Contacts of the helix formed by residues 220 - 233 (chain D) in PDB entry 1O1F
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 ASP 220 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206D LYS 5.5 0.3 - - - +
213D LYS* 2.8 65.6 + - + +
214D MET 3.5 4.0 - - - +
217D THR* 2.8 41.7 + - - +
218D LEU 2.9 1.2 - - - -
219D GLU* 1.3 88.1 - - - +
221D GLN* 1.3 50.8 - - - +
222D ILE 3.0 1.1 - - - -
223D ILE* 2.7 7.6 + - - +
224D SER* 2.3 41.8 + - - +
340D ILE* 4.8 0.4 - - + -
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Residues in contact with GLN 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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206D LYS* 4.5 3.8 - - - +
216D GLY* 3.6 6.7 + - - +
217D THR* 2.6 37.7 + - - +
218D LEU* 2.4 47.7 - - + +
220D ASP* 1.3 68.9 - - - +
222D ILE* 1.3 64.8 + - - +
224D SER* 4.2 4.5 - - - -
225D ALA* 2.8 24.0 + - - +
340D ILE* 3.6 21.1 - - + +
341D LEU* 3.4 21.0 - - + +
448D GLN* 4.0 23.5 - - - +
449D LEU* 3.6 15.0 - - + -
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Residues in contact with ILE 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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193D ILE* 4.0 27.3 - - + +
197D ALA* 5.2 6.1 - - + -
218D LEU* 2.9 37.9 - - + -
219D GLU* 3.5 19.7 - - - +
221D GLN* 1.3 80.7 - - - +
223D ILE* 1.3 69.4 + - + +
225D ALA* 3.3 13.0 - - - +
226D ASN* 4.2 5.4 - - - +
250D ILE* 6.0 1.1 - - + -
252D ILE* 5.0 9.9 - - + -
260D LEU* 5.3 10.3 - - + -
262D SER 5.1 1.1 - - - -
263D ALA* 3.2 30.7 - - + +
449D LEU* 4.7 7.2 - - + -
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Residues in contact with ILE 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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193D ILE* 5.3 4.3 - - + -
194D GLN* 3.2 49.6 - - + +
197D ALA* 4.9 6.3 - - + -
219D GLU 2.8 24.9 - - - +
220D ASP* 2.7 9.6 + - - +
222D ILE* 1.3 86.4 - - + +
224D SER* 1.3 56.8 + - - +
225D ALA 2.6 16.3 + - - -
226D ASN* 2.9 36.3 + - - +
227D PRO* 3.2 5.6 - - + +
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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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213D LYS 4.2 4.3 + - - -
220D ASP 2.3 32.9 + - - -
221D GLN* 3.7 5.8 - - - -
223D ILE* 1.3 67.6 - - - +
225D ALA* 1.3 62.4 - - - +
226D ASN 3.2 0.2 - - - -
227D PRO* 3.0 22.0 - - - +
228D LEU 3.9 0.3 + - - -
337D ALA* 3.7 17.3 - - - +
340D ILE* 3.8 24.6 - - - +
341D LEU* 3.4 22.0 - - - +
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Residues in contact with ALA 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 GLN 2.8 10.6 + - - +
222D ILE* 3.3 16.6 - - - +
223D ILE 2.6 5.3 + - - -
224D SER* 1.3 74.0 - - - +
226D ASN* 1.3 68.0 + - - +
228D LEU* 3.0 19.9 + - - +
229D LEU* 3.4 10.1 + - + +
265D ILE* 4.1 26.0 - - + -
341D LEU* 3.7 10.3 - - - -
445D ILE* 4.4 14.7 - - + +
449D LEU* 5.2 1.8 - - + -
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Residues in contact with ASN 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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190D MLY 4.1 23.7 - - + +
193D ILE* 5.6 8.7 - - - +
194D GLN* 6.0 0.4 + - - -
222D ILE 4.2 6.2 - - - +
223D ILE* 2.9 31.4 + - - +
225D ALA* 1.3 78.6 - - - +
227D PRO* 1.3 57.9 - - + +
228D LEU 2.8 11.8 + - - -
229D LEU* 3.0 9.0 + - - +
230D GLU* 2.8 41.2 + - + +
248D MLY 2.8 36.2 - - - -
250D ILE* 5.4 1.6 - - - +
