Contacts of the helix formed by residues 272 - 288 (chain K) in PDB entry 3HX0
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 272 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267K TYR* 3.4 22.7 + - + +
268K SER* 4.9 0.7 - - - -
270K GLN* 3.8 1.7 - - + +
271K GLY* 1.3 71.4 - - - +
273K LYS* 1.3 63.4 + - - +
274K TRP* 4.0 3.6 + - - +
275K ARG* 2.8 62.1 + - + +
276K ALA* 3.2 20.8 + - - +
1N G 5.0 1.6 - - - -
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Residues in contact with LYS 273 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268K SER* 5.3 4.5 - - - +
271K GLY 2.6 13.9 + - - +
272K ASP* 1.3 72.1 - - - +
274K TRP* 1.3 68.1 + - + +
276K ALA* 3.5 6.4 + - - +
277K ALA* 3.0 26.2 + - - +
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Residues in contact with TRP 274 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272K ASP* 3.3 3.5 + - - +
273K LYS* 1.3 82.8 - - + +
275K ARG* 1.3 61.3 + - - +
277K ALA* 3.5 20.5 - - + +
278K GLY 2.9 20.3 + - - -
4L C 3.1 72.9 - + + +
5L A 3.9 10.3 - - - -
1N G 3.3 32.7 + - + -
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Residues in contact with ARG 275 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267K TYR* 3.7 36.4 - - + -
272K ASP* 2.8 47.5 + - + +
274K TRP* 1.3 76.9 - - - +
276K ALA* 1.3 62.5 + - - +
278K GLY* 3.0 10.2 + - - -
279K TYR* 3.0 28.8 + - + -
308K ARG* 5.2 0.6 - - - +
1N G 2.7 89.5 + - + +
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Residues in contact with ALA 276 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264K ALA* 3.8 29.0 - - + +
267K TYR* 4.5 4.2 - - + +
268K SER* 3.8 18.6 - - - +
272K ASP 3.2 14.3 + - - +
273K LYS* 3.6 5.8 - - - +
275K ARG* 1.3 77.6 - - - +
277K ALA* 1.3 59.6 + - - +
278K GLY 3.2 0.2 + - - -
279K TYR* 3.3 8.9 + - - +
280K ALA* 2.8 31.2 + - - +
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Residues in contact with ALA 277 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273K LYS 3.0 17.5 + - - +
274K TRP* 3.5 31.4 - - + +
276K ALA* 1.3 76.4 - - - +
278K GLY* 1.3 63.5 + - - +
280K ALA* 3.4 7.5 - - - +
281K LYS* 3.0 23.7 + - - +
4L C 5.6 0.2 - - - +
1N G 4.7 4.9 - - - +
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Residues in contact with GLY 278 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274K TRP 2.9 10.3 + - - -
275K ARG 3.0 3.0 + - - -
277K ALA* 1.3 73.9 - - - +
279K TYR* 1.3 65.6 + - - +
281K LYS* 3.1 8.4 + - - +
282K ALA* 3.0 20.1 + - - +
304K GLY 4.9 1.7 - - - +
309K MET* 4.8 0.4 - - - -
1N G 3.1 41.3 - - - +
2N C 4.8 4.3 - - - +
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Residues in contact with TYR 279 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260K LEU* 4.7 15.7 - - + -
263K LEU* 3.9 23.6 - - + +
264K ALA* 4.2 16.2 - - + -
267K TYR* 3.3 31.3 + + - -
275K ARG* 3.0 32.2 + - + -
276K ALA* 3.7 6.3 - - - +
278K GLY* 1.3 73.1 - - - +
280K ALA* 1.3 54.2 + - - +
282K ALA* 2.7 3.7 + - - +
283K ILE* 2.6 42.6 + - + +
309K MET* 3.5 38.3 - - + +
312K LYS* 3.6 15.3 - - + -
1N G 2.6 48.1 + - - -
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Residues in contact with ALA 280 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264K ALA* 5.0 2.4 - - + +
276K ALA 2.8 18.6 + - - +
277K ALA* 3.4 10.5 - - - +
279K TYR* 1.3 76.4 - - - +
281K LYS* 1.3 63.1 + - - +
283K ILE* 3.2 12.1 + - - +
284K ASN* 3.0 32.0 + - - +
