8 1.2 - - - +
148C HIS* 3.4 63.9 + + + +
151C GLY* 3.6 13.9 - - - -
152C ILE 3.7 18.8 - - - -
153C MET* 4.0 10.3 - - + -
182C TYR* 3.5 30.9 + + + +
210C ASP* 1.3 77.5 + - + +
212C SER* 1.3 65.6 + - - +
214C ASP* 2.9 23.6 + - - +
215C MET* 3.9 2.6 + - - +
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Residues in contact with SER 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C GLU* 4.3 0.5 + - - -
209C TYR* 5.3 0.2 - - - +
210C ASP* 2.7 28.6 + - - -
211C TYR* 1.3 75.3 - - - +
213C LEU* 1.3 68.9 + - - +
215C MET* 2.8 25.3 + - - +
216C TRP 3.2 2.9 + - - -
309C HIS* 3.2 45.5 - - - +
312C ARG* 3.2 18.4 + - - -
313C LEU 5.6 0.9 - - - -
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Residues in contact with LEU 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C MET* 6.0 0.2 - - + -
155C ARG* 4.3 19.1 - - + +
192C VAL* 4.2 9.0 - - + -
193C ALA* 5.8 1.6 - - + -
197C PHE 5.2 0.4 - - - +
199C GLY* 4.0 14.1 - - - +
201C GLU* 3.6 22.0 - - - +
202C LEU* 3.8 34.3 - - + -
209C TYR* 3.6 35.0 - - + -
210C ASP 3.2 14.5 + - - +
211C TYR 3.0 0.2 - - - -
212C SER* 1.3 82.2 + - - +
214C ASP* 1.3 67.0 + - - +
216C TRP* 3.3 10.4 + - - +
217C SER* 3.4 15.6 + - - +
312C ARG* 3.8 0.8 - - - +
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Residues in contact with ASP 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 4.3 9.8 - - + +
148C HIS* 3.0 31.6 - - + +
153C MET* 3.8 5.4 - - - +
154C HIS* 2.3 40.9 + - - +
155C ARG* 3.8 6.2 - - - -
157C VAL* 3.4 22.5 + - + +
211C TYR 2.9 10.6 + - - +
213C LEU* 1.3 78.1 - - - +
215C MET* 1.3 61.6 + - - +
217C SER* 3.2 8.9 + - - -
218C LEU* 2.9 27.2 + - - +
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Residues in contact with MET 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LEU* 3.5 29.4 - - + -
144C LEU* 4.5 9.6 - - - -
148C HIS* 4.4 11.0 - - + +
211C TYR 4.3 8.3 - - - +
212C SER* 2.8 14.3 + - - +
214C ASP* 1.3 77.5 - - - +
216C TRP* 1.3 66.8 + - - +
218C LEU* 3.6 13.3 - - + +
219C GLY* 2.9 20.1 + - - -
304C LEU* 3.9 29.5 - - + +
312C ARG* 4.7 7.9 - - + -
313C LEU 3.4 20.2 - - - +
314C THR* 4.0 6.1 - - - +
315C ALA* 3.7 31.9 - - - +
318C ALA* 4.1 1.6 - - + -
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Residues in contact with TRP 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C TYR 5.2 0.4 + - - -
197C PHE 3.5 15.9 - - - -
198C LYS 3.3 12.7 + - - -
199C GLY* 3.4 18.6 - - - -
200C PRO* 3.5 25.1 - - + -
212C SER 3.2 5.3 + - - -
213C LEU 3.5 9.6 - - - +
214C ASP 3.3 0.2 - - - -
215C MET* 1.3 77.8 - - - +
217C SER* 1.3 62.4 + - - +
219C GLY* 2.9 4.3 + - - -
220C CYS* 2.9 37.9 + - - -
233C PHE* 3.9 13.0 - + - -
245C ILE* 3.8 31.5 - - + +
249C LEU* 3.7 19.7 - - + -
304C LEU 4.5 4.7 - - - -
305C LEU* 3.6 44.5 - - + +
306C ARG 3.6 19.7 - - - -
312C ARG* 3.6 18.6 - - - +
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Residues in contact with SER 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C ARG 5.4 1.0 + - - -
157C VAL* 3.4 38.4 + - - +
193C ALA* 5.0 5.5 - - - +
197C PHE* 3.2 30.3 + - - +
213C LEU* 3.4 13.2 + - - +
214C ASP* 3.2 11.9 + - - -
216C TRP* 1.3 78.1 - - - +
218C LEU* 1.3 64.4 + - - +
220C CYS* 2.9 17.7 + - - +
221C MET* 3.1 9.8 + - - +
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Residues in contact with LEU 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C MET* 3.5 37.5 - - + -
140C ILE* 3.8 33.4 - - + -
141C LEU* 3.3 35.0 - - + -
144C LEU* 4.4 8.3 - - + -
157C VAL* 4.4 8.6 - - + +
214C ASP 2.9 14.6 + - - +
215C MET* 3.6 20.4 - - + +
217C SER* 1.3 74.6 - - - +
219C GLY* 1.3 64.2 + - - +
221C MET* 2.9 20.9 + - - +
222C LEU* 2.9 12.8 + - - +
300C PHE* 4.9 0.4 - - + -
304C LEU* 4.3 7.6 - - + -
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Residues in contact with GLY 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C MET 2.9 13.3 + - - -
216C TRP 2.9 5.6 + - - -
218C LEU* 1.3 75.9 - - - +
220C CYS* 1.3 55.4 + - - +
