Contacts of the helix formed by residues 201 - 217 (chain D) in PDB entry 2IYL
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 ASN 201 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199D LYS 4.1 1.6 + - - -
200D HIS* 1.3 72.7 - - - +
202D LEU* 1.3 65.9 + - - +
203D MET* 2.9 35.3 + - - +
204D GLU* 3.0 32.2 + - + +
205D GLU* 3.3 20.6 + - - +
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Residues in contact with LEU 202 (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 ALA* 3.5 37.7 - - + +
194D GLY* 3.9 25.1 - - - -
195D ARG 4.0 15.0 - - - +
196D LEU* 3.8 34.6 + - + +
200D HIS 3.4 4.7 + - - -
201D ASN* 1.3 73.9 + - - +
203D MET* 1.3 66.7 + - + +
205D GLU* 3.2 12.6 + - - +
206D LEU* 3.0 36.0 + - + +
243D PHE* 4.0 18.8 - - + -
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Residues in contact with MET 203 (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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196D LEU* 5.4 2.7 - - + -
201D ASN* 2.9 11.9 + - - +
202D LEU* 1.3 83.6 - - + +
204D GLU* 1.3 56.6 + - - +
206D LEU* 3.4 12.7 + - + +
207D LYS* 3.0 37.7 + - - +
239D GLN* 5.2 4.3 - - - +
242D LYS* 3.3 29.8 - - + +
243D PHE* 3.4 42.0 - - + +
246D ALA* 3.0 39.7 - - + +
247D VAL* 5.1 0.2 - - + -
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Residues in contact with GLU 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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201D ASN* 3.0 33.2 + - + +
202D LEU 3.3 0.4 - - - -
203D MET* 1.3 73.9 - - - +
205D GLU* 1.3 60.3 + - - +
207D LYS* 3.3 37.6 + - - +
208D LYS* 3.1 44.6 + - - +
211D ARG* 4.9 7.8 + - - -
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Residues in contact with GLU 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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138D GLY 4.4 2.9 - - - +
140D THR* 5.5 0.5 + - - -
169D PRO* 3.4 34.0 - - + +
193D ALA* 3.6 30.0 + - - +
200D HIS* 5.3 9.7 - - + +
201D ASN 3.3 11.6 + - - +
202D LEU* 3.2 15.7 + - + +
204D GLU* 1.3 78.3 - - - +
206D LEU* 1.3 59.8 + - + +
208D LYS* 3.3 13.5 + - + +
209D VAL* 3.1 29.3 + - + +
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Residues in contact with LEU 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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106D LEU* 4.7 3.8 - - + +
108D VAL* 4.2 16.6 - - + -
192D THR* 3.9 31.4 - - + -
193D ALA 4.5 2.0 - - - +
202D LEU* 3.0 31.4 + - + +
203D MET* 3.4 20.4 - - + +
204D GLU 3.3 0.2 - - - -
205D GLU* 1.3 78.4 - - + +
207D LYS* 1.3 66.1 + - - +
209D VAL* 3.2 9.5 + - + +
210D LYS* 2.9 23.9 + - - +
243D PHE* 3.6 37.2 - - + -
247D VAL* 3.7 16.5 - - + +
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Residues in contact with LYS 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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203D MET* 3.0 21.3 + - - +
204D GLU* 3.3 35.1 + - - +
205D GLU 3.4 0.2 - - - -
206D LEU* 1.3 73.7 - - - +
208D LYS* 1.3 56.7 + - - +
210D LYS* 3.2 5.6 + - + +
211D ARG* 2.8 66.2 + - + +
245D GLU* 4.8 5.3 + - - +
246D ALA* 3.5 47.6 + - - +
247D VAL* 4.1 4.7 - - + -
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Residues in contact with LYS 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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170D ALA* 3.8 14.6 - - + +
200D HIS* 6.0 1.8 + - - -
204D GLU* 3.1 28.9 + - - +
205D GLU* 3.4 13.7 - - + +
207D LYS* 1.3 72.6 - - - +
209D VAL* 1.3 59.3 + - - +
211D ARG* 3.8 18.0 - - - +
212D ALA* 2.9 29.6 + - - +
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Residues in contact with VAL 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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106D LEU* 3.7 28.9 - - + -
169D PRO* 4.2 16.8 - - + +
170D ALA* 4.2 25.1 - - + +
173D ALA* 3.9 18.7 - - + +
190D VAL* 4.2 5.8 - - + -
192D THR* 5.1 3.4 - - + -