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Residues in contact with LYS 281 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277K ALA 3.0 13.5 + - - +
278K GLY* 3.4 10.8 - - - +
280K ALA* 1.3 74.7 - - - +
282K ALA* 1.3 58.0 + - - +
284K ASN* 3.6 7.7 - - - +
285K ALA* 2.9 27.9 + - - +
304K GLY* 5.1 7.0 - - - +
1N G 6.0 1.6 - - - +
2N C 6.1 1.3 - - - +
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Residues in contact with ALA 282 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260K LEU* 5.7 0.2 - - + -
278K GLY 3.0 9.6 + - - +
279K TYR* 2.7 18.4 + - - +
281K LYS* 1.3 68.2 - - - +
283K ILE* 1.3 61.0 + - + +
284K ASN 3.0 1.8 - - - -
285K ALA* 2.9 7.9 + - - +
286K LEU* 2.8 36.4 + - + +
304K GLY 3.5 23.9 + - - +
305K ILE* 4.4 4.0 - - + -
309K MET* 4.0 26.9 - - + -
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Residues in contact with ILE 283 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257K THR* 3.7 18.4 - - - -
260K LEU* 4.0 20.2 - - + -
261K GLU* 3.4 46.7 - - + +
264K ALA* 4.2 10.3 - - + -
279K TYR* 2.6 31.6 + - + +
280K ALA* 3.6 7.9 - - - +
282K ALA* 1.3 73.0 - - + +
284K ASN* 1.3 61.0 + - - +
286K LEU* 3.6 11.0 - - - +
287K LYS* 3.0 48.8 + - - +
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Residues in contact with ASN 284 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280K ALA* 3.0 22.6 + - - +
281K LYS* 3.6 7.8 - - - +
283K ILE* 1.3 78.2 - - - +
285K ALA* 1.3 65.8 + - - +
286K LEU 3.1 1.7 + - - -
287K LYS* 3.3 14.7 + - - +
288K SER* 3.1 21.1 + - - -
511K ALA* 4.5 8.3 - - - +
574K ASP 4.2 1.2 + - - -
575K TRP* 2.9 66.5 + - + +
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Residues in contact with ALA 285 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281K LYS 2.9 14.3 + - - +
282K ALA* 2.9 12.5 + - - +
284K ASN* 1.3 77.3 - - - +
286K LEU* 1.3 62.7 + - - +
288K SER* 3.6 6.6 + - - -
289K PHE* 3.4 16.6 + - - +
302K ILE* 4.0 18.4 - - + +
303K PRO* 3.6 24.2 - - + +
304K GLY* 4.9 1.6 - - - -
305K ILE* 5.0 1.1 - - + -
575K TRP* 5.8 0.2 - - - +
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Residues in contact with LEU 286 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251K ASN* 4.3 0.2 - - - -
253K ASN* 3.2 23.4 + - + +
256K ILE* 4.3 12.3 - - + -
257K THR* 4.0 19.5 - - + -
260K LEU* 3.6 31.2 - - + -
282K ALA* 2.8 20.5 + - + +
283K ILE* 3.6 7.2 - - - +
285K ALA* 1.3 75.7 - - - +
287K LYS* 1.3 67.5 + - - +
289K PHE* 2.8 26.4 + - + +
293K VAL* 5.2 9.6 - - + -
299K ALA* 6.2 0.4 - - + -
302K ILE* 5.3 4.3 - - + -
305K ILE* 3.6 25.1 - - + -
309K MET* 6.0 0.4 - - + -
313K ILE* 4.2 15.3 - - + -
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Residues in contact with LYS 287 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249K ALA 5.3 1.9 - - - +
250K THR 4.6 4.3 - - - +
251K ASN* 2.9 47.6 - - + +
252K HIS 4.7 1.7 + - - -
253K ASN* 5.1 0.2 + - - -
257K THR* 4.1 6.4 - - + -
261K GLU* 3.5 15.7 + - - -
283K ILE* 3.0 44.4 + - - +
284K ASN* 3.3 11.7 + - - +
286K LEU* 1.3 80.0 - - - +
288K SER* 1.3 58.7 + - - +
289K PHE 3.0 12.3 + - - +
575K TRP* 3.4 33.9 - - + -
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Residues in contact with SER 288 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284K ASN 3.1 12.9 + - - -
285K ALA* 3.9 6.7 - - - -
286K LEU 3.3 0.4 - - - -
287K LYS* 1.3 76.2 - - - +
289K PHE* 1.3 64.4 + - - +
290K HIS* 3.6 1.4 + - - -
575K TRP* 3.9 22.0 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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