Contacts of the helix formed by residues 272 - 288 (chain B) in PDB entry 5DKW
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B TYR* 3.0 26.6 + - + +
268B SER* 5.2 0.2 - - - -
270B GLN* 3.3 5.7 + - + +
271B GLY* 1.3 73.1 - - - +
273B LYS* 1.3 64.4 + - - +
274B TRP* 3.3 4.7 + - - +
275B ARG* 2.5 57.6 + - + +
276B ALA* 3.3 21.9 + - - +
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Residues in contact with LYS 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B SER* 5.7 2.5 - - - +
271B GLY* 2.9 13.6 + - - +
272B ASP* 1.3 72.3 - - - +
274B TRP* 1.3 106.1 + - + +
276B ALA* 3.5 6.8 - - - +
277B LEU* 3.2 23.8 + - + +
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Residues in contact with TRP 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ASP* 3.3 4.7 + - - +
273B LYS* 1.3 114.1 - - + +
275B ARG* 1.3 64.7 + - - +
277B LEU* 3.2 27.8 + - + +
278B GLY 3.1 17.3 + - - -
514B ARG* 5.5 1.6 - - - -
1C G 3.4 30.2 + - + -
4F C 3.5 74.0 - + + +
5F G 4.3 8.1 - - - -
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Residues in contact with ARG 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B TYR* 3.5 36.6 - - + -
272B ASP* 2.5 59.1 + - - +
274B TRP* 1.3 76.1 - - - +
276B ALA* 1.3 63.3 + - - +
278B GLY* 3.3 1.0 + - - -
279B TYR* 2.9 38.0 + - + -
1C G 3.3 73.0 + - + +
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ALA* 4.0 11.7 - - - +
267B TYR* 4.1 6.1 - - + -
268B SER* 3.8 32.3 - - - +
272B ASP 3.3 18.1 + - - +
273B LYS* 3.5 7.2 - - - +
275B ARG* 1.3 79.8 - - - +
277B LEU* 1.3 60.5 + - - +
279B TYR* 3.5 6.1 + - - +
280B ALA* 3.1 22.2 + - - +
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LYS* 3.2 14.7 + - + +
274B TRP* 3.2 36.5 + - + +
275B ARG 3.1 0.2 - - - -
276B ALA* 1.3 74.5 - - - +
278B GLY* 1.3 65.1 + - - +
280B ALA* 2.9 16.7 + - + +
281B LYS* 3.0 20.1 + - - +
511B HIS* 4.5 13.2 - - + -
514B ARG* 3.4 55.0 - - - +
1C G 5.3 2.5 - - - +
4F C 5.2 5.6 - - + +
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Residues in contact with GLY 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B TRP 3.1 10.1 + - - -
275B ARG 3.3 3.5 + - - -
277B LEU* 1.3 77.8 - - - +
279B TYR* 1.3 56.3 + - - +
281B LYS* 3.5 7.5 + - - +
282B ALA* 3.0 28.6 + - - +
304B GLY 4.3 4.2 - - - +
309B MET* 3.9 8.5 - - - +
1C G 4.2 23.8 + - - +
2C C 5.0 5.6 - - - -
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Residues in contact with TYR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B LEU* 4.1 29.2 - - + -
263B LEU* 3.5 25.3 - - + +
264B ALA* 3.7 23.6 - - + -
267B TYR* 3.6 17.5 - + - -
275B ARG* 2.9 30.4 + - + +
276B ALA 3.7 2.2 - - - +
277B LEU 3.2 0.2 - - - -
278B GLY* 1.3 73.9 - - - +
280B ALA* 1.3 60.1 + - - +
282B ALA* 3.5 1.4 + - - +
283B ILE* 3.0 37.0 + - + +
309B MET* 3.9 28.0 - - + -
312B LYS* 3.2 19.0 + - + +
1C G 2.6 50.6 + - - -
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Residues in contact with ALA 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ALA* 5.0 2.4 - - + +
276B ALA 3.1 12.9 + - - +
277B LEU* 2.9 12.6 + - + +
279B TYR* 1.3 78.8 - - - +
281B LYS* 1.3 60.7 + - - +
283B ILE* 3.4 8.6 + - - +
284B ASN* 3.1 18.4 + - - +
511B HIS* 4.3 13.5 - - + +
575B TRP* 3.3 23.7 - - + -
