Contacts of the helix formed by residues 286 - 299 (chain F) in PDB entry 2POZ
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 GLY 286 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94F SER* 3.1 13.4 + - - -
97F GLU* 3.2 12.8 - - - -
98F GLN* 4.9 0.2 - - - -
281F ILE* 3.4 19.0 + - - -
285F GLY* 1.3 79.9 - - - +
287F LEU* 1.3 58.5 + - - -
288F MSE 3.5 1.8 - - - -
289F GLU 4.0 1.1 - - - -
290F THR* 2.7 37.2 + - - -
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Residues in contact with LEU 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F GLU* 2.7 12.1 + - - +
98F GLN* 4.3 18.5 - - + +
101F TRP* 4.2 19.1 - - + -
112F VAL* 4.4 9.4 - - + -
116F PHE* 3.9 14.9 - - + -
281F ILE* 3.7 23.5 - - + +
286F GLY* 1.3 71.2 - - - +
288F MSE 1.3 57.1 + - - +
290F THR* 3.4 2.5 + - - -
291F LYS* 2.9 26.3 + - - +
317F ALA* 3.4 23.6 - - + +
320F GLN* 4.5 4.9 - - + -
321F LEU* 3.7 21.2 - - + +
366F LEU* 3.5 31.4 - - + -
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Residues in contact with MSE 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LEU 4.9 0.7 - - - +
116B PHE* 3.9 18.6 - - - +
288B MSE 4.7 15.5 - - + +
291B LYS* 4.0 11.7 - - - -
68F ILE* 6.0 0.2 - - + -
69F GLU* 4.0 10.5 - - - +
97F GLU* 2.8 19.6 + - - +
101F TRP* 3.7 28.5 - - + +
116F PHE* 3.9 28.2 - - + -
287F LEU* 1.3 72.2 - - - +
289F GLU* 1.3 64.6 + - - +
291F LYS* 3.1 19.0 + - + -
292F LYS* 2.9 52.6 + - - +
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Residues in contact with GLU 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F TRP* 3.7 22.3 - - + +
97F GLU* 3.8 3.0 + - - +
261F THR* 3.5 8.3 - - - -
262F ARG* 2.8 65.8 + - - +
263F PHE* 5.3 0.5 - - - -
284F ALA 3.5 22.9 - - - +
285F GLY* 3.7 26.7 - - - +
286F GLY 3.6 0.2 + - - -
287F LEU 3.4 0.4 - - - -
288F MSE 1.3 78.2 - - - +
290F THR* 1.3 57.7 + - - +
292F LYS* 3.2 12.3 + - - +
293F ILE* 2.9 31.3 + - + +
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Residues in contact with THR 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279F PRO* 3.7 30.1 - - + -
281F ILE* 3.6 24.3 - - + +
284F ALA* 3.7 12.5 - - - +
286F GLY 2.7 22.6 + - - -
287F LEU 3.7 4.3 - - - -
289F GLU* 1.3 75.8 - - - +
291F LYS* 1.3 65.3 + - - +
293F ILE* 3.1 8.2 + - - +
294F CYS* 2.9 23.6 + - - -
321F LEU* 3.5 26.7 - - + -
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Residues in contact with LYS 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLU* 2.7 25.5 + - - +
288B MSE 3.9 17.0 - - - -
292B LYS* 4.1 13.9 - - - +
116F PHE* 3.4 37.9 - - + -
287F LEU 2.9 15.2 + - - +
288F MSE 3.1 22.4 + - - +
290F THR* 1.3 75.0 - - - +
292F LYS* 1.3 58.4 + - + +
294F CYS* 3.2 6.4 + - - +
295F ALA* 2.9 27.3 + - - +
321F LEU* 3.7 13.9 - - + +
324F ASN* 2.6 29.4 + - - +
325F ILE* 4.7 8.1 - - + +
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Residues in contact with LYS 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B LYS* 4.2 11.3 - - - +
292B LYS* 5.8 6.1 - - + +
295B ALA* 3.7 27.8 - - + +
298B GLU* 4.9 3.0 + - - -
326B THR* 5.5 1.2 + - - -
69F GLU* 2.9 38.1 + - - -
262F ARG* 3.9 37.8 - - - +
288F MSE 2.9 36.6 + - - +
289F GLU* 3.3 15.4 + - - +
291F LYS* 1.3 76.7 - - + +
293F ILE* 1.3 63.1 + - - +
295F ALA* 3.1 9.3 + - - +
296F MSE 2.9 27.9 + - + +
