Contacts of the helix formed by residues 270 - 301 (chain Y) in PDB entry 5KHU
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 270 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269Y ASP* 3.8 29.4 - - - +
271Y VAL* 3.8 28.7 - - - +
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Residues in contact with VAL 271 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270Y ASN* 3.8 26.7 - - - +
272Y ASP* 3.8 29.8 - - - +
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Residues in contact with ASP 272 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271Y VAL* 3.8 26.5 - - - +
273Y LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 273 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272Y ASP* 3.8 25.4 - - - +
274Y LEU* 3.8 29.6 - - - +
276Y SER* 4.6 14.4 - - - +
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Residues in contact with LEU 274 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273Y LEU* 3.8 29.2 - - - +
275Y GLY* 3.8 27.4 - - - +
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Residues in contact with GLY 275 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274Y LEU* 3.8 24.7 - - - +
276Y SER* 3.8 29.6 - - - +
278Y ALA* 4.3 17.7 - - - +
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Residues in contact with SER 276 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273Y LEU* 4.6 17.3 - - - +
275Y GLY* 3.8 25.8 - - - +
277Y LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 277 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276Y SER* 3.8 28.7 - - - +
278Y ALA* 3.8 26.2 - - - +
280Y LEU* 4.7 16.8 - - - +
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Residues in contact with ALA 278 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275Y GLY* 4.3 20.0 - - - +
277Y LEU* 3.8 25.6 - - - +
279Y ASP* 3.8 28.9 - - - +
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Residues in contact with ASP 279 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278Y ALA* 3.8 29.4 - - - +
280Y LEU* 3.8 26.9 - - - +
282Y PHE* 4.6 15.7 - - - +
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Residues in contact with LEU 280 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277Y LEU* 4.7 16.2 - - - +
279Y ASP* 3.8 27.1 - - - +
281Y TYR* 3.8 28.9 - - - +
283Y ARG* 4.6 15.3 - - - +
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Residues in contact with TYR 281 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280Y LEU* 3.8 29.4 - - - +
282Y PHE* 3.8 24.2 - - - +
286Y ASP* 4.5 19.1 - - - +
290Y SER* 4.6 14.4 - - - +
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Residues in contact with PHE 282 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279Y ASP* 4.6 16.4 - - - +
281Y TYR* 3.8 29.4 - - - +
283Y ARG* 3.8 26.5 - - - +
285Y GLY* 4.2 16.2 - - - +
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Residues in contact with ARG 283 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280Y LEU* 4.6 13.0 - - - +
282Y PHE* 3.8 25.6 - - - +
284Y ALA* 3.8 29.2 - - - +
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Residues in contact with ALA 284 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283Y ARG* 3.8 29.4 - - - +
285Y GLY* 3.8 24.2 - - - +
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Residues in contact with GLY 285 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282Y PHE* 4.2 18.4 - - - +
284Y ALA* 3.8 29.6 - - - +
286Y ASP* 3.8 28.7 - - - +
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Residues in contact with ASP 286 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281Y TYR* 4.5 17.9 - - - +
285Y GLY* 3.8 27.4 - - - +
287Y ASN* 3.7 29.4 - - - +
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Residues in contact with ASN 287 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286Y ASP* 3.7 29.4 - - - +
288Y LYS* 3.8 28.0 - - - +
290Y SER* 4.3 17.9 - - - +
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Residues in contact with LYS 288 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287Y ASN* 3.8 29.6 - - - +
289Y ASN* 3.8 25.6 - - - +
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Residues in contact with ASN 289 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288Y LYS* 3.8 28.5 - - - +
290Y SER* 3.8 25.4 - - - +
292Y LEU* 4.5 15.7 - - - +
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Residues in contact with SER 290 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281Y TYR* 4.6 19.7 - - - +
287Y ASN* 4.3 19.1 - - - +
289Y ASN* 3.8 27.4 - - - +
291Y VAL* 3.8 29.4 - - - +
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Residues in contact with VAL 291 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290Y SER* 3.8 29.2 - - - +
292Y LEU* 3.8 25.4 - - - +
294Y PHE* 4.6 15.5 - - - +
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Residues in contact with LEU 292 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289Y ASN* 4.5 18.8 - - - +
291Y VAL* 3.8 28.3 - - - +
293Y LYS* 3.8 29.4 - - - +
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Residues in contact with LYS 293 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292Y LEU* 3.8 29.6 - - - +
294Y PHE* 3.8 24.9 - - - +
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Residues in contact with PHE 294 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291Y VAL* 4.6 16.2 - - - +
293Y LYS* 3.8 29.2 - - - +
295Y GLU* 3.8 26.0 - - - +
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Residues in contact with GLU 295 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294Y PHE* 3.8 25.1 - - - +
296Y GLN* 3.8 28.7 - - - +
298Y GLN* 4.1 21.1 - - - +
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Residues in contact with GLN 296 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F GLY* 4.2 24.5 - - - +
295Y GLU* 3.8 24.2 - - - +
297Y ALA* 3.8 29.8 - - - +
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Residues in contact with ALA 297 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296Y GLN* 3.8 29.6 - - - +
298Y GLN* 3.8 25.6 - - - +
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Residues in contact with GLN 298 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295Y GLU* 4.1 18.6 - - - +
297Y ALA* 3.8 25.8 - - - +
299Y MET* 3.8 29.6 - - - +
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Residues in contact with MET 299 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298Y GLN* 3.8 29.6 - - - +
300Y LEU* 3.8 27.8 - - - +
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Residues in contact with LEU 300 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299Y MET* 3.8 28.9 - - - +
301Y ASP* 3.8 27.4 - - - +
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Residues in contact with ASP 301 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300Y LEU* 3.8 29.4 - - - +
302Y PRO* 3.8 29.2 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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