Contacts of the helix formed by residues 275 - 289 (chain B) in PDB entry 4EVI
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 275 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274B PRO* 1.3 74.4 - - - +
276B GLU* 1.3 55.0 + - - +
278B VAL* 3.7 0.8 - - - +
279B LEU* 2.7 38.3 + - - +
335B ARG* 2.7 41.5 + - - +
339B GLN* 5.7 5.0 + - - +
343B LEU* 3.8 22.0 - - + +
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Residues in contact with GLU 276 (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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274B PRO* 4.6 1.7 - - + +
275B ASP* 1.3 77.6 - - - +
277B PRO* 1.3 73.0 - - + +
279B LEU* 3.5 6.0 + - - +
280B LYS* 3.1 23.4 + - + +
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Residues in contact with PRO 277 (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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254B PHE* 3.6 30.1 - - + -
273B TRP* 4.5 7.6 - - + -
274B PRO* 3.2 38.8 - - + +
276B GLU* 1.3 99.3 - - + +
278B VAL* 1.3 59.9 + - - +
280B LYS* 3.7 9.6 - - + +
281B MET* 3.1 23.6 + - - +
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Residues in contact with VAL 278 (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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270B LEU* 3.9 35.0 - - + +
273B TRP* 3.7 28.9 - - + +
274B PRO 3.1 19.5 + - - +
275B ASP* 3.7 3.4 - - - +
277B PRO* 1.3 73.9 - - - +
279B LEU* 1.3 60.5 + - - +
281B MET* 3.1 11.0 + - + +
282B LEU* 2.8 52.5 + - + +
335B ARG* 3.8 8.7 - - - +
340B TRP* 5.3 1.3 - - + -
343B LEU* 4.4 14.6 - - + -
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Residues in contact with LEU 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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275B ASP 2.7 21.2 + - - +
276B GLU* 3.8 5.6 - - - +
278B VAL* 1.3 73.2 - - - +
280B LYS* 1.3 65.1 + - - +
282B LEU* 3.1 6.3 + - - +
283B LYS* 2.9 52.5 + - + +
343B LEU* 3.8 20.1 - - + +
346B GLU* 3.7 19.5 - - + -
347B ALA* 3.5 36.3 - - + +
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Residues in contact with LYS 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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254B PHE 4.3 12.8 + - - +
276B GLU* 3.1 17.6 + - + +
277B PRO* 3.7 8.7 - - + +
279B LEU* 1.3 76.9 - - - +
281B MET* 1.3 61.1 + - - +
283B LYS* 3.5 10.3 + - - +
284B GLN* 3.0 56.8 + - + +
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Residues in contact with MET 281 (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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253B MET* 3.5 55.0 - - + +
254B PHE* 3.9 23.6 - - + -
258B ILE* 4.2 13.2 - - + -
266B PHE* 3.8 16.2 - - + -
270B LEU* 3.4 33.2 - - + -
277B PRO 3.1 15.0 + - - +
278B VAL* 3.5 6.7 - - + +
280B LYS* 1.3 76.0 - - - +
282B LEU* 1.3 60.0 + - + +
284B GLN* 3.3 13.1 + - - +
285B CYS* 2.9 26.6 + - - -
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Residues in contact with LEU 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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266B PHE* 4.8 7.2 - - + -
270B LEU* 4.3 21.5 - - + -
278B VAL* 2.8 36.3 + - + +
279B LEU* 3.6 3.8 - - - +
281B MET* 1.3 74.4 - - + +
283B LYS* 1.3 55.7 + - - +
285B CYS* 3.0 6.3 + - + +
286B LYS 2.8 30.3 + - - -
298B LEU* 3.7 29.6 - - + -
300B ILE* 4.9 0.4 - - + -
340B TRP* 5.7 1.1 - - + -
343B LEU* 4.3 22.4 - - + +
344B PHE* 4.5 17.5 - - + -
347B ALA* 3.6 21.3 - - + -
349B PHE* 3.4 9.7 - - + -
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Residues in contact with LYS 283 (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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279B LEU* 2.9 42.8 + - + +
280B LYS* 3.6 9.2 - - - +
282B LEU* 1.3 75.4 - - - +
284B GLN* 1.3 63.0 + - + +
286B LYS* 3.3 3.8 + - - +
287B LYS* 3.1 21.8 + - - +
346B GLU* 3.7 19.1 - - - -
347B ALA* 3.8 24.5 - - - +
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Residues in contact with GLN 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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253B MET 4.2 9.7 + - - -
254B PHE 4.2 14.4 + - - +
256B ASP 5.1 5.3 + - - -
257B GLU* 6.1 1.4 - - - +
258B ILE* 5.7 5.4 - - + +
280B LYS* 3.0 41.4 + - + +
281B MET* 3.5 20.0 + - - +
282B LEU 3.2 0.4 - - - -
283B LYS* 1.3 79.5 - - + +
285B CYS* 1.3 61.8 + - - +
287B LYS* 3.4 7.3 + - - +
288B ALA* 3.1 22.7 + - - +
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Residues in contact with CYS 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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258B ILE* 3.6 29.2 - - - -
264B VAL* 4.2 12.6 - - + -
266B PHE* 4.0 22.9 - - - -
281B MET 2.9 21.7 + - - +
282B LEU* 3.0 11.9 + - - +
284B GLN* 1.3 78.5 - - - +
286B LYS* 1.3 57.6 + - - +
288B ALA* 3.3 5.0 + - - +
289B LEU* 2.9 45.4 + - + +
298B LEU* 4.9 4.9 - - + -
349B PHE* 4.3 7.6 - - + -
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Residues in contact with LYS 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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282B LEU 2.8 12.8 + - - +
283B LYS 3.6 6.5 - - - +
285B CYS* 1.3 69.7 - - - +
287B LYS* 1.3 59.2 + - - +
289B LEU* 4.0 1.5 - - - -
290B THR* 2.7 50.8 + - - +
347B ALA 3.7 13.5 - - - +
348B GLY* 3.3 25.3 + - - +
349B PHE* 3.6 26.2 - - + -
350B LYS* 3.8 8.0 - - - +
368B PRO* 3.2 35.1 + - + -
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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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283B LYS 3.1 12.5 + - - +
284B GLN* 3.6 10.8 - - - +
285B CYS 3.3 0.2 - - - -
286B LYS* 1.3 80.2 - - - +
288B ALA* 1.3 64.1 + - - +
290B THR* 3.1 22.5 + - - -
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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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258B ILE* 5.0 13.7 - - + +
259B PRO 5.8 0.7 - - - +
260B HIS* 5.6 13.0 - - + +
264B VAL* 6.0 3.4 - - + -
284B GLN 3.1 14.2 + - - +
285B CYS* 3.7 6.3 - - - +
287B LYS* 1.3 81.2 - - - +
289B LEU* 1.3 61.6 + - + +
290B THR 3.0 12.3 + - - -
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Residues in contact with LEU 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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261B ALA 3.7 23.6 - - - +
262B ASP 4.5 0.2 - - - +
264B VAL* 3.8 24.7 - - + +
285B CYS* 2.9 27.8 + - + +
286B LYS* 4.3 1.8 - - - +
288B ALA* 1.3 73.9 - - + +
290B THR* 1.3 58.6 + - - +
294B VAL 3.0 3.3 - - - +
295B LYS* 3.0 7.4 - - - +
296B GLY* 2.7 35.3 + - - +
297B LYS* 3.5 43.1 - - - +
298B LEU* 3.6 15.5 - - + +
349B PHE* 4.3 11.2 - - + -
368B PRO* 4.2 9.4 - - + -
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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
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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