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Residues in contact with ILE 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F THR* 3.7 18.2 - - - -
262F ARG* 3.7 20.9 - - + +
265F PHE* 3.7 38.1 - - + -
269F PHE* 3.6 2.9 - - + -
277F ILE* 3.6 22.9 - - + -
279F PRO* 4.6 6.7 - - + -
284F ALA* 3.9 22.9 - - + +
289F GLU 2.9 20.5 + - - +
290F THR* 3.4 11.9 - - - +
292F LYS* 1.3 75.7 - - - +
294F CYS* 1.3 58.3 + - - +
296F MSE 3.1 12.6 + - - +
297F ALA* 2.9 23.2 + - - +
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Residues in contact with CYS 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277F ILE* 5.0 0.7 - - - -
279F PRO* 4.6 3.8 - - - -
290F THR* 2.9 33.6 + - - +
291F LYS 3.6 4.0 - - - +
293F ILE* 1.3 74.0 - - - +
295F ALA* 1.3 66.0 + - - +
297F ALA* 3.2 7.6 + - - -
298F GLU* 3.2 9.6 + - - +
304F VAL* 3.7 32.3 - - + -
321F LEU* 4.5 1.6 - - - -
325F ILE* 4.0 26.0 - - + -
327F ASN* 3.2 35.8 + - - +
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Residues in contact with ALA 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B ARG* 2.9 35.8 + - - +
292B LYS* 3.7 40.2 - - + +
296B MSE 5.5 0.4 - - + -
291F LYS 2.9 13.8 + - - +
292F LYS* 3.4 11.2 - - - +
294F CYS* 1.3 76.4 - - - +
296F MSE 1.3 63.6 + - + +
298F GLU* 3.3 13.1 + - - +
299F ALA* 3.8 2.1 + - - +
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Residues in contact with MSE 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B LYS 5.6 0.2 - - - +
295B ALA* 6.4 0.4 - - + -
296B MSE 3.8 50.5 - - + +
299B ALA* 4.8 6.7 - - - -
300B TYR* 6.0 1.6 - - - -
262F ARG* 3.2 56.8 - - + +
265F PHE* 4.4 0.7 - - + -
266F ARG* 5.6 2.2 - - - -
269F PHE* 3.4 31.2 - - + -
292F LYS* 2.9 14.7 + - + +
293F ILE* 3.4 15.0 - - + +
295F ALA* 1.3 77.4 - - - +
297F ALA* 1.3 57.0 + - - +
299F ALA* 2.9 26.9 + - - +
300F TYR* 3.4 9.7 - - + -
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Residues in contact with ALA 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269F PHE* 3.7 17.9 - - + -
277F ILE* 3.7 25.1 - - + -
293F ILE 2.9 13.4 + - - +
294F CYS* 3.2 11.2 + - - +
296F MSE 1.3 76.0 - - - +
298F GLU* 1.3 56.8 + - - +
300F TYR* 2.9 17.2 + - - +
302F MSE 3.2 29.2 + - + +
304F VAL* 4.6 0.2 - - + -
327F ASN* 3.8 11.9 - - - +
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Residues in contact with GLU 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B TRP* 6.0 0.7 - - - -
262B ARG* 3.0 30.2 + - - +
263B PHE* 3.7 11.6 - - + -
292B LYS* 5.0 3.8 + - - -
294F CYS 3.2 6.1 + - - +
295F ALA* 3.4 15.9 - - - +
296F MSE 3.1 0.8 - - - -
297F ALA* 1.3 71.7 - - - +
299F ALA* 1.3 59.1 + - - +
300F TYR 2.9 9.1 + - - -
301F ASN 3.1 2.3 + - - -
302F MSE 4.4 1.6 - - - -
326F THR* 3.8 36.9 + - - +
327F ASN* 3.4 28.1 - - + +
175H ARG* 2.8 39.2 + - - +
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Residues in contact with ALA 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B ARG* 4.4 19.7 - - + +
263B PHE* 3.5 27.6 - - + -
266B ARG* 2.6 39.4 + - + -
296B MSE 4.7 5.4 - - - -
295F ALA 3.8 0.6 + - - -
296F MSE 2.9 15.2 + - - +
298F GLU* 1.3 78.8 - - - +
300F TYR* 1.3 61.6 + - + +
301F ASN 3.6 0.7 - - - -
238H ASP* 3.5 6.4 - - - +
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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