Contacts of the helix formed by residues 267 - 281 (chain D) in PDB entry 3OP5
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 267 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221C HIS 5.5 1.7 - - - +
264D ASN* 3.3 26.3 + - - +
265D LEU 3.3 0.6 - - - -
266D LYS* 1.4 77.1 - - - +
268D PRO* 1.4 67.5 - - - +
269D LYS* 3.5 12.7 + - - +
270D TYR* 3.4 31.0 + - + +
271D VAL* 3.2 24.9 + - - +
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Residues in contact with PRO 268 (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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221C HIS* 4.0 26.9 - - + +
225C ILE* 4.4 5.2 - - + -
265C LEU 6.0 0.2 - - - +
268C PRO* 3.6 26.0 - - + -
221D HIS* 3.4 37.3 + - + +
225D ILE* 4.2 12.8 - - + -
233D HIS* 4.1 0.5 + - - -
265D LEU 5.3 1.1 - - - +
266D LYS 3.4 12.1 - - - +
267D ASP* 1.4 84.5 - - - +
269D LYS* 1.3 56.5 + - + +
271D VAL* 3.4 4.5 + - + +
272D ARG* 3.0 29.1 + - - +
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Residues in contact with LYS 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C LYS 4.6 6.3 - - - +
220C CYS 4.1 15.3 - - - +
221C HIS 5.2 4.5 - - - +
222C ASP* 3.9 20.9 - - - +
221D HIS* 5.2 2.5 - - - +
267D ASP* 3.4 9.1 + - - +
268D PRO* 1.3 78.0 - - + +
270D TYR* 1.4 52.5 + - - +
272D ARG* 3.4 30.5 + - - +
273D ASP* 2.8 44.1 + - - +
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Residues in contact with TYR 270 (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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260D PRO 3.8 16.5 + - - -
261D TRP* 3.8 26.8 - - + -
263D ASP* 6.1 0.5 - - - +
264D ASN* 3.6 41.5 - - + +
267D ASP* 3.4 28.5 + - + +
268D PRO 3.3 0.6 - - - -
269D LYS* 1.4 77.5 - - - +
271D VAL* 1.4 55.9 + - - +
273D ASP* 3.3 6.5 + - + +
274D SER* 2.8 45.1 + - - -
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Residues in contact with VAL 271 (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 ILE* 3.5 33.4 - - + +
233D HIS* 3.7 11.7 - - + -
261D TRP* 3.7 26.0 - - + +
264D ASN 3.4 16.6 - - - +
265D LEU* 3.9 21.5 - - + -
267D ASP 3.2 16.0 + - - +
268D PRO 3.7 5.8 - - - +
270D TYR* 1.4 79.6 - - + +
272D ARG* 1.4 56.4 + - - +
274D SER* 3.4 2.4 + - - -
275D LYS* 3.1 34.9 + - - +
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Residues in contact with ARG 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C PRO 5.9 0.8 + - - -
218C LYS* 4.2 19.7 + - - +
221D HIS* 4.4 5.2 + - + -
230D ILE* 4.7 1.7 - - + +
233D HIS* 3.7 47.0 - - + +
234D ASN* 3.5 22.5 + - - +
268D PRO 3.0 16.2 + - - +
269D LYS* 3.5 32.2 + - - +
271D VAL* 1.4 76.6 - - - +
273D ASP* 1.3 86.3 + - - +
275D LYS* 3.4 4.0 + - - +
276D ILE* 3.1 47.1 + - + +
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Residues in contact with ASP 273 (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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269D LYS* 2.8 26.0 + - - +
270D TYR* 3.8 6.1 - - + +
272D ARG* 1.3 105.6 + - - +
274D SER* 1.3 63.8 + - - +
276D ILE* 3.4 9.2 + - - +
277D ARG* 3.1 26.3 + - - +
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Residues in contact with SER 274 (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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260D PRO* 4.6 0.5 - - - +
261D TRP* 3.3 33.0 - - - +
270D TYR* 2.8 31.0 + - - -
271D VAL 3.5 5.2 - - - -
273D ASP* 1.3 75.8 - - - +
275D LYS* 1.3 56.8 + - - +
277D ARG* 3.4 8.6 + - - +
