Contacts of the helix formed by residues 278 - 292 (chain B) in PDB entry 3DYQ
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 SER 278 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B LYS 4.4 0.2 + - - -
277B PHE* 1.3 78.4 - - - +
279B GLN* 1.3 65.4 + - - +
280B THR* 3.4 11.4 + - - -
281B ASP* 3.0 32.8 + - - +
282B ILE* 3.0 20.7 + - - +
351B GLN* 5.3 1.4 + - - -
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Residues in contact with GLN 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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222B LEU 2.9 24.9 + - - +
223B GLY* 4.0 8.9 + - - -
224B LEU* 3.8 6.4 - - + +
226B ARG* 4.4 3.4 - - - +
227B ASP* 3.1 30.1 + - + +
228B PHE* 3.6 19.6 - - + -
274B GLN* 3.5 22.5 + - - +
277B PHE 5.2 1.4 - - - +
278B SER* 1.3 70.6 - - - +
280B THR* 1.3 67.3 + - - +
282B ILE* 3.0 14.8 + - - +
283B LEU* 2.8 24.6 + - - +
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Residues in contact with THR 280 (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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228B PHE* 3.3 22.5 - - + -
278B SER* 3.2 10.6 + - - -
279B GLN* 1.3 79.0 - - - +
281B ASP* 1.3 61.5 + - - +
283B LEU* 3.1 3.3 + - - +
284B ILE* 3.0 29.4 + - + +
348B GLY* 5.2 2.0 - - - +
351B GLN* 3.6 30.3 + - + +
352B ILE* 3.8 27.6 - - + -
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Residues in contact with ASP 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B PHE* 3.6 27.8 - - + -
278B SER* 3.0 30.7 + - - +
280B THR* 1.3 79.5 - - - +
282B ILE* 1.3 56.9 + - - +
284B ILE* 3.3 12.8 + - - +
285B LEU* 2.9 32.9 + - - +
351B GLN* 5.5 2.7 - - - +
390B MET* 4.7 4.7 - - - +
394B LYS* 2.8 36.4 + - + +
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Residues in contact with ILE 282 (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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222B LEU* 4.3 27.4 - - + -
224B LEU* 3.9 15.3 - - + -
268B VAL* 4.0 28.9 - - + -
273B LEU* 4.2 21.1 - - + +
274B GLN* 4.6 6.7 - - + +
277B PHE* 4.2 14.4 - - + +
278B SER 3.0 16.9 + - - +
279B GLN* 3.0 24.9 + - - +
281B ASP* 1.3 76.5 - - - +
283B LEU* 1.3 62.5 + - - +
285B LEU* 3.3 11.7 + - + +
286B MET* 3.0 26.6 + - + +
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B TYR* 3.8 22.2 - - + -
224B LEU* 3.9 19.0 - - + +
228B PHE* 3.7 31.6 - - + -
230B ILE* 4.6 6.7 - - + -
279B GLN 2.8 13.0 + - - +
280B THR 3.4 8.1 - - - +
282B ILE* 1.3 77.0 - - - +
284B ILE* 1.3 55.9 + - - +
286B MET* 3.8 0.3 - - - +
287B THR* 2.6 54.3 + - - +
341B PHE* 3.9 22.4 - - + -
344B ILE* 4.2 1.8 - - + -
352B ILE* 3.7 31.4 - - + -
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Residues in contact with ILE 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 THR* 3.0 25.5 + - + +
281B ASP* 3.5 24.0 - - - +
282B ILE 3.3 0.2 - - - -
283B LEU* 1.3 72.2 - - - +
285B LEU* 1.3 66.3 + - - +
288B ALA* 2.9 28.2 + - - +
351B GLN* 3.9 22.7 - - + +
352B ILE* 3.9 24.9 - - + +
355B GLY* 3.6 27.1 - - - -
356B MET* 3.8 10.2 - - - +
359B LEU* 3.5 24.2 - - + -
394B LYS* 4.6 9.2 - - + +
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Residues in contact with LEU 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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264B MET* 3.9 35.7 - - + +
268B VAL* 5.5 0.9 - - + -
273B LEU* 4.5 9.4 - - + -
277B PHE* 4.8 7.0 - - + -
281B ASP 2.9 23.6 + - - +
282B ILE* 3.7 20.6 - - + +
284B ILE* 1.3 75.2 - - - +
286B MET* 1.3 59.4 + - + +
288B ALA* 3.7 1.7 - - - +
289B ALA* 2.9 30.2 + - - +
359B LEU* 3.9 15.0 - - + -
394B LYS* 3.8 43.1 - - + +
397B LEU* 4.1 17.9 - - + -
398B ILE* 4.6 0.2 - - - +
