Contacts of the helix formed by residues 314 - 332 (chain B) in PDB entry 2OZB
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 314 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B PRO* 4.9 3.4 - - - -
218B ASN* 3.2 19.3 - - - -
221B ILE* 3.8 18.8 - - - -
311B SER 3.1 7.2 + - - -
312B THR 3.2 2.4 + - - -
313B GLU* 1.3 78.6 - - - +
315B LYS* 1.3 66.3 + - - +
317B GLY* 3.1 2.1 + - - -
318B TYR* 3.0 29.0 + - - -
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Residues in contact with LYS 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B SER* 3.2 12.3 + - - +
313B GLU* 3.4 6.2 + - + +
314B GLY* 1.3 76.6 - - - +
316B VAL* 1.3 68.7 + - + +
318B TYR* 3.5 5.6 + - - +
319B GLU* 3.1 52.4 + - + +
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Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PRO* 3.9 29.8 - - + -
65A ILE* 6.3 0.2 - - + -
218B ASN* 3.5 15.5 - - + +
301B LEU* 5.5 0.4 - - + -
302B ALA* 4.7 2.9 - - - +
305B VAL* 4.2 19.7 - - + -
311B SER* 3.0 23.1 + - - +
315B LYS* 1.3 82.0 - - + +
317B GLY* 1.3 57.1 + - - +
319B GLU* 3.2 15.2 + - - +
320B LEU* 2.9 49.3 + - + +
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Residues in contact with GLY 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ASN* 2.7 43.4 + - - -
221B ILE* 3.6 11.3 - - - +
222B ILE* 3.8 11.3 - - - +
314B GLY 3.1 2.2 + - - -
316B VAL* 1.3 73.9 - - - +
318B TYR* 1.3 56.3 + - - +
320B LEU 3.4 0.5 + - - -
321B LYS* 2.8 30.0 + - - +
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Residues in contact with TYR 318 (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 ILE* 3.5 40.7 - - + +
313B GLU 4.0 12.8 - - - -
314B GLY 3.0 27.1 + - - +
315B LYS* 4.0 4.9 - - - +
317B GLY* 1.3 74.0 - - - +
319B GLU* 1.3 59.1 + - - +
321B LYS* 3.6 16.5 - - + +
322B ASP* 2.9 28.8 + - - +
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Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LYS* 3.1 54.0 + - + +
316B VAL* 3.2 16.9 + - - +
318B TYR* 1.3 74.3 - - + +
320B LEU* 1.3 62.9 + - + +
322B ASP* 3.3 7.6 + - - +
323B GLU* 3.0 27.6 + - - +
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ILE* 3.9 20.2 - - + -
298B LYS* 3.6 44.6 - - + +
301B LEU* 4.4 14.8 - - + -
302B ALA* 4.2 7.6 - - + +
316B VAL* 2.9 38.7 + - + +
317B GLY 3.9 0.2 - - - +
319B GLU* 1.3 77.5 - - + +
321B LYS* 1.3 58.1 + - - +
323B GLU* 3.1 22.8 + - - +
324B ILE* 2.8 36.0 + - - +
31C U 5.5 2.5 - - - +
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Residues in contact with LYS 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ILE* 3.7 32.9 + - + +
222B ILE* 4.5 8.5 + - + +
279B ILE* 4.6 11.7 - - + +
317B GLY 2.8 18.8 + - - +
318B TYR* 3.6 17.0 - - + +
319B GLU 3.3 0.2 - - - -
320B LEU* 1.3 77.2 - - - +
322B ASP* 1.3 58.0 + - - +
324B ILE* 3.3 10.3 + - - +
325B GLU* 3.0 58.0 + - + +
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Residues in contact with ASP 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B TYR 2.9 17.7 + - - +
319B GLU* 3.6 7.7 - - - +
320B LEU 3.3 0.2 - - - -
321B LYS* 1.3 73.2 - - - +
323B GLU* 1.3 67.3 + - - +
325B GLU* 3.9 6.4 - - - +
326B ARG* 3.1 57.8 + - - +
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Residues in contact with GLU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LEU* 6.0 0.7 - - - -
298B LYS* 3.7 23.9 + - - -
319B GLU 3.0 13.6 + - - +
320B LEU* 3.1 28.6 + - + +
322B ASP* 1.3 80.4 - - - +
324B ILE* 1.3 64.2 + - + +
326B ARG* 3.4 7.1 + - - +
327B LYS* 2.8 52.8 + - + +
29C A 4.8 3.3 + - - -
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Residues in contact with ILE 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ILE* 3.7 30.1 - - + -
