Contacts of the helix formed by residues 211 - 225 (chain D) in PDB entry 3H90
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 PRO 211 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209D ALA 3.9 1.3 - - - +
210D LEU* 1.3 89.4 - - + +
212D ASP* 1.3 67.3 + - - +
213D GLU* 3.1 7.6 - - + +
214D GLU* 2.9 40.9 + - + +
215D ARG 3.1 9.0 + - - -
238D GLN* 5.3 4.0 - - - +
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Residues in contact with ASP 212 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B ASP* 5.1 3.1 - - - +
210D LEU 3.6 1.6 + - - -
211D PRO* 1.3 70.6 - - - +
213D GLU* 1.3 53.1 + - - +
215D ARG* 3.6 33.2 + - - +
216D GLN* 2.8 37.1 + - - +
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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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211D PRO* 3.1 6.4 - - + +
212D ASP* 1.3 78.1 - - - +
214D GLU* 1.3 67.1 + - + +
216D GLN* 3.2 6.9 + - - +
217D GLU* 3.0 53.3 + - - +
274D ARG* 5.4 0.8 + - - +
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Residues in contact with GLU 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 LEU* 3.9 15.1 - - + +
211D PRO* 2.9 34.1 + - + +
213D GLU* 1.3 77.3 - - + +
215D ARG* 1.3 66.4 + - - +
217D GLU* 3.2 6.2 + - - +
218D ILE* 3.0 29.4 + - - +
238D GLN* 5.5 0.2 - - - -
243D ARG* 2.9 46.2 + - - -
274D ARG* 5.8 0.4 - - - +
275D PHE* 3.7 25.6 - - + -
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Residues in contact with ARG 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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69B ASP* 3.2 36.6 + - - -
70B ASN* 4.0 12.7 - - - +
72B SER* 6.5 0.2 - - - -
209D ALA* 3.3 31.5 - - - +
210D LEU* 3.5 17.6 + - + +
211D PRO 3.1 8.5 + - - +
212D ASP* 3.6 33.0 + - - +
214D GLU* 1.3 79.3 - - - +
216D GLN* 1.3 59.8 + - - +
218D ILE* 3.6 9.9 + - - +
219D ILE* 3.2 25.2 + - + +
234D LEU* 3.7 27.9 - - + +
236D THR* 4.3 11.6 + - + +
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Residues in contact with GLN 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 ASP* 2.8 19.4 + - - +
213D GLU* 3.4 8.7 - - - +
214D GLU 3.2 0.2 - - - -
215D ARG* 1.3 75.3 - - - +
217D GLU* 1.3 65.2 + - + +
219D ILE* 3.1 16.9 + - - +
220D ASP* 3.0 59.1 + - - +
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Residues in contact with GLU 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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213D GLU* 3.0 44.1 + - - +
214D GLU* 3.2 8.4 + - - +
216D GLN* 1.3 73.4 - - + +
218D ILE* 1.3 60.6 + - - +
220D ASP* 3.1 9.5 + - - +
221D ILE* 2.9 37.9 + - + +
274D ARG* 2.6 45.1 + - - +
275D PHE* 3.5 15.0 - - + -
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Residues in contact with ILE 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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210D LEU* 4.0 20.2 - - + -
214D GLU 3.0 22.3 + - - +
215D ARG* 3.8 5.6 - - - +
217D GLU* 1.3 74.5 - - - +
219D ILE* 1.3 61.3 + - - +
221D ILE* 3.5 8.3 + - - +
222D VAL* 2.9 44.0 + - + +
234D LEU* 4.4 21.8 - - + -
236D THR* 4.2 9.9 - - + -
245D ILE* 3.6 34.3 - - + -
247D ILE* 4.8 1.1 - - + -
271D ILE* 4.2 14.1 - - + -
275D PHE* 3.6 20.9 - - + -
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Residues in contact with ILE 219 (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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215D ARG* 3.2 9.4 + - + +
216D GLN* 3.1 33.9 + - - +
218D ILE* 1.3 80.0 - - - +
220D ASP* 1.3 63.1 + - - +
222D VAL* 3.5 3.8 + - - +
223D THR* 2.8 45.2 + - + +
231D ALA* 5.7 5.6 - - + +
232D HIS 5.4 2.7 - - - +
234D LEU* 3.7 41.5 - - + -
247D ILE* 4.7 6.1 - - + -
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Residues in contact with ASP 220 (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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216D GLN* 3.0 45.8 + - - +
217D GLU* 3.1 10.5 + - - +
219D ILE* 1.3 78.4 - - - +
221D ILE* 1.3 56.8 + - + +
223D THR* 3.7 5.4 + - - -
224D SER* 2.8 36.6 + - - -
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Residues in contact with ILE 221 (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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217D GLU* 2.9 26.9 + - + +
218D ILE* 3.8 8.5 - - - +
220D ASP* 1.3 76.2 - - + +
222D VAL* 1.3 66.2 + - - +
224D SER* 3.5 10.5 + - - -
225D TRP* 3.6 14.8 + - + +
267D VAL* 5.3 0.4 - - + +
270D ALA* 3.6 38.1 - - + +
271D ILE* 4.0 14.4 - - + +
274D ARG* 3.6 42.0 - - + -
275D PHE* 4.5 3.1 - - + -
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Residues in contact with VAL 222 (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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218D ILE* 2.9 26.8 + - + +
219D ILE 3.8 3.4 - - - +
221D ILE* 1.3 79.0 - - - +
223D THR* 1.3 60.7 + - - +
224D SER 3.4 0.3 + - - -
225D TRP* 3.5 4.5 + - - +
228D VAL* 3.1 26.3 - - + +
231D ALA* 3.7 18.8 - - + -
247D ILE* 3.8 20.2 - - + -
249D LEU* 3.4 32.5 - - + -
267D VAL* 3.9 10.3 - - + -
271D ILE* 3.8 26.2 - - + -
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Residues in contact with THR 223 (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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219D ILE* 2.8 29.9 + - + +
220D ASP* 3.7 9.4 + - - -
222D VAL* 1.3 78.7 - - - +
224D SER* 1.3 61.3 + - - +
225D TRP 4.1 0.9 - - - +
228D VAL* 3.5 20.2 - - - +
229D SER 5.8 0.5 - - - -
230D GLY* 5.0 3.1 - - - -
231D ALA* 4.2 29.4 - - + +
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Residues in contact with SER 224 (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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220D ASP 2.8 21.2 + - - -
221D ILE* 3.5 6.1 + - - -
223D THR* 1.3 79.3 + - - +
225D TRP* 1.3 69.1 + - - +
226D PRO* 3.4 5.9 - - - +
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Residues in contact with TRP 225 (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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221D ILE* 3.6 10.0 + - + +
222D VAL 3.5 13.9 + - - +
223D THR 3.4 0.7 - - - +
224D SER* 1.3 82.7 + - - +
226D PRO* 1.4 84.4 - - + +
227D GLY 4.0 9.6 - - - -
228D VAL* 3.3 24.1 + - + +
263D VAL* 4.5 2.5 - - + -
266D GLN* 3.0 55.2 + - + +
267D VAL* 3.9 20.4 - - + -
270D ALA* 3.8 27.6 - - + -
273D ARG* 5.0 10.5 - - - -
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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