Contacts of the helix formed by residues 181 - 197 (chain D) in PDB entry 1Y8Q
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 GLU 181 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179D PRO 3.7 0.4 - - - -
180D SER* 1.3 94.9 - - - +
182D PRO* 1.3 76.7 - - + +
183D ILE* 3.6 15.2 - - + +
184D HIS* 2.9 47.0 + - + +
185D CYS 3.4 3.6 + - - -
368D MET* 3.6 10.3 - - - +
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Residues in contact with PRO 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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181D GLU* 1.3 99.9 - - + +
183D ILE* 1.3 62.7 + - + +
185D CYS* 3.0 5.9 + - - +
186D ILE* 2.9 29.4 + - + +
363D MET* 3.7 30.6 - - + +
368D MET* 3.6 13.9 - - + -
369D ASN 4.9 5.6 - - - +
371D LYS* 3.9 31.0 - - + -
379D MET* 5.4 1.8 - - - -
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Residues in contact with ILE 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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168D ARG* 3.9 28.9 - - + +
170D PHE* 3.5 28.5 - - + -
181D GLU* 3.6 22.0 - - + +
182D PRO* 1.3 79.6 - - + +
184D HIS* 1.3 70.3 + - + +
186D ILE* 3.4 11.3 + - + +
187D VAL* 3.0 37.3 + - + +
379D MET* 4.5 28.8 - - + +
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Residues in contact with HIS 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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170D PHE* 3.7 35.1 - + - -
174D THR* 3.9 19.9 - - + +
175D ILE* 3.4 30.4 - - + +
179D PRO* 3.8 18.5 - - + +
180D SER* 3.2 22.0 + - - -
181D GLU* 2.9 44.3 + - + +
183D ILE* 1.3 80.6 - - + +
185D CYS* 1.3 62.5 + - - +
188D TRP* 3.1 20.4 + - - +
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Residues in contact with CYS 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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179D PRO* 4.8 7.4 - - - -
181D GLU 4.0 1.8 - - - -
182D PRO 3.0 7.0 + - - +
184D HIS* 1.3 77.1 - - - +
186D ILE* 1.3 55.1 + - - +
188D TRP* 2.9 12.3 + - - +
189D ALA* 2.8 33.4 + - - +
359D ALA* 3.5 21.3 - - - +
362D ARG* 3.8 17.5 - - + +
363D MET* 3.3 39.9 - - + -
366D PHE* 5.5 0.4 - - - -
368D MET* 3.6 20.0 - - - -
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Residues in contact with ILE 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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168D ARG* 6.2 0.9 - - - +
182D PRO* 2.9 16.5 + - + +
183D ILE* 3.7 11.2 - - + +
184D HIS 3.4 0.2 - - - -
185D CYS* 1.3 76.5 - - - +
187D VAL* 1.3 63.9 + - + +
189D ALA* 3.0 3.8 + - - +
190D LYS* 2.9 25.9 + - + +
355D VAL* 4.2 7.4 - - + -
359D ALA* 3.8 18.6 - - + -
363D MET* 4.5 6.3 - - + -
371D LYS* 5.4 0.2 - - + -
376D ILE* 4.3 16.8 - - + -
379D MET* 3.7 45.8 - - + +
380D ALA* 3.8 34.1 - - + +
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Residues in contact with VAL 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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168D ARG* 4.4 10.1 - - - +
170D PHE* 3.9 29.4 - - + -
175D ILE* 4.0 11.7 - - + -
183D ILE* 3.0 26.4 + - + +
184D HIS 3.9 4.7 - - - +
186D ILE* 1.3 75.9 - - + +
188D TRP* 1.3 56.4 + - - +
190D LYS* 3.4 11.8 + - + +
191D TYR* 2.9 62.7 + - + +
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Residues in contact with TRP 188 (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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175D ILE* 3.7 23.8 - - + +
176D ARG* 5.1 0.7 - - - -
184D HIS 3.1 14.7 + - - +
185D CYS* 2.9 15.9 + - - +
187D VAL* 1.3 75.9 - - - +
189D ALA* 1.3 71.8 + - - +
191D TYR* 3.0 7.6 + - + +
192D LEU* 2.8 52.5 + - + +
205D GLU 5.4 0.9 - - - -
206D VAL* 3.1 44.8 + - + +
258D LEU* 4.4 19.5 - - + -
259D PHE* 3.8 22.0 - + - -
358D ALA* 3.7 16.8 - - + -
362D ARG* 3.0 61.0 - - + +
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Residues in contact with ALA 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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185D CYS 2.8 9.2 + - - +
186D ILE 3.3 8.5 - - - +
188D TRP* 1.3 82.0 - - - +
190D LYS* 1.3 62.2 + - - +
192D LEU* 3.2 6.7 + - - +
193D PHE* 3.0 19.4 + - - +
354D PHE* 3.8 7.4 - - - -
355D VAL* 3.5 37.3 - - + +
358D ALA* 4.1 4.9 - - + -
359D ALA* 3.6 21.8 - - + +
