Contacts of the helix formed by residues 253 - 271 (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 ASN 253 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251K ASN* 3.0 7.3 + - - +
252K HIS* 1.3 82.4 - - - +
254K LEU* 1.3 58.1 + - - +
255K HIS* 3.2 10.2 + - - -
256K ILE* 2.8 24.8 + - + +
257K THR* 2.8 36.2 + - + +
286K LEU* 3.2 38.8 + - + +
287K LYS 5.1 0.2 + - - -
289K PHE* 4.2 3.2 + - - +
291K LYS 3.7 14.6 + - - -
292K PRO* 3.0 9.8 - - - +
293K VAL 3.0 27.4 + - - +
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Residues in contact with LEU 254 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251K ASN* 2.8 33.3 + - + +
253K ASN* 1.3 73.2 - - - +
255K HIS* 1.3 62.4 + - - +
257K THR* 3.6 7.4 - - - +
258K GLU* 2.9 45.9 + - + +
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Residues in contact with HIS 255 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252K HIS 3.3 27.4 + - - -
253K ASN* 3.8 8.1 + - - -
254K LEU* 1.3 76.6 + - - +
256K ILE* 1.3 81.8 + - + +
258K GLU* 4.5 3.9 - - - +
259K LYS* 4.2 10.0 + - - +
292K PRO* 5.0 7.1 - - + +
293K VAL 5.9 0.2 + - - -
316K ILE* 4.1 13.6 - - + +
317K LEU* 5.0 9.7 - - + +
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Residues in contact with ILE 256 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253K ASN* 2.8 30.0 + - + +
255K HIS* 1.3 94.5 - - + +
257K THR* 1.3 66.1 + - - +
258K GLU 3.1 1.3 - - - -
259K LYS* 2.9 15.6 + - - +
260K LEU* 3.2 28.0 + - + +
286K LEU* 4.3 10.1 - - + -
293K VAL* 4.4 8.5 - - + +
313K ILE* 4.3 25.6 - - + -
316K ILE* 4.3 26.0 - - + -
317K LEU* 3.9 25.8 - - + -
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Residues in contact with THR 257 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251K ASN* 3.0 35.4 + - - +
253K ASN* 2.8 20.4 + - + +
254K LEU* 3.4 6.2 + - - +
256K ILE* 1.3 72.2 - - - +
258K GLU* 1.3 72.3 + - - +
259K LYS 3.2 0.2 + - - -
260K LEU* 3.3 7.8 + - - +
261K GLU* 3.1 33.6 + - - +
283K ILE* 3.7 33.4 - - - +
286K LEU* 4.0 19.1 - - + -
287K LYS* 4.1 6.5 + - + -
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Residues in contact with GLU 258 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254K LEU* 2.9 30.0 + - + +
255K HIS* 4.6 4.9 - - - +
257K THR* 1.3 84.3 + - - +
259K LYS* 1.3 63.1 + - - +
261K GLU* 3.9 13.5 + - - +
262K VAL* 3.7 13.5 - - - +
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Residues in contact with LYS 259 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255K HIS 4.2 9.1 + - - +
256K ILE 2.9 10.1 + - - +
258K GLU* 1.3 77.8 - - - +
260K LEU* 1.3 68.3 + - - +
262K VAL* 3.2 22.7 + - - +
316K ILE* 3.8 22.9 - - + -
321K HIS 6.3 0.2 - - - -
322K LEU* 4.7 3.1 - - + -
325K LEU* 3.8 25.5 - - + +
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Residues in contact with LEU 260 (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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256K ILE* 3.2 19.8 + - + +
257K THR* 3.7 5.6 - - - +
259K LYS* 1.3 76.3 - - - +
261K GLU* 1.3 54.3 + - - +
263K LEU* 2.7 34.1 + - + +
264K ALA 3.2 6.4 + - - -
279K TYR* 4.7 12.6 - - + -
283K ILE* 4.0 21.1 - - + +
286K LEU* 3.6 31.4 - - + -
309K MET* 4.5 26.5 - - + +
312K LYS* 4.6 15.0 - - + +
313K ILE* 5.1 4.3 - - + -
316K ILE* 4.4 14.4 - - + -
322K LEU* 4.6 12.3 - - + -
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Residues in contact with GLU 261 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257K THR* 3.1 24.8 + - - +
258K GLU* 4.0 10.2 + - - +
259K LYS 3.4 0.2 - - - -
260K LEU* 1.3 78.2 - - - +
262K VAL* 1.3 56.0 + - + +
264K ALA* 3.0 4.5 + - + +
265K LYS* 2.8 58.7 + - + +
283K ILE* 3.4 28.7 - - + -
287K LYS* 3.5 22.3 + - - -
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Residues in contact with VAL 262 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258K GLU 3.7 11.4 - - - +
259K LYS* 3.3 17.7 - - - +
260K LEU 2.7 4.4 + - - -
261K GLU* 1.3 74.2 - - + +
263K LEU* 1.3 51.2 + - - +
265K LYS* 3.4 8.1 + - - +
266K ALA* 2.8 34.8 + - + +
325K LEU* 3.5 22.0 - - + -
328K ILE* 4.1 11.7 - - + -
332K VAL* 5.8 1.1 - - + +
