Contacts of the helix formed by residues 181 - 195 (chain C) 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 SER 181 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B GLN* 3.6 29.8 - - - -
160B ASP* 4.6 2.5 + - - -
180C LEU* 1.3 76.0 - - - +
182C ALA* 1.3 65.2 + - - +
183C LYS* 3.7 6.0 + - - +
184C ASN* 3.3 28.4 + - - +
185C TYR* 2.9 22.3 + - - +
211C PHE 3.7 9.6 - - - -
212C MET* 3.9 1.3 - - - -
109T GLN* 2.9 24.0 + - - +
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Residues in contact with ALA 182 (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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156B GLN* 5.0 1.6 + - - -
157B VAL* 5.9 3.8 - - + -
181C SER* 1.3 73.8 - - - +
183C LYS* 1.3 63.0 + - - +
185C TYR* 3.3 4.2 + - - +
186C GLY 3.2 17.3 + - - -
211C PHE 4.5 0.6 + - - -
212C MET* 3.7 24.1 - - + +
213C ARG 5.6 0.2 - - - +
216C ASP* 3.7 33.4 - - + -
217C ARG* 3.8 15.3 - - - +
220C PHE* 3.7 17.8 - - + +
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Residues in contact with LYS 183 (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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160B ASP* 3.5 43.5 + - + +
163B ASN* 3.3 21.4 + - - -
165B TYR* 2.7 33.3 + - - +
181C SER* 3.3 2.7 + - - +
182C ALA* 1.3 80.3 - - - +
184C ASN* 1.3 62.8 + - - +
187C ARG* 3.1 25.6 + - - +
220C PHE* 3.9 13.9 - - + -
65T ARG* 5.0 9.5 + - - +
66T TYR* 2.7 42.8 + - + +
100T ARG* 6.0 0.8 - - - +
111T GLN* 4.0 15.7 + - - +
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Residues in contact with ASN 184 (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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180C LEU* 4.4 15.1 - - + +
181C SER* 3.3 13.4 + - - +
183C LYS* 1.3 76.7 - - - +
185C TYR* 1.3 64.8 + - - +
187C ARG* 2.9 35.9 + - - +
188C ALA* 3.0 24.3 + - - +
104T PHE* 4.1 12.9 - - - -
109T GLN* 2.8 44.2 + - - +
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Residues in contact with TYR 185 (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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174C ILE* 3.7 37.6 + - + +
176C PRO 5.0 2.5 - - - -
177C LYS 4.8 5.1 + - - -
180C LEU* 4.0 22.2 - - + +
181C SER 2.9 10.8 + - - +
182C ALA* 3.4 9.6 - - - +
183C LYS 3.2 0.4 - - - -
184C ASN* 1.3 77.6 - - - +
186C GLY* 1.3 56.2 + - - +
188C ALA* 3.3 7.0 + - - +
189C VAL* 3.0 34.5 + - + +
202C ASP* 3.3 40.1 - - - -
203C ASP 3.3 9.4 + - - -
206C VAL* 3.9 10.7 - - + +
212C MET* 3.7 29.2 - - + -
217C ARG* 3.7 16.8 - - + -
221C CYS* 3.9 14.1 - - - -
238C HIS* 4.1 4.7 - + - -
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Residues in contact with GLY 186 (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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182C ALA 3.2 9.2 + - - -
183C LYS 3.3 0.2 + - - -
184C ASN 3.3 0.2 - - - -
185C TYR* 1.3 76.1 - - - +
187C ARG* 1.3 64.0 + - - +
189C VAL* 4.2 4.9 - - - -
190C TYR* 3.0 21.1 + - - +
220C PHE 4.1 9.9 - - - -
221C CYS* 4.4 3.7 - - - -
224C ALA* 3.1 19.9 - - - +
66T TYR* 3.2 19.9 - - - -
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Residues in contact with ARG 187 (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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183C LYS* 3.1 36.0 + - - +
184C ASN* 2.9 36.6 + - - +
186C GLY* 1.3 77.7 - - - +
188C ALA* 1.3 63.5 + - - +
190C TYR* 3.4 4.4 + - - +
191C GLU* 3.3 29.5 + - + +
43T GLU* 2.9 31.7 + - - -
66T TYR* 3.4 20.3 + - + -
69T MET* 4.0 27.7 - - + +
102T ILE* 3.9 3.8 - - - +
104T PHE* 3.7 17.4 - - - -
111T GLN* 2.9 29.7 + - - +
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Residues in contact with ALA 188 (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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174C ILE* 4.1 25.8 - - + -
180C LEU* 5.2 4.3 - - + -
184C ASN 3.0 13.2 + - - +
185C TYR 3.3 8.5 + - - +
187C ARG* 1.3 79.5 - - - +
189C VAL* 1.3 60.7 + - - +
