Contacts of the helix formed by residues 285 - 298 (chain B) in PDB entry 3OPY
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 285 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189B SER 4.1 2.6 + - - -
190B GLY* 5.3 1.5 - - - -
284B GLY* 1.3 74.0 - - - -
286B ASP* 1.3 60.2 + - - +
287B GLY 3.7 1.1 - - - -
288B SER* 3.3 16.3 + - - -
289B LEU* 3.0 30.4 + - - +
329B VAL* 4.3 10.3 - - - -
330B GLY 3.7 8.8 + - - -
331B SER* 4.4 7.9 - - - -
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Residues in contact with ASP 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLY* 1.3 69.3 - - - +
287B GLY* 1.3 53.0 + - - +
288B SER* 4.4 0.2 + - - -
289B LEU* 3.1 7.4 + - - +
290B THR* 2.8 41.1 + - + +
331B SER* 4.8 5.9 + - - -
333B ASP* 4.4 1.8 - - - +
335B ASP* 2.9 38.3 - - - +
336B MET* 3.6 32.8 + - - +
378B HIS* 3.7 19.2 + - - -
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Residues in contact with GLY 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ASP* 1.3 74.9 - - - +
288B SER* 1.3 57.6 + - - +
290B THR* 3.1 15.8 + - - +
291B GLY* 2.7 32.9 + - - -
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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
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189B SER* 3.6 23.3 + - - -
190B GLY* 4.0 14.9 + - - -
221B TYR* 2.7 38.3 + - - -
282B VAL* 4.3 3.5 - - - +
284B GLY* 4.1 2.0 - - - -
285B GLY* 3.3 31.3 + - - -
287B GLY* 1.3 75.4 + - - +
289B LEU* 1.4 58.7 + - - +
292B ALA* 3.5 2.1 + - - +
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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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282B VAL* 3.9 27.6 - - + +
284B GLY 4.0 8.3 - - - +
285B GLY 3.0 20.8 + - - +
286B ASP* 3.6 3.1 - - - +
288B SER* 1.4 74.8 - - - +
290B THR* 1.4 58.7 + - - +
291B GLY 3.3 1.6 - - - -
292B ALA* 3.3 7.8 + - + +
293B ASP* 2.9 27.9 + - - +
327B GLY* 3.7 26.7 - - - -
328B ALA 4.1 9.2 - - - +
329B VAL* 3.8 29.2 - - + -
336B MET* 4.7 12.6 - - + -
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Residues in contact with THR 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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286B ASP* 2.8 38.3 + - + +
287B GLY* 3.1 15.2 + - - -
289B LEU* 1.4 71.2 - - + +
291B GLY* 1.3 55.0 + - - +
293B ASP* 3.1 10.7 + - - +
294B ARG* 2.8 38.4 + - - +
336B MET* 6.1 2.5 - - - -
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Residues in contact with GLY 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B TYR* 4.1 5.2 - - - -
259B PHE* 3.5 16.5 - - - -
265B ARG* 4.7 5.5 + - - -
287B GLY 2.7 20.6 + - - -
288B SER 4.3 1.6 - - - -
290B THR* 1.3 72.0 + - - +
292B ALA* 1.3 56.9 + - - +
294B ARG* 3.7 8.5 + - - +
295B PHE* 3.1 26.2 + - - +
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Residues in contact with ALA 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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221B TYR* 3.1 24.8 + - + +
282B VAL* 4.1 11.2 - - + -
288B SER 3.5 3.5 + - - +
289B LEU* 3.3 16.1 + - + +
290B THR 3.3 0.4 - - - -
291B GLY* 1.3 72.4 - - - +
293B ASP* 1.3 59.1 + - - +
295B PHE* 3.4 9.0 + - - +
296B ARG* 3.0 26.5 + - - +
325B ILE* 3.7 26.4 - - + +
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Residues in contact with ASP 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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289B LEU 2.9 13.7 + - - +
290B THR* 3.2 14.0 - - - +
292B ALA* 1.3 73.7 - - - +
294B ARG* 1.4 64.6 + - - +
296B ARG* 3.0 60.3 + - - +
297B SER 3.2 4.3 + - - -
325B ILE* 6.2 0.2 - - - -
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Residues in contact with ARG 294 (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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265B ARG* 3.6 34.1 - - - +
290B THR* 2.8 19.9 + - - +
291B GLY* 3.9 5.4 - - - +
292B ALA 3.4 0.2 - - - -
293B ASP* 1.4 76.6 - - - +
295B PHE* 1.4 56.7 + - - +
297B SER* 3.0 14.2 + - - -
298B GLU* 2.9 62.7 + - - +
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Residues in contact with PHE 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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221B TYR* 5.9 0.2 - + - -
224B LEU* 5.0 1.3 - - + -
259B PHE* 3.5 29.8 - + + -
265B ARG* 3.2 40.6 - - + +
268B ALA* 4.6 4.0 - - + -
269B CYS* 4.1 13.2 - - + -
272B MET* 3.9 20.6 - - - -
280B LEU* 4.6 9.6 - - + -
291B GLY 3.1 19.4 + - - +
292B ALA* 3.4 8.3 - - - +
293B ASP 3.3 0.2 - - - -
294B ARG* 1.4 75.1 - - - +
296B ARG* 1.3 56.0 + - - +
298B GLU* 3.7 2.4 - - + -
299B TRP* 3.0 55.1 + + - +
323B LEU* 3.7 23.3 - - + -
325B ILE* 4.4 7.2 - - + -
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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 ALA 3.0 12.9 + - - +
293B ASP* 3.0 41.3 + - - +
295B PHE* 1.3 74.3 - - - +
297B SER* 1.3 90.2 + - - +
299B TRP* 3.3 17.7 + - - +
300B PRO* 4.2 2.6 - - - +
323B LEU* 3.7 21.3 - - + +
325B ILE* 4.2 19.3 - - + -
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Residues in contact with SER 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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293B ASP 3.2 4.5 + - - -
294B ARG* 3.0 29.1 + - - -
296B ARG* 1.3 101.4 + - - +
298B GLU* 1.4 60.2 + - - +
299B TRP 3.3 0.2 - - - -
300B PRO* 3.2 17.8 - - - +
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Residues in contact with GLU 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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262B ARG* 4.4 13.1 - - - +
265B ARG* 3.0 35.6 + - + +
294B ARG* 2.9 55.8 + - - +
295B PHE* 3.7 7.2 - - + +
297B SER* 1.4 78.3 + - - +
299B TRP* 1.4 64.6 + - - +
300B PRO* 3.3 11.2 - - - +
301B SER* 3.9 9.7 + - - -
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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