Contacts of the helix formed by residues 290 - 305 (chain B) in PDB entry 3C6M
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 290 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B THR* 1.3 81.8 + - - +
292B TRP* 3.2 9.7 - - - +
293B GLU* 3.2 28.4 + - - +
294B PHE* 3.0 22.6 + - - +
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Residues in contact with THR 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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280B VAL* 4.3 27.1 - - + -
281B PRO* 5.7 0.7 - - - +
290B SER* 1.3 84.5 + - - +
292B TRP* 1.3 76.3 + - - +
294B PHE* 3.3 11.7 - - + +
295B LEU* 3.1 31.6 + - - +
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Residues in contact with TRP 292 (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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290B SER 3.2 6.2 - - - +
291B THR* 1.3 88.6 + - - +
293B GLU* 1.3 58.5 + - - +
294B PHE 3.2 0.4 - - - -
295B LEU* 3.2 28.3 + - + +
296B ARG 2.9 24.3 + - - -
317B ASN* 5.6 2.5 - - - -
324B ALA* 3.4 32.8 - - + -
327B LEU* 3.5 37.5 - - + +
328B TYR* 3.7 23.8 - - + -
331B GLN* 3.5 37.8 - - + +
334B ARG* 5.8 0.7 - - - +
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Residues in contact with GLU 293 (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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290B SER* 3.2 25.7 + - - +
292B TRP* 1.3 77.2 - - + +
294B PHE* 1.3 58.8 + - - +
296B ARG* 3.3 20.6 + - - +
297B LEU* 2.8 29.9 + - - +
331B GLN* 5.0 0.7 - - - -
231D LYS* 3.2 46.4 + - - +
232D TYR* 3.9 22.8 + - + -
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Residues in contact with PHE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ILE* 4.0 33.0 - - + -
280B VAL* 5.9 1.3 - - + -
281B PRO* 3.5 47.1 - - + -
282B ILE 3.7 20.4 - - - -
283B SER* 3.8 20.6 - - - -
285B SER* 6.6 0.2 - - - -
290B SER 3.0 11.9 + - - +
291B THR* 3.3 14.6 - - + +
292B TRP 3.2 0.2 - - - -
293B GLU* 1.3 78.8 - - - +
295B LEU* 1.3 62.2 + - + +
297B LEU* 3.2 19.6 + - + +
298B ILE* 3.1 32.3 + - + +
401B MTA 5.0 1.3 - - - -
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Residues in contact with LEU 295 (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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275B ASN* 6.3 1.3 - - - +
279B ALA 4.4 10.3 - - - +
281B PRO* 3.8 34.5 - - + -
291B THR* 3.1 20.0 + - - +
292B TRP* 3.2 35.2 + - + +
294B PHE* 1.3 74.0 - - - +
296B ARG* 1.3 63.9 + - - +
298B ILE* 3.2 17.3 + - + +
299B LEU* 3.2 19.2 + - - +
328B TYR* 4.0 24.0 - - + -
331B GLN* 4.7 6.5 - - + -
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Residues in contact with ARG 296 (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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292B TRP 2.9 8.1 + - - +
293B GLU* 3.6 22.8 + - - +
295B LEU* 1.3 77.4 - - - +
297B LEU* 1.3 76.9 + - - +
299B LEU* 3.3 5.9 + - - +
300B ASP* 2.4 58.7 + - - +
331B GLN* 3.5 36.2 - - + +
334B ARG* 3.2 32.3 - - + +
335B LEU* 3.8 14.5 - - + +
231D LYS 5.6 2.2 + - - -
234D ARG* 3.4 34.5 - - - +
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Residues in contact with LEU 297 (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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257B ILE* 4.5 14.6 - - + -
261B LYS* 5.6 5.4 - - - -
293B GLU 2.8 17.4 + - - +
294B PHE* 3.2 31.6 + - + +
296B ARG* 1.3 93.5 - - - +
298B ILE* 1.3 59.8 - - - +
300B ASP* 3.4 3.5 + - + +
301B LEU* 3.1 49.5 + - + +
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Residues in contact with ILE 298 (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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197B LEU* 3.7 18.4 - - + -
256B CYS* 5.1 1.3 - - - -
257B ILE* 3.9 21.1 - - + -
