Contacts of the helix formed by residues 217 - 229 (chain D) in PDB entry 3BUW
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 217 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262B ALA 4.0 7.4 - - - -
263B VAL 2.5 28.6 + - - -
264B THR* 4.1 0.8 - - - -
265B HIS 3.7 22.9 - - - -
266B PRO* 4.5 2.9 - - - -
268B TYR 5.9 0.2 - - - -
343B ARG* 5.2 1.3 - - - +
215D ILE* 3.4 8.5 - - - +
216D SER* 1.3 81.1 - - - +
218D GLY* 1.3 59.2 + - - +
219D LEU 3.6 1.4 + - - -
220D GLU* 3.0 16.9 + - - +
221D ALA* 3.0 24.6 + - - +
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Residues in contact with GLY 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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268B TYR* 5.0 10.9 + - - -
269B MET* 6.3 0.4 - - - +
217D SER* 1.3 74.9 - - - +
219D LEU* 1.3 62.4 + - - +
221D ALA* 3.2 9.8 + - - +
222D MET* 3.0 27.6 + - - +
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Residues in contact with LEU 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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223B ALA* 4.2 21.2 - - + +
226B SER* 3.5 25.8 - - - +
227B THR* 4.0 16.6 - - - +
258B TRP* 4.5 0.9 - - - +
262B ALA* 3.8 33.6 + - + +
263B VAL* 4.0 20.9 - - + +
268B TYR* 4.2 15.1 - - + -
270B ALA* 5.8 6.3 - - + -
217D SER* 3.3 6.3 + - - +
218D GLY* 1.3 76.3 - - - +
220D GLU* 1.3 61.3 - - - +
222D MET* 3.3 12.2 + - + +
223D ALA* 3.1 22.2 + - - +
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Residues in contact with GLU 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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263B VAL* 4.1 5.9 + - - +
264B THR* 5.7 1.2 - - - +
214D PRO 4.8 1.4 - - - +
215D ILE* 4.0 10.8 - - + +
216D SER* 2.8 40.4 + - - -
217D SER* 3.0 22.1 + - - +
218D GLY 3.2 0.2 - - - -
219D LEU* 1.3 74.0 - - - +
221D ALA* 1.3 60.3 + - - +
223D ALA* 3.1 5.9 + - - -
224D LEU* 2.9 26.2 + - - +
255D LEU* 4.5 12.5 - - - +
258D TRP* 3.4 32.6 - - + -
259D ASN* 4.3 12.7 - - - +
263D VAL* 5.7 2.7 - - + -
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Residues in contact with ALA 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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202D TRP* 3.4 22.9 - - + +
206D ARG* 4.6 16.6 - - + +
215D ILE* 3.8 16.3 - - + +
217D SER 3.0 13.5 + - - +
218D GLY* 3.2 12.1 + - - +
220D GLU* 1.3 77.4 - - - +
222D MET* 1.3 59.9 + - + +
224D LEU* 3.2 5.5 + - - +
225D LYS 2.9 24.3 + - - -
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Residues in contact with MET 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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202D TRP* 5.3 5.4 - - - -
218D GLY 3.0 19.4 + - - +
219D LEU* 3.7 15.5 - - + +
220D GLU 3.2 0.2 - - - -
221D ALA* 1.3 76.6 - - - +
223D ALA* 1.3 66.0 + - - +
225D LYS* 3.4 34.7 + - - +
226D SER* 3.1 23.7 + - - -
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Residues in contact with ALA 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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219B LEU* 4.2 25.0 - - + +
223B ALA* 6.3 1.8 - - + -
219D LEU 3.1 13.6 + - - +
220D GLU* 3.6 10.5 - - - +
222D MET* 1.3 76.1 - - - +
224D LEU* 1.3 59.1 + - - +
226D SER* 2.6 22.7 + - - -
227D THR* 2.8 16.1 + - - -
258D TRP* 3.4 15.0 - - + -
263D VAL* 4.9 6.5 - - + -
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Residues in contact with LEU 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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202D TRP* 4.1 11.9 - - + -
206D ARG* 6.1 0.2 - - - -
209D LEU* 3.8 26.7 - - + -
215D ILE* 4.0 22.7 - - + -
220D GLU 2.9 13.6 + - - +
221D ALA* 3.4 8.3 - - - +
223D ALA* 1.3 75.5 - - - +
225D LYS* 1.3 65.7 + - - +
227D THR* 3.0 11.3 + - - -
228D ILE* 3.0 44.4 + - + +
244D PHE* 3.5 23.1 - - + -
255D LEU* 4.0 14.6 - - + -
258D TRP* 3.3 21.1 - - + -
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Residues in contact with LYS 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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202D TRP* 3.6 58.0 - - + +
221D ALA 2.9 16.5 + - - +
222D MET* 3.7 34.9 - - - +
223D ALA 3.4 0.2 - - - -
224D LEU* 1.3 77.3 - - - +
226D SER* 1.3 58.7 + - - +
229D ASP* 2.9 51.9 + - + +
234D ASP* 3.8 21.4 + - - +
236D ILE* 5.7 0.2 - - + -
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Residues in contact with SER 226 (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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219B LEU* 3.4 21.5 - - - +
222D MET 3.1 12.7 + - - -
223D ALA* 2.6 21.8 + - - -
225D LYS* 1.3 79.4 - - - +
227D THR* 1.3 59.8 + - - +
229D ASP* 4.4 5.3 + - - +
271D PHE* 3.6 28.2 - - - -
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Residues in contact with THR 227 (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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219B LEU* 4.0 10.9 - - - +
223D ALA 2.8 13.7 + - - -
224D LEU 3.0 7.9 + - - -
226D SER* 1.3 82.4 + - - +
228D ILE* 1.3 58.2 + - - +
230D LEU* 3.2 18.7 - - - +
244D PHE* 3.8 16.8 - - + -
248D PHE* 3.8 14.8 - - + -
258D TRP* 3.1 28.0 + - + +
268D TYR* 4.0 22.0 + - + +
271D PHE* 5.5 2.8 - - - -
295D LEU* 5.3 6.7 - - + +
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Residues in contact with ILE 228 (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 TRP* 4.8 1.6 - - + -
205D PHE* 3.8 25.8 - - + -
209D LEU* 5.2 0.9 - - + -
224D LEU* 3.0 39.6 + - + +
225D LYS* 4.5 0.9 - - - +
227D THR* 1.3 72.5 - - - +
229D ASP* 1.3 59.6 + - - +
230D LEU* 2.7 25.9 + - - +
236D ILE* 4.1 27.4 - - + -
240D GLU* 3.6 19.8 - - - +
241D PHE* 4.8 2.2 - - - +
244D PHE* 3.1 50.5 - - + -
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Residues in contact with ASP 229 (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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225D LYS* 2.9 32.8 + - + +
226D SER* 4.4 5.3 - - - +
228D ILE* 1.3 72.8 - - - +
230D LEU* 1.3 62.6 + - - +
232D CYS* 3.0 35.3 + - - -
233D ASN* 3.1 21.6 + - - +
234D ASP* 2.9 31.2 + - - +
235D TYR 3.5 8.9 - - - +
236D ILE* 4.2 12.1 - - + +
240D GLU* 3.5 5.8 - - - +
271D PHE* 4.2 3.5 - - - -
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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