Contacts of the helix formed by residues 181 - 194 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156C GLN* 3.6 35.2 + - - -
160C ASP* 4.7 2.9 + - - -
180D LEU* 1.3 77.5 - - - +
182D ALA* 1.3 64.4 + - - +
183D LYS* 3.8 5.5 + - - +
184D ASN* 3.3 28.1 + - - +
185D TYR* 2.9 21.7 + - - +
211D PHE 3.7 9.4 - - - -
212D MET* 3.9 1.3 - - - -
109U GLN* 2.8 18.7 + - - +
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Residues in contact with ALA 182 (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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156C GLN* 5.1 1.4 + - - -
157C VAL* 5.7 5.8 - - + +
181D SER* 1.3 73.1 - - - +
183D LYS* 1.3 64.2 + - - +
185D TYR* 3.2 4.2 + - - +
186D GLY 3.1 17.7 + - - -
211D PHE 4.5 0.8 + - - -
212D MET* 3.7 23.5 - - + +
216D ASP* 3.7 37.2 - - + -
217D ARG* 3.9 5.0 - - - +
220D PHE* 3.7 22.9 - - + +
221D CYS* 5.6 0.2 - - - -
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Residues in contact with LYS 183 (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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160C ASP* 3.3 53.0 + - + +
163C ASN* 3.3 20.6 + - - -
165C TYR* 3.0 18.5 + - - +
181D SER* 3.3 4.6 + - - +
182D ALA* 1.3 78.6 - - - +
184D ASN* 1.3 58.5 + - - +
187D ARG* 3.0 30.8 + - - +
220D PHE* 3.8 13.8 - - + -
65U ARG* 4.8 12.5 + - - +
66U TYR* 2.6 46.1 + - + +
100U ARG* 5.8 1.0 - - - +
111U GLN* 3.7 17.0 - - - +
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Residues in contact with ASN 184 (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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180D LEU* 4.1 17.1 - - + +
181D SER* 3.3 13.8 + - - +
183D LYS* 1.3 75.3 - - - +
185D TYR* 1.3 65.2 + - - +
187D ARG* 2.9 36.5 + - - +
188D ALA* 3.1 23.7 + - - +
104U PHE* 4.2 11.5 - - - -
109U GLN* 2.9 42.5 + - - +
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Residues in contact with TYR 185 (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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174D ILE* 3.6 40.8 + - + +
176D PRO 5.1 2.9 - - - -
177D LYS 5.0 4.3 - - - -
180D LEU* 4.0 20.4 - - + +
181D SER 2.9 10.7 + - - +
182D ALA 3.4 9.9 - - - +
183D LYS 3.2 0.2 - - - -
184D ASN* 1.3 76.9 - - - +
186D GLY* 1.3 59.1 + - - +
188D ALA* 3.3 6.7 + - - +
189D VAL* 3.0 33.4 + - + +
202D ASP* 3.3 40.3 - - - -
203D ASP* 3.3 9.4 + - - +
206D VAL* 3.8 11.2 - - + +
212D MET* 3.7 32.3 - - + -
217D ARG* 3.8 14.6 - - + -
221D CYS* 3.9 12.3 - - - -
238D HIS* 4.1 4.9 - + - -
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Residues in contact with GLY 186 (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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182D ALA 3.1 8.6 + - - -
183D LYS 3.2 0.2 + - - -
185D TYR* 1.3 78.3 - - - +
187D ARG* 1.3 63.5 + - - +
189D VAL* 3.2 4.6 + - - -
190D TYR* 3.0 21.7 + - - +
220D PHE 4.2 9.6 - - - -
221D CYS* 4.6 3.1 - - - -
224D ALA* 3.2 18.2 - - - +
66U TYR* 3.2 20.6 - - - -
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Residues in contact with ARG 187 (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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183D LYS* 3.0 36.6 + - - +
184D ASN* 2.9 31.3 + - - +
185D TYR 3.3 0.2 - - - -
186D GLY* 1.3 76.0 - - - +
188D ALA* 1.3 64.5 + - - +
190D TYR* 3.6 5.2 + - + +
191D GLU* 3.3 30.1 + - + +
43U GLU* 2.9 28.4 + - - -
66U TYR* 3.5 18.7 + - + -
69U MET* 3.6 31.9 - - + -
104U PHE* 3.5 20.6 - - - -
111U GLN* 3.1 26.8 + - - +
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Residues in contact with ALA 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D ILE* 4.1 26.2 - - + -
180D LEU* 5.2 3.8 - - + -