279B ILE* 4.5 9.4 - - + -
294B LEU* 3.7 19.5 - - + -
295B VAL* 4.3 13.7 - - + -
298B LYS* 4.0 30.1 - - + -
320B LEU 2.8 23.5 + - - +
321B LYS* 3.7 6.3 - - - +
322B ASP 3.3 0.2 - - - -
323B GLU* 1.3 78.1 - - + +
325B GLU* 1.3 58.2 + - - +
327B LYS* 2.9 5.8 + - - +
328B PHE* 2.9 61.9 + - + -
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Residues in contact with GLU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ILE* 3.7 21.7 - - - +
321B LYS* 3.0 53.3 + - + +
322B ASP* 3.9 7.6 - - - +
324B ILE* 1.3 76.5 - - - +
326B ARG* 1.3 58.1 + - + +
328B PHE* 3.4 16.4 + - - +
329B ASP* 2.9 38.9 + - - +
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Residues in contact with ARG 326 (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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322B ASP* 3.1 43.7 + - - +
323B GLU* 3.9 6.5 - - - +
324B ILE 3.2 0.2 - - - -
325B GLU* 1.3 77.2 - - + +
327B LYS* 1.3 62.0 + - + +
329B ASP* 3.7 10.4 + - - +
330B LYS* 3.3 22.5 + - - +
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Residues in contact with LYS 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LEU* 4.1 32.9 - - + +
298B LYS* 5.0 1.8 - - - +
323B GLU* 2.8 43.8 + - + +
324B ILE 2.9 8.5 + - - +
326B ARG* 1.3 75.4 - - + +
328B PHE* 1.3 66.5 + - - +
330B LYS* 3.1 6.9 + - - +
331B TRP* 3.0 47.7 + - + +
28C C 4.5 14.1 - - - -
29C A 4.2 23.9 + - - -
33C A 5.7 3.8 - - - +
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Residues in contact with PHE 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ILE* 3.9 25.8 - - + -
280B VAL* 5.3 0.2 - - - -
282B SER* 5.2 0.9 - - - -
283B LEU* 3.5 32.5 - - + -
291B ALA* 3.9 14.4 - - + -
294B LEU* 3.6 15.3 - - + -
295B VAL* 4.2 11.0 - - + -
324B ILE* 2.9 40.9 + - + -
325B GLU* 3.6 22.0 - - - +
327B LYS* 1.3 75.5 - - - +
329B ASP* 1.3 64.4 + - - +
331B TRP* 3.2 38.4 + + - +
332B GLN* 3.2 28.8 + - - +
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Residues in contact with ASP 329 (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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325B GLU* 2.9 28.0 + - - +
326B ARG* 3.9 9.8 - - - +
327B LYS 3.3 0.2 - - - -
328B PHE* 1.3 77.2 - - - +
330B LYS* 1.3 61.9 + - - +
332B GLN* 3.3 30.2 + - - +
333B GLU* 4.7 0.7 - - - +
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Residues in contact with LYS 330 (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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326B ARG 3.3 15.9 + - - +
327B LYS* 3.1 8.9 + - - +
329B ASP* 1.3 77.3 - - - +
331B TRP* 1.3 68.0 + - + +
332B GLN 4.1 3.5 - - - +
333B GLU* 4.5 8.5 + - - +
27C C 5.7 4.7 - - - -
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Residues in contact with TRP 331 (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 LEU* 4.6 5.6 - - + -
287B LEU* 4.0 35.7 - - + +
290B LYS* 3.3 59.1 - - + +
291B ALA* 3.9 16.8 - - + -
294B LEU* 3.7 28.5 - - + -
327B LYS* 3.0 33.5 + - + +
328B PHE* 3.2 34.0 + + - +
330B LYS* 1.3 85.6 - - + +
332B GLN* 1.3 61.8 + - - +
333B GLU* 4.3 4.3 - - - +
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Residues in contact with GLN 332 (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 SER 5.3 1.0 - - - +
283B LEU* 4.7 10.3 - - - +
284B PRO* 3.4 27.2 - - + +
287B LEU* 3.8 20.9 - - + -
328B PHE* 3.2 30.7 + - - +
329B ASP* 3.3 21.2 + - - +
330B LYS 4.1 0.5 - - - +
331B TRP* 1.3 76.7 - - - +
333B GLU* 1.3 93.6 + - - +
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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
------------------------------------------------------------
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