222C LEU* 3.3 1.2 + - - -
223C ALA* 2.9 30.7 + - - +
301C LEU* 3.5 6.4 - - - +
304C LEU* 3.6 22.3 - - - +
305C LEU* 3.8 17.9 - - - -
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Residues in contact with CYS 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C TYR 3.9 17.0 - - - +
197C PHE* 3.7 22.9 - - + -
216C TRP* 2.9 49.5 + - - -
217C SER 2.9 7.8 + - - +
219C GLY* 1.3 75.3 - - - +
221C MET* 1.3 60.4 + - - +
223C ALA* 3.8 6.4 - - - +
224C SER* 3.2 22.5 + - - -
232C PHE* 4.3 6.0 + - + +
233C PHE* 4.0 19.1 - - + +
305C LEU* 4.4 1.6 - - - -
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Residues in contact with MET 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PHE* 3.9 32.5 - - + -
137C MET* 5.2 2.2 - - - -
140C ILE* 3.9 18.2 - - + -
157C VAL* 4.4 13.0 - - - -
158C LYS* 3.8 12.8 - - - +
159C PRO* 3.6 43.7 - - + -
162C VAL* 4.7 2.7 - - + -
197C PHE* 3.7 10.5 - - + -
217C SER 3.1 7.6 + - - +
218C LEU* 2.9 12.1 + - - +
220C CYS* 1.3 73.0 - - - +
222C LEU* 1.3 67.9 + - - +
223C ALA 3.0 1.6 - - - -
224C SER* 3.0 10.2 + - - -
225C MET* 2.8 42.7 + - + +
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Residues in contact with LEU 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C ILE* 4.1 5.6 - - + -
137C MET* 4.0 21.3 - - + -
218C LEU 2.9 10.6 + - - +
219C GLY* 3.7 7.6 - - - +
221C MET* 1.3 76.3 - - - +
223C ALA* 1.3 62.2 + - - +
225C MET* 3.7 8.9 - - - +
226C ILE* 3.1 38.4 + - + +
297C ALA* 4.3 4.0 - - + +
300C PHE* 3.4 31.6 - - + -
301C LEU* 3.8 31.0 - - + +
304C LEU* 4.4 3.6 - - + -
323C TYR* 3.7 31.4 - - + +
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Residues in contact with ALA 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C GLY 2.9 18.1 + - - +
220C CYS* 3.8 5.2 - - - +
221C MET 3.0 0.2 - - - -
222C LEU* 1.3 77.9 - - - +
224C SER* 1.3 63.1 + - - +
226C ILE* 4.4 2.0 - - - -
227C PHE* 3.0 38.9 + - + +
232C PHE* 3.7 35.0 - - + -
301C LEU* 3.9 16.1 - - + +
305C LEU* 4.7 2.0 - - + -
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Residues in contact with SER 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C TYR* 3.6 25.0 + - - -
159C PRO* 5.5 1.7 - - - +
197C PHE* 5.8 3.5 - - - -
220C CYS 3.2 11.5 + - - -
221C MET* 3.0 12.0 + - - -
223C ALA* 1.3 80.3 - - - +
225C MET* 1.3 58.8 + - - +
228C ARG* 3.2 7.8 - - - -
229C LYS* 3.0 50.8 + - - +
230C GLU* 4.1 6.6 + - - -
231C PRO 4.4 2.0 - - - -
232C PHE* 4.0 10.0 - - - +
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Residues in contact with MET 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C PHE* 3.4 35.0 - - + -
125C TYR* 3.6 41.5 - - + +
133C ILE* 3.8 28.6 - - + +
137C MET* 3.5 37.0 - - + -
221C MET* 2.8 38.5 + - + +
222C LEU* 3.7 5.2 - - - +
224C SER* 1.3 79.6 + - - +
226C ILE* 1.3 62.2 + - - +
228C ARG* 3.7 7.8 + - - +
292C LEU* 3.7 14.7 - - - +
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Residues in contact with ILE 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C ILE* 4.3 11.0 - - + -
222C LEU* 3.1 41.0 + - + +
223C ALA 3.7 4.3 - - - +
225C MET* 1.3 73.5 - - - +
227C PHE* 1.3 78.8 + - + +
228C ARG 3.1 5.1 + - - -
289C ASN* 3.1 28.8 - - - +
292C LEU* 3.6 29.4 - - + +
293C VAL* 3.9 5.1 - - + +
297C ALA* 4.4 20.0 - - + +
298C LEU* 4.7 6.1 - - + -
301C LEU* 4.1 24.0 - - + -
323C TYR* 4.2 10.5 - - - +
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Residues in contact with PHE 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C ALA 3.0 19.8 + - - +
226C ILE* 1.3 81.2 - - + +
228C ARG* 1.3 71.3 + - - +
229C LYS* 4.0 14.6 - - + +
232C PHE* 3.3 27.8 - + + -
281C TRP* 3.8 26.9 - + - -
284C PHE* 3.7 31.6 - - + +
285C VAL* 4.1 5.2 - - + -
286C HIS* 4.3 5.4 - - - -
289C ASN* 2.9 23.1 + - - +
293C VAL* 4.0 23.3 - - + -
298C LEU* 3.8 24.2 - - + -
301C LEU* 3.6 23.1 - - + -
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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