Contacts of the helix formed by residues 203 - 218 (chain D) in PDB entry 1Y1V
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 203 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202D ILE* 1.3 80.4 - - - +
204D ASP* 1.3 67.4 + - - +
205D ASP* 4.0 7.1 + - - +
206D GLU* 3.3 26.3 + - - +
207D LEU 3.3 12.8 + - - -
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Residues in contact with ASP 204 (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 ALA* 3.9 19.7 - - + +
189D ASP 5.3 0.9 + - - -
192D LYS* 2.4 38.2 + - - +
202D ILE 3.4 1.2 + - - -
203D SER* 1.3 73.8 - - - +
205D ASP* 1.3 69.6 + - - +
207D LEU* 3.2 4.2 + - - +
208D GLU* 3.1 23.0 + - - +
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Residues in contact with ASP 205 (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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203D SER* 3.3 6.3 - - - +
204D ASP* 1.3 79.9 + - - +
206D GLU* 1.3 57.8 + - - +
208D GLU* 2.9 32.5 + - - +
209D ARG* 3.1 11.5 + - - +
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Residues in contact with GLU 206 (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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202D ILE* 4.4 18.9 - - + +
203D SER* 3.3 21.9 + - - +
205D ASP* 1.3 73.9 - - - +
207D LEU* 1.3 67.9 + - - +
208D GLU 2.9 1.8 - - - -
209D ARG* 2.8 31.4 + - - +
210D ILE* 3.0 22.4 + - - +
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Residues in contact with LEU 207 (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 LEU* 5.8 0.2 - - + -
180D LEU* 3.8 33.9 - - + -
188D ALA* 4.2 10.8 - - + -
191D ALA* 4.0 18.2 - - + -
192D LYS* 3.6 35.4 - - + -
198D LEU* 4.1 9.2 - - + -
202D ILE* 3.6 24.3 - - + +
203D SER 3.3 3.2 + - - +
204D ASP* 3.2 10.6 + - - +
206D GLU* 1.3 79.3 - - - +
208D GLU* 1.3 56.8 + - - +
210D ILE* 3.2 18.3 + - + +
211D LEU* 2.9 29.7 + - + +
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Residues in contact with GLU 208 (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 ASP 4.2 12.8 - - - +
187D THR* 3.5 14.1 - - - +
188D ALA* 2.9 35.2 + - - +
204D ASP* 3.1 10.2 + - - +
205D ASP* 2.9 18.9 + - - +
206D GLU 2.9 0.8 - - - -
207D LEU* 1.3 75.2 - - - +
209D ARG* 1.3 59.2 + - - +
210D ILE 3.1 1.3 - - - -
211D LEU* 3.8 5.0 - - + +
212D LYS* 2.9 51.8 + - + +
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Residues in contact with ARG 209 (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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205D ASP 3.1 12.5 + - - +
206D GLU* 2.8 23.8 + - + +
208D GLU* 1.3 76.5 - - - +
210D ILE* 1.3 61.9 + - + +
212D LYS* 3.7 15.4 - - + +
213D GLU* 3.3 26.2 + - - +
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Residues in contact with ILE 210 (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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166D LEU* 4.3 19.8 - - + +
167D LEU* 3.5 31.6 - - + -
169D SER* 6.1 0.4 - - - +
170D THR* 3.9 21.5 - - + +
180D LEU* 5.5 4.0 - - + -
202D ILE* 4.2 21.5 - - + -
206D GLU* 3.0 23.4 + - - +
207D LEU* 3.3 19.5 - - + +
209D ARG* 1.3 80.2 - - + +
211D LEU* 1.3 60.4 + - - +
213D GLU* 3.5 2.9 + - - +
214D LEU* 3.0 36.0 + - + +
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Residues in contact with LEU 211 (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 ARG* 5.8 1.3 - - - +
180D LEU* 4.3 10.3 - - + -