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Residues in contact with LYS 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU* 3.0 18.9 + - - +
278B GLY* 3.9 7.2 - - - +
280B ALA* 1.3 73.4 - - - +
282B ALA* 1.3 65.1 + - - +
284B ASN* 3.5 5.9 + - - +
285B ALA* 3.2 21.5 + - - +
303B PRO 5.1 3.1 - - - +
304B GLY* 4.4 21.8 - - - -
514B ARG* 5.9 6.4 - - - +
575B TRP* 3.8 21.5 - - + -
2C C 6.3 1.1 - - - -
3C C 6.3 2.3 - - - -
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU* 5.4 2.0 - - + -
278B GLY 3.0 18.4 + - - +
279B TYR 3.7 4.3 - - - +
280B ALA 3.3 0.2 - - - -
281B LYS* 1.3 78.6 - - - +
283B ILE* 1.3 63.1 + - + +
285B ALA* 3.2 6.5 + - - +
286B LEU* 3.1 26.3 + - + +
304B GLY 3.7 18.3 + - - +
305B ILE* 4.0 10.0 - - + +
309B MET* 3.8 29.8 - - + -
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Residues in contact with ILE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B THR* 4.2 9.6 - - - -
260B LEU* 3.6 30.1 - - + +
261B GLU* 3.6 48.7 - - + +
264B ALA* 4.3 6.7 - - + -
279B TYR* 3.0 27.5 + - + +
280B ALA* 3.8 6.7 - - - +
281B LYS 3.4 0.2 - - - -
282B ALA* 1.3 74.8 - - - +
284B ASN* 1.3 63.8 + - - +
286B LEU* 3.3 8.5 + - - +
287B LYS* 3.1 46.5 + - + +
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Residues in contact with ASN 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B ALA 3.1 9.1 + - - +
281B LYS* 3.8 7.5 + - - +
282B ALA 3.2 0.2 - - - -
283B ILE* 1.3 77.1 - - - +
285B ALA* 1.3 67.3 + - - +
287B LYS* 3.2 9.1 + - - +
288B SER* 2.9 36.2 + - - -
575B TRP* 3.0 71.5 + - + +
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B LYS 3.2 10.0 + - - +
282B ALA* 3.2 11.3 + - - +
284B ASN* 1.3 82.7 - - - +
286B LEU* 1.3 62.1 + - - +
288B SER* 3.6 7.9 + - - +
289B PHE* 3.5 25.6 + - - +
302B ILE* 3.6 28.6 - - + +
303B PRO 4.0 11.0 - - - +
305B ILE* 4.5 4.0 - - + -
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B ASN* 4.0 2.5 - - - +
252B HIS 5.2 0.3 + - - -
253B ASN* 3.0 32.3 + - + +
256B ILE* 3.6 29.8 - - + -
257B THR* 3.7 13.9 - - + -
260B LEU* 3.9 13.7 - - + -
282B ALA* 3.1 15.9 + - + +
283B ILE* 3.6 8.7 - - - +
284B ASN 3.2 0.2 - - - -
285B ALA* 1.3 75.7 - - - +
287B LYS* 1.3 63.3 + - - +
289B PHE* 3.4 9.6 + - + +
293B VAL* 3.6 31.0 - - + -
302B ILE* 4.7 3.1 - - + -
305B ILE* 4.0 17.0 - - + -
313B ILE* 3.7 20.2 - - + -
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Residues in contact with LYS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B ALA* 4.7 4.5 - - - +
250B THR 3.6 20.8 - - - +
251B ASN* 3.2 33.1 - - + +
252B HIS 4.9 0.2 + - - -
257B THR* 4.0 17.0 - - + -
261B GLU* 3.0 29.7 + - - -
283B ILE* 3.1 31.3 + - + +
284B ASN* 3.2 9.2 + - - +
286B LEU* 1.3 76.8 - - - +
288B SER* 1.3 57.9 + - - +
289B PHE 3.4 2.3 + - - +
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Residues in contact with SER 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ALA* 5.2 13.5 - - - -
250B THR 5.5 0.2 - - - -
284B ASN* 2.9 27.0 + - - -
285B ALA* 3.8 8.0 + - - +
286B LEU 3.2 0.2 - - - -
287B LYS* 1.3 76.6 - - - +
289B PHE* 1.3 59.8 + - - +
290B HIS 4.1 1.2 + - - -
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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) + - + + + + + -
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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