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Residues in contact with LYS 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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168D ARG* 5.2 9.5 - - - +
186D ILE* 2.9 21.2 + - + +
187D VAL* 3.6 13.9 - - + +
189D ALA* 1.3 76.0 - - - +
191D TYR* 1.3 61.8 + - + +
193D PHE* 3.2 9.7 + - - +
194D ASN* 2.6 28.4 + - - +
204D GLN* 4.9 0.2 - - - -
344D TRP* 4.0 25.7 - - + +
355D VAL* 4.0 22.4 - - + -
380D ALA* 2.8 40.6 + - + +
382D ASN* 4.5 9.3 - - - +
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Residues in contact with TYR 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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170D PHE* 4.8 9.2 + - - +
172D GLY* 6.3 2.7 - - - -
175D ILE* 4.1 24.9 - - + -
176D ARG* 6.0 1.1 - - + -
187D VAL* 2.9 40.9 + - + +
188D TRP* 3.3 8.7 - + + +
190D LYS* 1.3 77.4 - - + +
192D LEU* 1.3 59.7 + - - +
194D ASN* 3.1 3.8 + - - +
195D GLN* 2.8 32.1 + - - +
203D ASP* 4.3 8.5 + - - +
204D GLN* 3.3 65.6 - - + +
205D GLU 4.3 6.3 - - - -
206D VAL* 4.0 6.7 - - + -
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Residues in contact with LEU 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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188D TRP* 2.8 31.8 + - + +
189D ALA* 3.4 9.0 - - - +
191D TYR* 1.3 76.7 - - - +
193D PHE* 1.3 58.3 + - - +
195D GLN* 3.4 1.0 + - + -
196D LEU* 2.8 50.1 + - + +
206D VAL* 3.6 22.6 - - + +
240D THR* 5.2 0.9 - - + -
258D LEU* 3.4 44.4 - - + -
259D PHE* 5.2 0.4 - - + -
322D PHE* 4.4 5.2 - - + -
354D PHE* 3.4 25.8 - - + -
358D ALA* 4.1 8.7 - - + -
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Residues in contact with PHE 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 ALA 3.0 12.6 + - - +
190D LYS* 3.3 11.4 - - - +
192D LEU* 1.3 76.9 - - - +
194D ASN* 1.3 65.1 + - - +
196D LEU 3.2 0.3 + - - -
197D PHE* 2.8 38.9 + + + -
198D GLY 3.2 4.1 + - - -
329D LEU* 3.7 34.3 - - + -
342D LEU* 4.3 25.6 - - + -
343D ILE 4.2 3.1 - - - -
344D TRP* 3.6 59.2 - + + -
351D ALA* 4.0 13.0 - - + -
354D PHE* 3.6 28.9 - + + -
355D VAL* 4.7 0.2 - - + -
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Residues in contact with ASN 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 LYS* 2.6 23.6 - - - +
191D TYR 3.1 1.5 + - - +
193D PHE* 1.3 83.7 - - - +
195D GLN* 1.3 63.3 + - + +
198D GLY* 2.6 39.9 + - - +
199D GLU* 3.4 26.1 + - - +
200D GLU 4.1 0.2 + - - -
201D ASP* 6.0 0.4 - - - +
204D GLN* 3.5 31.9 + - - +
344D TRP* 4.8 7.7 - - - +
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Residues in contact with GLN 195 (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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191D TYR 2.8 15.9 + - - +
192D LEU* 3.7 3.8 - - - +
194D ASN* 1.3 77.2 - - - +
196D LEU* 1.3 58.9 + - - +
200D GLU* 3.6 19.1 - - - +
201D ASP 2.8 43.6 + - - +
204D GLN* 3.0 29.8 + - + +
205D GLU* 3.3 21.4 - - - +
206D VAL* 3.7 15.7 - - + -
239D SER* 5.5 0.3 + - - -
240D THR* 4.3 16.2 + - + -
241D LYS* 3.2 32.4 + - - +
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Residues in contact with LEU 196 (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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192D LEU* 2.8 32.2 + - + +
195D GLN* 1.3 78.5 - - - +
197D PHE* 1.3 81.9 + - + +
240D THR* 3.5 28.9 - - + -
241D LYS* 3.3 15.7 - - - +
243D TRP* 5.6 0.2 - - + -
244D ALA* 4.4 19.3 - - + -
249D TYR* 3.2 24.0 + - + -
254D LEU* 4.2 28.0 - - + -
258D LEU* 4.9 2.7 - - + -
322D PHE* 5.7 0.2 - - + -
326D ILE* 5.2 0.7 - - + -
354D PHE* 3.8 27.6 - - + -
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Residues in contact with PHE 197 (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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193D PHE* 2.8 32.1 + + + +
196D LEU* 1.3 100.2 - - + +
198D GLY* 1.3 62.0 + - - +
241D LYS* 3.8 9.7 - - - +
249D TYR* 4.0 23.1 - + - -
326D ILE* 4.5 19.3 - - + -
329D LEU* 3.8 37.9 - - + -
330D ARG* 4.0 11.0 - - + -
333D LEU* 4.0 25.0 - - + +
341D GLU* 3.5 7.3 - - - -
342D LEU* 3.2 38.8 + - + -
354D PHE* 4.0 10.3 - + - -
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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