183D LEU 5.0 2.2 - - - +
185D CYS* 3.2 52.8 - - + +
186D ASP 3.7 13.7 - - - +
187D THR 3.5 21.3 - - - +
188D ALA* 4.6 2.7 - - - -
191D ALA* 4.1 10.5 - - + -
207D LEU* 2.9 25.5 + - + +
208D GLU* 3.4 5.8 + - + +
210D ILE* 1.3 74.6 - - - +
212D LYS* 1.3 64.6 + - - +
214D LEU* 3.7 26.0 - - + +
215D SER* 3.4 21.5 + - - -
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Residues in contact with LYS 212 (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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208D GLU* 2.9 40.6 + - + +
209D ARG* 3.7 15.2 - - + +
210D ILE 3.2 0.4 - - - -
211D LEU* 1.3 78.4 - - - +
213D GLU* 1.3 61.7 + - + +
215D SER* 3.2 12.4 + - - -
216D ASN* 3.1 22.3 - - - +
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Residues in contact with GLU 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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166D LEU* 4.3 16.1 - - + +
209D ARG 3.3 16.7 + - - +
210D ILE 3.5 4.0 + - - +
211D LEU 3.3 0.2 - - - -
212D LYS* 1.3 78.1 - - + +
214D LEU* 1.3 61.9 + - - +
216D ASN* 4.0 12.1 + - + +
217D LEU* 3.0 40.4 + - + +
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Residues in contact with LEU 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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153D ARG* 4.5 18.5 + - - +
154D PHE* 4.7 9.5 - - + -
163D VAL* 4.9 20.6 - - + -
166D LEU* 4.1 18.2 - - + -
167D LEU* 4.5 14.4 - - + -
180D LEU* 3.5 25.4 - - + +
181D GLY* 5.3 2.0 - - - -
210D ILE* 3.0 27.3 + - + +
211D LEU* 3.7 29.6 - - + +
212D LYS 3.2 0.6 - - - -
213D GLU* 1.3 76.8 - - - +
215D SER* 1.3 56.9 + - - +
216D ASN 3.1 1.6 - - - -
217D LEU* 3.2 5.5 + - + +
218D GLU* 2.8 34.0 + - - +
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Residues in contact with SER 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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153D ARG* 4.9 4.0 - - - +
185D CYS 5.9 1.8 - - - -
211D LEU 3.4 10.7 + - - -
212D LYS* 3.2 11.7 + - - -
214D LEU* 1.3 80.6 - - - +
216D ASN* 1.3 67.3 + - - +
218D GLU* 3.0 37.4 - - - +
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Residues in contact with ASN 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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212D LYS 3.1 20.2 + - - +
213D GLU* 4.2 14.5 + - - +
214D LEU 3.1 0.6 - - - -
215D SER* 1.3 89.9 + - - +
217D LEU* 1.3 66.5 + - + +
218D GLU 3.4 3.8 + - - +
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Residues in contact with LEU 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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154D PHE* 4.0 16.9 - - + -
159D THR* 4.3 17.3 - - + +
162D ALA* 3.6 32.8 - - + +
163D VAL* 4.0 17.0 - - + +
166D LEU* 5.2 7.6 - - + -
213D GLU* 3.0 33.8 + - + +
214D LEU* 3.2 6.5 + - + +
216D ASN* 1.3 78.8 - - + +
218D GLU* 1.3 52.9 + - - +
219D THR* 2.5 27.7 + - - -
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Residues in contact with GLU 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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153D ARG* 3.6 46.6 + - + +
154D PHE* 4.3 8.3 - - - -
214D LEU 2.8 13.2 + - - +
215D SER* 3.0 28.5 - - - +
216D ASN 3.1 4.4 - - - +
217D LEU* 1.3 72.9 - - - +
219D THR* 1.3 75.7 + - - +
220D LEU* 3.5 6.4 + - - +
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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