191C GLU* 3.5 1.1 + - - -
192C CYS* 3.1 21.5 + - - -
407C LEU* 4.9 4.7 - - + -
413C ASN* 3.1 27.0 + - - +
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Residues in contact with VAL 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ILE* 4.0 16.6 - - + -
185C TYR* 3.0 24.3 + - + +
186C GLY* 3.6 7.4 - - - +
187C ARG 3.2 0.2 - - - -
188C ALA* 1.3 74.1 - - - +
190C TYR* 1.3 66.8 + - - +
192C CYS* 3.2 1.6 + - - +
193C LEU* 3.0 39.2 + - + +
200C THR* 3.3 20.4 - - - +
221C CYS* 4.1 11.9 - - - +
224C ALA* 4.2 10.8 - - + -
238C HIS* 3.6 35.0 - - + +
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Residues in contact with TYR 190 (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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186C GLY 3.0 16.7 + - - +
187C ARG* 3.4 5.6 + - - +
189C VAL* 1.3 76.1 - - - +
191C GLU* 1.3 89.1 + - + +
193C LEU* 4.0 0.7 - - - +
194C ARG* 3.0 44.2 + - + +
224C ALA* 3.9 20.2 - - + +
227C LYS* 3.5 36.1 - - + -
228C ALA* 3.9 21.1 - - + -
231C GLU* 2.6 28.2 + - - -
66T TYR* 5.1 7.2 - + + -
67T TRP 3.8 19.5 - - - -
68T THR* 2.9 20.4 + - - +
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Residues in contact with GLU 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C ARG* 3.3 22.8 + - + +
188C ALA* 3.9 1.6 - - - +
190C TYR* 1.3 94.6 - - + +
192C CYS* 1.3 62.4 + - - +
194C ARG* 2.9 36.1 + - - +
195C GLY 3.7 0.2 + - - -
413C ASN* 3.6 23.8 - - + +
414C ALA* 3.2 32.4 + - - +
67T TRP 4.4 0.5 - - - +
68T THR* 3.9 1.0 - - - +
69T MET* 3.1 47.3 + - + +
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Residues in contact with CYS 192 (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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172C CYS* 3.9 23.1 - - - -
174C ILE* 4.2 6.5 - - - -
188C ALA 3.1 23.5 + - - +
189C VAL 3.2 0.6 + - - +
191C GLU* 1.3 74.9 - - - +
193C LEU* 1.3 66.3 + - - +
195C GLY 3.2 2.1 + - - -
197C LEU* 3.8 13.9 - - + +
200C THR* 3.5 20.0 - - + -
406C THR* 4.0 8.1 - - - -
407C LEU* 4.0 5.2 - - - -
413C ASN* 3.5 29.4 - - - -
417C ALA* 3.2 25.3 - - - +
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Residues in contact with LEU 193 (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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189C VAL* 3.0 39.3 + - + +
192C CYS* 1.3 78.1 - - - +
194C ARG* 1.3 62.6 + - - +
195C GLY 3.1 1.4 + - - -
196C GLY 3.3 4.5 + - - -
197C LEU* 3.6 18.1 - - + +
198C ASP 3.8 9.9 - - - +
199C PHE* 3.7 28.7 - - - +
200C THR* 3.8 10.3 - - + +
225C LEU* 3.8 29.8 - - + -
228C ALA* 3.6 12.6 - - + -
236C LYS* 3.0 39.6 + - + -
237C GLY 3.9 4.7 - - - +
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Residues in contact with ARG 194 (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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190C TYR* 3.0 47.5 + - + +
191C GLU* 2.9 34.7 + - - +
193C LEU* 1.3 75.7 - - - +
195C GLY* 1.3 61.3 + - - +
196C GLY 3.3 1.1 + - - -
228C ALA* 4.0 4.8 - - + +
231C GLU* 3.1 30.4 + - - +
232C THR* 3.6 22.0 - - + +
414C ALA* 3.9 10.9 - - + +
68T THR* 3.6 22.4 - - - +
69T MET 4.9 1.4 + - - -
3U VAL* 4.4 5.5 - - - +
4U TRP* 2.8 59.1 + - - +
5U PRO 3.4 9.5 + - - -
6U THR* 3.6 5.1 - - - +
17U TYR* 4.3 2.4 + - - -
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Residues in contact with GLY 195 (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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191C GLU 3.7 1.0 + - - -
192C CYS 3.2 4.2 + - - -
193C LEU 3.1 1.6 - - - -
194C ARG* 1.3 82.2 - - - +
196C GLY* 1.3 56.2 + - - +
414C ALA* 3.7 16.4 - - - -
417C ALA* 3.6 18.2 - - - -
418C VAL* 3.2 37.1 + - - +
421C ARG* 4.5 0.2 - - - +
4U TRP* 4.5 2.9 - - - -
17U TYR* 3.8 8.5 - - - -
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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
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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