184D ASN 3.1 13.4 + - - +
185D TYR* 3.6 8.7 - - - +
186D GLY 3.2 0.2 - - - -
187D ARG* 1.3 80.4 - - - +
189D VAL* 1.3 61.5 + - - +
191D GLU* 3.4 1.4 + - - -
192D CYS* 3.1 22.0 + - - -
407D LEU* 4.8 4.9 - - + -
413D ASN* 3.2 27.0 + - - +
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Residues in contact with VAL 189 (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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174D ILE* 4.0 15.3 - - + -
185D TYR* 3.0 19.2 + - + +
186D GLY* 3.2 9.8 + - - +
188D ALA* 1.3 76.3 - - - +
190D TYR* 1.3 64.7 + - - +
192D CYS* 3.2 2.1 + - - +
193D LEU* 3.0 38.0 + - + +
200D THR* 3.4 20.2 - - - +
221D CYS* 4.1 13.5 - - - +
224D ALA* 4.1 11.4 - - + -
225D LEU 4.6 2.5 - - - +
238D HIS* 3.5 34.3 - - + +
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Residues in contact with TYR 190 (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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186D GLY 3.0 16.0 + - - +
187D ARG* 3.9 6.1 - - - +
189D VAL* 1.3 76.7 - - - +
191D GLU* 1.3 87.5 + - + +
193D LEU* 3.9 0.7 - - - +
194D ARG* 3.0 44.0 + - + +
224D ALA* 3.8 20.6 - - + +
227D LYS* 3.6 36.1 - - + -
228D ALA* 3.9 19.7 - - + -
231D GLU* 2.6 29.9 + - - -
66U TYR* 5.2 7.0 - + + -
67U TRP 3.8 19.1 - - - -
68U THR* 2.9 21.6 + - - +
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Residues in contact with GLU 191 (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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187D ARG* 3.3 24.0 + - + +
188D ALA* 3.9 2.0 - - - +
189D VAL 3.3 0.2 - - - -
190D TYR* 1.3 95.8 - - + +
192D CYS* 1.3 62.2 + - - +
194D ARG* 3.0 40.1 + - - +
195D GLY 3.7 0.2 + - - -
413D ASN* 3.6 22.4 - - + +
414D ALA* 3.2 29.6 + - - +
67U TRP 4.3 1.0 - - - +
68U THR* 3.8 0.9 - - - +
69U MET* 3.1 47.1 + - + +
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Residues in contact with CYS 192 (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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172D CYS* 3.9 23.3 - - - -
174D ILE* 4.3 6.1 - - - -
188D ALA 3.1 24.3 + - - +
189D VAL 3.2 0.4 + - - +
191D GLU* 1.3 76.8 - - - +
193D LEU* 1.3 64.0 + - - +
195D GLY* 3.2 1.9 + - - -
197D LEU* 3.8 13.9 - - + +
200D THR* 3.6 19.3 - - + -
406D THR* 4.0 5.8 - - - -
407D LEU* 3.9 7.9 - - - -
413D ASN* 3.4 31.4 - - - -
417D ALA* 3.2 24.4 - - - +
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Residues in contact with LEU 193 (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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189D VAL* 3.0 37.2 + - + +
192D CYS* 1.3 74.2 - - - +
194D ARG* 1.3 61.7 + - - +
195D GLY 3.0 6.5 + - - -
196D GLY 3.2 4.3 + - - -
197D LEU* 3.6 11.3 - - + +
198D ASP 3.8 22.2 - - - +
199D PHE 3.8 21.3 - - - +
200D THR* 3.8 9.9 - - + +
225D LEU* 3.7 30.3 - - + -
228D ALA* 3.5 15.3 - - + -
236D LYS* 3.0 39.4 + - + -
237D GLY 3.9 6.3 - - - +
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Residues in contact with ARG 194 (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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190D TYR* 3.0 42.7 + - + +
191D GLU* 3.0 31.1 + - - +
192D CYS 3.4 0.2 - - - -
193D LEU* 1.3 76.8 - - - +
195D GLY* 1.3 61.6 + - - +
196D GLY 3.4 0.6 + - - -
228D ALA* 3.9 5.1 - - + +
231D GLU* 2.9 34.4 + - - +
232D THR* 3.6 21.5 - - + +
414D ALA* 3.9 12.8 - - + +
68U THR* 3.6 23.8 - - - +
69U MET 4.9 1.2 + - - -
3V VAL* 4.4 5.5 - - - +
4V TRP* 2.8 60.6 + - - +
5V PRO 3.3 10.3 + - - -
6V THR* 3.5 3.6 - - - +
17V TYR* 4.5 1.7 + - - -
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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