205D GLU* 3.1 20.1 + - + +
206D LEU* 3.2 13.7 + - + +
208D LYS* 1.3 74.1 - - - +
210D LYS* 1.3 59.1 + - - +
212D ALA* 3.2 2.8 + - - +
213D ILE* 3.0 32.4 + - + +
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Residues in contact with LYS 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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106D LEU* 4.4 8.5 - - + -
206D LEU 2.9 16.5 + - - +
207D LYS* 3.6 7.0 - - - +
209D VAL* 1.3 78.0 - - - +
211D ARG* 1.3 61.7 + - + +
213D ILE* 3.5 10.3 + - - +
214D ALA* 3.2 22.5 + - - +
221D PRO* 3.7 34.3 - - + +
224D VAL* 4.6 5.8 - - + +
246D ALA 5.5 0.6 + - - +
247D VAL* 2.6 45.7 + - + +
248D GLY* 4.8 3.0 + - - -
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Residues in contact with ARG 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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204D GLU* 4.9 8.3 + - - -
207D LYS* 2.8 59.0 + - - +
208D LYS* 3.8 20.1 - - - +
209D VAL 3.3 0.2 - - - -
210D LYS* 1.3 77.3 - - + +
212D ALA* 1.3 60.9 + - - +
214D ALA* 3.3 9.0 + - - +
215D LYS* 3.2 33.8 + - - +
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Residues in contact with ALA 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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170D ALA* 3.2 34.1 - - + +
174D TYR* 3.3 30.8 - - + +
208D LYS 2.9 18.7 + - - +
209D VAL 3.2 4.7 + - - +
211D ARG* 1.3 74.1 - - - +
213D ILE* 1.3 65.2 + - - +
215D LYS* 3.2 21.3 + - + +
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Residues in contact with ILE 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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104D VAL* 4.0 19.7 - - + -
106D LEU* 4.2 8.1 - - + -
173D ALA* 3.9 15.7 - - + -
174D TYR* 5.1 0.7 - - - +
177D VAL* 3.8 25.5 - - + +
190D VAL* 4.1 12.6 - - + -
209D VAL* 3.0 37.7 + - + +
210D LYS* 3.7 4.7 - - - +
211D ARG 3.4 0.2 - - - -
212D ALA* 1.3 74.3 - - - +
214D ALA* 1.3 58.2 + - - +
216D ALA* 3.1 6.9 + - - +
217D ASP* 2.9 24.6 + - - +
220D GLU* 3.7 13.0 - - + -
221D PRO* 3.6 35.9 - - + -
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Residues in contact with ALA 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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210D LYS 3.2 11.2 + - - +
211D ARG* 3.7 11.0 - - - +
212D ALA 3.2 0.4 - - - -
213D ILE* 1.3 78.7 - - - +
215D LYS* 1.3 57.7 + - - +
216D ALA 3.3 0.2 - - - -
217D ASP 3.4 9.9 - - - +
218D PRO* 3.1 34.8 - - + +
220D GLU 3.4 15.3 - - - +
221D PRO* 5.2 0.2 - - + -
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Residues in contact with LYS 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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174D TYR* 3.6 20.6 + - + -
211D ARG* 3.2 23.5 + - - +
212D ALA* 3.2 14.6 + - + +
214D ALA* 1.3 75.7 - - - +
216D ALA* 1.3 61.3 + - - +
218D PRO* 5.4 2.4 - - - +
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Residues in contact with ALA 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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174D TYR* 3.5 31.9 - - + +
177D VAL* 3.6 26.5 - - + -
178D GLN* 4.2 9.6 - - - +
181D LYS* 2.7 29.6 + - - -
212D ALA 3.4 1.9 + - - +
213D ILE 3.1 9.1 + - - +
215D LYS* 1.3 81.8 - - - +
217D ASP* 1.3 58.1 + - - +
218D PRO* 4.6 1.6 - - - +
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Residues in contact with ASP 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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103D ARG* 4.8 13.3 + - - -
177D VAL* 4.0 13.7 - - + -
180D MET* 5.1 1.7 - - - +
181D LYS* 4.4 12.2 - - + +
213D ILE 2.9 5.5 + - - -
214D ALA* 3.4 10.5 - - - -
216D ALA* 1.3 78.7 - - - +
218D PRO* 1.3 67.9 - - - +
219D GLU* 3.1 23.5 + - - +
220D GLU* 2.9 46.7 + - + +
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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