278D TYR* 3.0 49.5 + - - -
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Residues in contact with LYS 275 (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 ILE 2.9 24.5 + - - -
226D GLU 3.4 10.1 + - - -
227D PHE 3.8 0.4 - - - -
228D THR 2.6 30.1 + - - +
230D ILE* 3.5 11.9 - - + +
233D HIS* 3.1 23.9 + - + +
245D GLU* 4.7 1.6 - - - +
249D TYR* 3.6 25.7 + - + +
261D TRP* 3.6 44.4 - - + +
271D VAL* 3.1 19.0 + - - +
272D ARG 3.7 4.9 - - - +
273D ASP 3.4 0.2 - - - -
274D SER* 1.3 73.4 - - - +
276D ILE* 1.3 58.4 + - - +
278D TYR* 3.8 2.4 - - - +
279D ARG* 3.0 29.6 + - - +
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Residues in contact with ILE 276 (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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230D ILE* 3.9 32.1 - - + -
234D ASN* 4.7 6.7 - - - +
272D ARG* 3.1 53.1 + - + +
273D ASP* 3.8 7.9 - - - +
274D SER 3.4 0.2 - - - -
275D LYS* 1.3 74.0 - - - +
277D ARG* 1.3 58.9 + - - +
279D ARG* 3.3 4.6 + - - +
280D GLU* 3.0 30.7 + - + +
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Residues in contact with ARG 277 (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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273D ASP 3.1 17.8 + - - +
274D SER* 3.6 7.6 - - - +
276D ILE* 1.3 77.6 - - - +
278D TYR* 1.3 70.4 + - + +
280D GLU* 3.4 9.2 + - - +
281D ASN* 3.1 28.0 + - + +
284D SER* 4.7 2.5 + - - +
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Residues in contact with TYR 278 (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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249D TYR* 6.4 1.1 - - + -
260D PRO* 3.6 20.9 - - + +
261D TRP* 3.8 15.7 - + + -
274D SER* 3.0 43.9 + - - +
275D LYS 4.2 3.6 - - - +
276D ILE 3.4 0.2 - - - -
277D ARG* 1.3 84.5 - - + +
279D ARG* 1.4 58.6 + - - +
281D ASN 3.1 20.6 - - - +
282D ILE* 3.3 11.4 + - - +
284D SER* 3.6 28.9 - - - -
285D LEU* 3.5 43.8 - - + +
288D LYS* 3.5 25.7 - - + +
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Residues in contact with ARG 279 (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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81B PHE* 4.8 7.5 - - - -
366B GOL 5.3 7.5 + - - -
230D ILE* 3.7 23.8 - - + -
241D ARG* 4.4 18.5 - - - +
245D GLU* 5.5 4.8 + - - -
249D TYR* 5.5 1.6 - - - +
275D LYS 3.0 20.1 + - - +
276D ILE* 3.6 5.8 - - - +
278D TYR* 1.4 73.1 - - - +
280D GLU* 1.3 62.3 + - - +
281D ASN 3.3 1.0 + - - -
282D ILE* 3.6 12.8 - - + +
306D VAL 5.1 0.4 + - - -
307D LYS* 2.8 83.5 + - + +
309D LEU 4.5 1.2 + - - -
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Residues in contact with GLU 280 (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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218B LYS* 6.4 1.8 - - + -
276D ILE* 3.0 19.3 + - + +
277D ARG* 3.4 9.4 + - - +
279D ARG* 1.3 78.1 - - - +
281D ASN* 1.3 57.5 + - + +
307D LYS* 3.4 19.1 + - - +
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Residues in contact with ASN 281 (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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76B ASP* 5.5 2.6 - - - +
277D ARG* 3.1 12.9 + - + +
278D TYR 3.1 10.4 - - - +
280D GLU* 1.3 78.7 - - + +
282D ILE* 1.3 62.6 + - - +
283D ALA* 3.7 12.8 + - - +
284D SER* 2.7 53.9 + - - +
285D LEU 3.4 2.9 + - - -
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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