260B LEU* 4.5 5.8 - - + -
275B ASN* 3.5 26.5 - - - +
277B LEU* 4.1 10.1 - - + -
281B PRO* 3.7 35.4 - - + -
294B PHE* 3.1 28.6 + - + +
295B LEU* 3.2 11.2 + - + +
297B LEU* 1.3 75.8 - - - +
299B LEU* 1.3 51.8 + - + +
301B LEU* 3.4 8.4 + - - +
302B SER* 2.7 41.6 + - - +
312B TYR* 4.7 0.4 - - - +
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Residues in contact with LEU 299 (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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295B LEU 3.2 15.0 + - - +
296B ARG* 3.5 7.2 - - - +
298B ILE* 1.3 76.8 - - + +
300B ASP* 1.3 66.9 + - - +
302B SER* 3.7 3.2 - - - -
303B MET* 2.9 36.4 + - + +
312B TYR* 3.6 40.4 - - + +
328B TYR* 3.8 26.2 - - + +
331B GLN* 4.2 18.8 - - + -
332B LEU* 3.9 29.2 - - + -
335B LEU* 3.7 16.4 - - + -
360B VAL* 5.0 0.2 - - + -
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Residues in contact with ASP 300 (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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296B ARG* 2.4 42.8 + - - +
297B LEU* 3.6 10.3 - - + +
299B LEU* 1.3 77.1 - - - +
301B LEU* 1.3 67.0 + - + +
303B MET* 3.2 5.6 + - - +
304B LYS* 3.0 30.5 + - + +
334B ARG 4.5 0.7 - - - +
335B LEU* 3.4 11.4 - - - +
336B TYR* 2.8 45.2 + - + +
234D ARG* 4.7 5.7 + - - -
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Residues in contact with LEU 301 (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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257B ILE* 3.8 39.0 - - + +
260B LEU* 3.8 26.5 - - + +
261B LYS* 4.0 28.9 - - + +
264B ALA* 5.4 5.3 - - + +
297B LEU* 3.1 34.4 + - + +
298B ILE 3.7 3.8 - - - +
300B ASP* 1.3 82.1 - - + +
302B SER* 1.3 61.2 + - - +
304B LYS* 3.3 22.0 + - + +
305B VAL* 3.4 17.8 + - - +
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Residues in contact with SER 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU* 3.6 19.4 - - - +
260B LEU* 4.3 4.8 - - - +
273B VAL* 3.9 7.8 - - - +
298B ILE* 2.7 26.5 + - - +
299B LEU 3.7 3.4 - - - -
301B LEU* 1.3 69.3 - - - +
303B MET* 1.3 68.5 + - - +
305B VAL* 3.2 14.6 + - - +
306B LEU* 3.1 21.8 + - - +
312B TYR* 3.4 37.9 - - - -
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Residues in contact with MET 303 (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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299B LEU* 2.9 25.2 + - + +
300B ASP 3.5 4.7 - - - +
302B SER* 1.3 77.3 - - - +
304B LYS* 1.3 54.2 + - - +
306B LEU* 2.9 32.4 + - + +
312B TYR* 3.7 44.4 - - + -
335B LEU* 4.1 19.1 - - + -
336B TYR* 3.6 17.3 - - + -
337B CYS* 4.1 12.1 - - - -
339B VAL* 4.0 17.3 - - - -
360B VAL* 4.6 11.7 - - + -
362B LYS* 2.7 36.6 + - - -
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Residues in contact with LYS 304 (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 ALA* 4.3 22.5 - - + +
268B ARG 4.6 0.9 - - - +
269B GLU* 4.4 12.5 - - - +
300B ASP* 3.0 20.1 + - + +
301B LEU* 3.7 18.2 - - + +
302B SER 3.3 0.6 - - - -
303B MET* 1.3 75.1 - - - +
305B VAL* 1.3 60.8 + - - +
336B TYR* 3.5 54.1 - - + +
362B LYS* 4.8 1.4 + - - -
239D ASP* 4.7 7.5 + - - +
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Residues in contact with VAL 305 (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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195B LEU* 4.1 15.5 - - + -
260B LEU* 3.9 26.0 - - + +
263B TYR* 3.9 6.1 - - + -
264B ALA* 3.5 32.1 - - + +
268B ARG 3.5 17.3 - - - +
269B GLU* 3.1 5.3 - - - +
270B PHE* 2.8 41.4 + - + +
273B VAL* 4.2 3.5 - - + +
301B LEU 3.4 12.5 + - - +
302B SER* 3.3 13.9 - - - +
303B MET 3.0 0.8 - - - -
304B LYS* 1.3 79.9 - - - +
306B LEU* 1.3 54.1 + - - +
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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