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Residues in contact with LEU 263 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260K LEU* 2.7 16.9 + - + +
262K VAL* 1.3 71.4 - - - +
264K ALA* 1.3 57.6 + - - +
266K ALA* 2.8 6.6 + - + -
267K TYR* 2.5 60.2 + - + +
279K TYR* 3.9 28.9 - - + +
312K LYS* 4.4 8.5 - - + -
322K LEU* 4.0 20.9 - - + -
324K LYS* 4.0 29.2 - - + -
325K LEU* 3.7 19.5 - - + -
328K ILE* 4.2 14.8 - - + -
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Residues in contact with ALA 264 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260K LEU 3.2 2.4 + - - +
261K GLU* 3.0 20.6 + - - +
263K LEU* 1.3 80.0 - - - +
265K LYS* 1.3 55.1 + - + +
267K TYR* 3.1 1.9 + - - +
268K SER* 2.7 37.7 + - - -
276K ALA* 3.8 15.1 - - + +
279K TYR* 4.2 18.2 - - + -
280K ALA* 5.0 3.1 - - + +
283K ILE* 4.2 13.9 - - + -
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Residues in contact with LYS 265 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261K GLU* 2.8 45.7 + - + +
262K VAL* 3.8 6.1 - - - +
264K ALA* 1.3 75.1 - - + +
266K ALA* 1.3 59.4 + - - +
268K SER* 3.9 7.2 - - - -
269K VAL* 3.1 34.4 + - + +
332K VAL* 5.0 2.2 - - + +
336K GLU* 4.3 21.9 - - - +
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Residues in contact with ALA 266 (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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262K VAL* 2.8 15.8 + - + +
263K LEU* 2.8 17.1 + - + +
265K LYS* 1.3 74.3 - - - +
267K TYR* 1.3 66.3 + - + +
269K VAL* 3.1 13.3 - - - +
270K GLN* 3.0 26.2 - - - +
328K ILE* 4.2 17.0 - - + -
332K VAL* 4.2 25.4 - - + -
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Residues in contact with TYR 267 (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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263K LEU* 2.5 44.7 + - + +
264K ALA 3.8 2.0 - - - +
266K ALA* 1.3 72.8 - - + +
268K SER* 1.3 66.3 + - - +
270K GLN* 3.0 26.3 + - + +
271K GLY 3.1 9.0 + - - -
272K ASP* 3.4 26.7 + - + +
275K ARG* 3.7 18.4 - - + -
276K ALA* 4.5 7.2 - - + +
279K TYR* 3.3 41.6 + + - -
324K LYS* 3.3 25.0 + - - +
1N G 2.7 19.9 + - - -
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Residues in contact with SER 268 (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 2.7 22.8 + - - -
265K LYS* 3.7 10.3 - - - -
267K TYR* 1.3 74.2 - - - +
269K VAL* 1.3 63.1 + - - +
270K GLN 2.9 6.2 + - - -
271K GLY* 3.0 11.8 + - - -
272K ASP 4.4 3.7 - - - -
273K LYS* 5.1 3.4 + - - +
276K ALA* 3.8 18.7 - - - +
346K THR* 3.4 8.8 + - - -
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Residues in contact with VAL 269 (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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265K LYS* 3.1 20.4 - - + +
266K ALA* 3.1 15.3 - - - +
268K SER* 1.3 82.1 - - - +
270K GLN* 1.3 63.9 + - + +
271K GLY 3.5 0.2 - - - -
332K VAL* 4.3 22.4 - - + +
335K LEU* 4.0 19.7 - - + +
336K GLU* 3.9 24.0 - - + +
339K SER* 3.7 27.5 - - - +
346K THR* 3.4 22.3 + - - +
349K ALA* 5.2 0.9 - - - +
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Residues in contact with GLN 270 (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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266K ALA* 3.0 24.5 - - - +
267K TYR* 3.0 26.9 + - + +
268K SER 3.0 1.0 - - - -
269K VAL* 1.3 83.4 - - + +
271K GLY* 1.3 56.7 + - - +
272K ASP* 3.8 2.2 - - + +
328K ILE* 5.5 1.4 - - - +
329K SER* 3.7 28.3 - - - +
331K SER* 5.8 0.6 - - - -
332K VAL* 4.4 10.2 - - + +
335K LEU* 4.4 16.5 - - + +
346K THR* 3.3 3.1 - - - -
350K GLN* 3.2 21.7 + - - +
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Residues in contact with GLY 271 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267K TYR 4.1 0.2 - - - -
268K SER 3.0 9.1 + - - -
270K GLN* 1.3 80.6 - - - +
272K ASP* 1.3 55.8 + - - +
273K LYS* 2.6 21.3 + - - +
346K THR* 3.3 18.3 - - - +
347K LYS* 6.1 2.2 - - - -
350K GLN* 4.8 0.4 - - - -
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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
------------------------------------------------------------
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