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Residues in contact with PRO 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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190D MLY 6.2 1.6 - - - -
223D ILE* 3.2 9.9 - - + +
224D SER* 3.0 21.8 - - - +
226D ASN* 1.3 97.8 - - + +
228D LEU* 1.3 59.2 + - - +
230D GLU* 4.1 12.2 - - + +
231D ALA* 3.7 8.3 + - - +
333D ALA* 4.9 16.2 - - + +
334D THR* 3.8 20.0 + - - -
337D ALA* 4.8 9.0 - - + -
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Residues in contact with LEU 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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224D SER 3.9 6.0 + - - +
225D ALA 3.0 10.0 + - - +
226D ASN 2.8 3.2 + - - -
227D PRO* 1.3 74.8 - - - +
229D LEU* 1.3 70.6 + - + +
230D GLU 3.0 0.9 - - - -
231D ALA* 2.8 14.7 + - - +
232D PHE* 3.2 39.5 - - + -
334D THR* 4.2 8.7 - - + +
337D ALA* 4.6 6.3 - - + -
338D ILE* 3.5 31.6 - - + -
341D LEU* 4.5 8.5 - - + -
343D PHE* 4.1 21.3 - - + -
441D MET* 4.3 14.8 - - - -
445D ILE* 3.9 24.5 - - + -
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Residues in contact with LEU 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 ALA* 3.4 14.5 + - + +
226D ASN* 3.4 9.2 - - - +
228D LEU* 1.3 82.8 - - + +
230D GLU* 1.3 53.7 + - + +
232D PHE* 3.1 3.0 + - - +
233D GLY* 2.4 38.6 + - - -
246D PHE* 4.1 20.0 - - + -
248D MLY 5.4 9.9 - - + +
265D ILE* 4.2 29.6 - - + -
267D THR* 5.6 0.7 - - - +
438D PHE* 3.9 21.5 - - + -
441D MET* 5.1 6.1 - - + -
442D VAL* 4.1 22.9 - - + +
445D ILE* 3.9 22.9 - - + -
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Residues in contact with GLU 230 (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 THR* 3.6 12.2 - - + +
190D MLY 2.8 46.4 - - - +
226D ASN* 2.8 30.7 + - + +
227D PRO* 4.1 9.9 - - + +
229D LEU* 1.3 75.9 - - + +
231D ALA* 1.3 63.1 + - - +
232D PHE 3.1 0.7 - - - -
234D ASN* 2.9 45.6 + - + +
242D ASN* 2.6 31.9 + - - +
246D PHE* 6.1 0.9 - - + -
248D MLY 5.0 3.8 - - - -
286D HIS* 3.3 9.9 - - + -
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Residues in contact with ALA 231 (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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227D PRO 3.7 5.4 + - - +
228D LEU 2.8 11.1 + - - +
230D GLU* 1.3 81.0 - - - +
232D PHE* 1.3 65.9 - - + +
285D TYR 4.0 0.2 - - - -
286D HIS* 3.2 17.1 + - - -
287D ILE* 2.7 37.7 + - + +
290D GLN* 3.5 28.9 - - - +
334D THR* 3.8 10.3 - - + +
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Residues in contact with PHE 232 (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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228D LEU* 3.2 45.0 + - + -
229D LEU* 3.1 4.6 + - - +
231D ALA* 1.3 81.8 - - + +
233D GLY* 1.3 58.7 + - - +
270D LEU* 5.0 0.3 - - - +
285D TYR* 2.8 20.8 - - - -
287D ILE* 3.0 38.4 - - + -
334D THR* 4.9 1.1 - - + -
338D ILE* 5.5 1.1 - - + -
351D ILE* 3.7 21.1 - - + -
355D THR* 3.8 20.2 - - - -
434D TYR* 2.8 38.2 + + + +
437D MET* 4.0 9.2 - - + -
438D PHE* 3.8 19.9 - - + -
441D MET* 3.8 21.8 - - + -
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Residues in contact with GLY 233 (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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229D LEU 2.4 20.1 + - - -
232D PHE* 1.3 72.9 - - - +
234D ASN* 1.3 60.5 + - - +
245D ARG* 2.9 27.4 + - - -
246D PHE* 3.0 22.3 - - - -
270D LEU* 4.1 3.4 - - - -
285D TYR* 3.3 12.8 - - - -
438D PHE* 3.8 6.9 - - - -
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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