Contacts of the helix formed by residues 267 - 281 (chain A) in PDB entry 2KTY
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A ILE* 5.0 0.9 - - - -
264A ASN 3.7 2.4 + - - +
265A LEU 3.3 3.7 - - - +
266A LYS* 1.3 102.2 - - + +
268A PRO* 1.3 74.6 - - + +
269A LYS* 3.4 17.1 + - + +
270A TYR* 3.6 17.5 + - + +
271A VAL* 3.2 23.6 + - - +
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Residues in contact with PRO 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ARG* 4.7 15.3 - - - +
225A ILE* 3.7 13.9 - - + -
233A HIS* 3.2 33.0 + - + +
266A LYS 4.6 1.1 - - - +
267A ASP* 1.3 94.6 - - + +
269A LYS* 1.3 81.9 + - + +
271A VAL* 3.1 3.5 + - - +
272A ARG* 2.9 24.1 + - - +
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Residues in contact with LYS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ASP* 3.4 15.3 + - + +
268A PRO* 1.3 90.0 - - + +
270A TYR* 1.3 58.5 + - + +
272A ARG* 3.4 7.4 + - - +
273A ASP* 3.0 40.4 + - - +
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Residues in contact with TYR 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A TRP* 5.7 0.9 - - - -
264A ASN* 2.8 58.8 - - + +
266A LYS* 5.2 8.3 - - + -
267A ASP* 3.6 17.3 + - + +
268A PRO 3.1 0.6 - - - -
269A LYS* 1.3 78.6 - - + +
271A VAL* 1.3 52.2 + - - +
272A ARG 3.1 0.2 + - - -
273A ASP* 3.1 10.2 + - + +
274A SER* 2.6 38.9 + - - -
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ILE* 3.3 48.0 - - + +
229A SER 5.5 0.7 - - - -
230A ILE* 5.4 1.1 - - + -
233A HIS* 5.1 1.8 - - + -
261A TRP* 4.8 8.1 - - + -
264A ASN 5.2 0.2 - - - -
265A LEU* 3.5 27.1 - - + +
267A ASP 3.2 17.0 - - - +
268A PRO 3.1 1.0 + - - +
270A TYR* 1.3 75.9 - - - +
272A ARG* 1.3 57.5 + - - +
274A SER* 2.6 17.9 + - - +
275A LYS* 2.9 53.2 + - + +
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Residues in contact with ARG 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ILE* 4.7 10.1 - - + -
233A HIS* 4.4 18.2 + - + -
234A ASN* 3.1 34.2 + - - +
268A PRO 2.9 11.7 + - - +
269A LYS* 3.5 11.2 - - - +
271A VAL* 1.3 74.3 - - - +
273A ASP* 1.3 70.4 + - - +
274A SER 3.2 0.2 + - - -
275A LYS* 3.2 6.1 + - - +
276A ILE* 3.0 42.4 + - + +
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Residues in contact with ASP 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A LYS* 3.0 22.2 + - - +
270A TYR* 3.7 10.5 - - + +
272A ARG* 1.3 79.1 - - - +
274A SER* 1.3 58.2 + - - +
276A ILE* 4.1 8.8 - - - +
277A ARG* 2.9 34.0 + - - +
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Residues in contact with SER 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A TRP* 3.2 36.3 - - - +
270A TYR* 2.6 17.4 + - - -
271A VAL* 2.6 29.1 + - - -
273A ASP* 1.3 73.3 - - - +
275A LYS* 1.3 54.2 + - - -
277A ARG* 4.4 1.3 - - - -
278A TYR* 2.7 53.5 + - - +
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Residues in contact with LYS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ILE 4.2 4.2 + - - -
226A GLU 4.8 2.4 + - - -
229A SER* 3.8 18.7 - - - +
230A ILE* 3.2 42.4 - - + +
249A TYR* 3.2 57.4 + - + +
261A TRP* 4.4 19.0 - - + +
271A VAL* 2.9 52.1 + - - +
272A ARG 3.2 2.2 + - - +
274A SER* 1.3 74.7 - - - +
276A ILE* 1.3 54.0 + - + +
278A TYR* 3.7 2.1 - - - +
279A ARG* 2.7 41.7 + - - +
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Residues in contact with ILE 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ILE* 5.9 1.8 - - + -
272A ARG* 3.0 35.7 + - + +
273A ASP* 4.1 8.5 - - - +
275A LYS* 1.3 74.3 - - + +
277A ARG* 1.3 67.1 + - - +
279A ARG* 2.9 30.9 + - + +
280A GLU* 2.9 30.4 + - + +
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Residues in contact with ARG 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ASP* 2.9 21.6 + - - +
274A SER* 3.9 2.2 - - - +
276A ILE* 1.3 78.7 - - - +
278A TYR* 1.3 74.3 + - + +
280A GLU* 3.5 32.6 + - - +
281A ASN* 4.2 2.1 + - - +
285A LEU* 4.6 6.7 - - + +
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Residues in contact with TYR 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A TYR* 5.3 9.2 - + + +
260A PRO* 2.9 43.9 - - + +
261A TRP* 4.2 20.0 - + + -
274A SER* 2.7 45.8 + - - +
275A LYS* 4.0 3.8 - - - +
277A ARG* 1.3 84.4 - - + +
279A ARG* 1.3 55.2 + - - +
281A ASN 3.3 1.2 - - - -
282A ILE* 2.8 42.9 + - + +
285A LEU* 3.2 46.3 - - + +
286A MET* 5.2 6.3 - - + -
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Residues in contact with ARG 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ILE* 3.3 31.9 - - - +
241A ARG* 3.3 31.8 - - - +
245A GLU* 4.3 8.7 - - - +
249A TYR* 3.9 13.2 - - - +
275A LYS 2.7 27.6 + - - +
276A ILE* 2.9 19.8 + - + +
278A TYR* 1.3 76.4 - - - +
280A GLU* 1.3 66.9 + - - +
281A ASN 3.1 0.7 + - - -
282A ILE* 3.5 20.0 + - + +
307A LYS* 3.9 34.5 + - + +
311A TYR* 5.4 6.5 - - - +
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Residues in contact with GLU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A ILE* 2.9 31.7 + - + +
277A ARG* 3.5 26.5 + - - +
278A TYR 3.2 0.4 - - - -
279A ARG* 1.3 77.8 - - - +
281A ASN* 1.3 63.3 + - + +
282A ILE* 5.5 0.5 - - - +
307A LYS* 4.8 8.3 + - - +
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Residues in contact with ASN 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ARG 4.2 1.8 + - - +
278A TYR 3.3 4.7 + - - -
279A ARG 4.1 0.2 - - - -
280A GLU* 1.3 83.9 - - + +
282A ILE* 1.3 68.2 + - - +
283A ALA* 2.9 15.1 - - - +
284A SER* 2.9 43.0 + - - +
285A LEU* 3.2 16.0 + - + +
304A GLU* 4.9 1.0 - - - +
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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