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Residues in contact with MET 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B MET* 3.9 28.9 - - + -
219B TYR* 3.5 24.0 - - + +
222B LEU* 3.9 22.7 - - + -
224B LEU* 4.4 4.7 - - + -
261B ALA* 3.7 26.2 - - + +
264B MET* 3.7 23.8 - - + +
265B TYR* 3.9 16.2 - - + -
268B VAL* 5.2 2.5 - - + -
282B ILE* 3.0 23.3 + - + +
283B LEU 4.0 1.3 - - - +
285B LEU* 1.3 78.7 - - + +
287B THR* 1.3 58.3 + - - +
289B ALA* 3.1 5.6 + - - +
290B ILE* 2.9 32.8 + - + +
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Residues in contact with THR 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B TYR* 2.9 14.4 + - - -
238B TRP* 3.6 30.3 - - + -
283B LEU* 2.6 36.5 + - - +
286B MET* 1.3 72.9 - - - +
288B ALA* 1.3 65.9 + - - +
290B ILE* 3.3 2.7 + - - +
291B CYS* 3.0 30.8 + - - -
333B LEU* 5.1 1.8 - - + -
340B ILE* 4.4 2.0 - - + -
341B PHE* 4.1 13.3 - - + -
356B MET* 3.5 29.8 - - + -
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Residues in contact with ALA 288 (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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284B ILE 2.9 18.4 + - - +
285B LEU 3.7 1.6 - - - +
287B THR* 1.3 75.3 - - - +
289B ALA* 1.3 58.9 + - - +
291B CYS 3.1 0.5 + - - -
292B HIS* 2.9 35.3 + - - +
356B MET* 4.1 11.0 - - - +
359B LEU* 4.0 20.2 - - + -
360B ILE* 4.0 17.6 - - + +
398B ILE* 3.5 19.7 - - + -
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Residues in contact with ALA 289 (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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246B TYR* 4.6 0.2 + - - -
257B CYS* 4.3 5.7 - - - +
260B VAL* 4.1 16.4 - - + +
261B ALA* 4.0 23.1 - - - -
264B MET* 4.3 15.7 - - + -
285B LEU 2.9 19.7 + - - +
286B MET* 3.1 9.6 + - - +
288B ALA* 1.3 77.7 - - - +
290B ILE* 1.3 57.5 + - - +
292B HIS* 3.1 25.2 + - - -
398B ILE* 3.9 8.7 - - + -
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Residues in contact with ILE 290 (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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215B LEU* 4.2 18.4 - - + -
219B TYR* 3.3 42.4 - - + +
238B TRP* 3.8 20.9 - - + -
239B LEU* 4.4 10.8 - - + -
242B VAL* 3.7 22.9 - - + -
246B TYR* 2.6 29.6 + - - -
257B CYS* 3.4 14.7 - - - -
261B ALA* 3.9 20.2 - - + -
286B MET* 2.9 16.5 + - + +
287B THR 3.8 4.5 - - - +
288B ALA 3.3 0.2 - - - -
289B ALA* 1.3 76.4 - - - +
291B CYS* 1.3 55.5 + - - +
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Residues in contact with CYS 291 (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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238B TRP* 3.9 26.9 - - - -
242B VAL* 4.6 4.5 - - - -
246B TYR* 3.5 2.7 - - - -
287B THR* 3.0 25.2 + - - +
288B ALA 3.1 1.8 + - - +
290B ILE* 1.3 82.8 - - - +
292B HIS* 1.3 58.5 + - - +
293B ASP 2.9 10.0 + - - -
294B LEU* 3.1 39.1 + - + +
325B HIS* 3.9 6.4 - - - +
329B ALA* 3.7 20.6 - - + -
333B LEU* 5.7 0.9 - - - -
356B MET* 4.5 3.1 - - + -
360B ILE* 4.3 7.7 - - + +
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Residues in contact with HIS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B TYR* 4.4 1.2 + - - -
256B HIS* 3.6 5.8 - + - -
257B CYS* 4.7 5.4 - - - -
260B VAL* 3.6 32.8 - - + +
288B ALA 2.9 16.1 + - - +
289B ALA 3.1 18.7 + - - -
290B ILE 3.5 0.4 - - - -
291B CYS* 1.3 76.5 - - - +
293B ASP* 1.3 77.4 + - + +
294B LEU 3.6 0.4 - - - -
325B HIS* 2.9 23.3 - - - +
360B ILE* 3.8 19.4 - - + +
363B THR* 4.2 24.2 + - + -
398B ILE* 4.4 3.8 - - + -
402B ASP* 2.9 17.4 + - + -
901B NA 2.4 30.6 - - - -
902B NA 4.3 2.0 - - - -
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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