Contacts of the helix formed by residues 275 - 289 (chain A) in PDB entry 4OQB
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 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LYS* 6.2 3.8 - - - -
273A PRO 3.7 1.2 + - - -
274A SER* 1.3 76.8 + - - +
276A GLU* 1.3 64.1 + - - -
277A SER* 3.6 3.4 - - - -
278A ALA* 4.1 5.4 - - - -
279A ILE* 3.2 30.8 + - - +
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Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LYS* 6.3 0.2 - - - +
30A LYS* 4.4 16.5 + - - -
253A LYS* 3.6 32.7 - - - +
258A THR* 4.5 21.0 + - + +
261A LEU* 5.9 1.0 - - + +
275A GLY* 1.3 70.6 - - - +
277A SER* 1.3 66.3 + - - +
279A ILE* 3.1 17.5 + - - +
280A LEU* 3.1 16.6 + - + +
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Residues in contact with SER 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LYS* 3.8 27.6 - - - +
249A LYS* 4.0 8.3 + - - +
253A LYS* 4.9 4.2 - - - +
275A GLY* 5.1 1.0 - - - -
276A GLU* 1.3 79.0 + - - +
278A ALA* 1.3 64.0 + - - +
280A LEU* 3.4 15.2 - - - +
281A ASP* 3.2 23.7 + - - +
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A PRO* 3.8 14.4 - - + +
274A SER 4.2 18.2 - - - +
275A GLY* 3.9 4.2 + - - +
276A GLU 3.2 1.0 - - - -
277A SER* 1.3 80.0 + - - +
279A ILE* 1.3 64.7 + - - +
281A ASP* 3.6 7.2 - - - +
282A ARG* 3.2 32.3 + - - +
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Residues in contact with ILE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A THR* 3.8 25.6 - - + +
261A LEU* 3.5 42.4 - - + +
262A LYS* 3.9 21.3 - - + +
265A LEU* 4.1 4.9 - - + +
272A VAL* 4.4 2.2 - - + -
273A PRO* 3.5 35.9 - - + +
275A GLY 3.2 22.2 + - - +
276A GLU* 3.1 9.4 + - - +
278A ALA* 1.3 77.1 - - - +
280A LEU* 1.3 59.8 + - - +
282A ARG* 3.2 6.2 + - - +
283A VAL* 3.0 28.4 + - - +
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A TRP* 6.0 0.9 - - + -
249A LYS* 3.2 56.7 - - + +
250A ASP* 4.4 0.7 - - - +
252A LEU* 5.0 4.7 - - + +
253A LYS* 3.6 38.8 - - + +
261A LEU* 4.3 20.9 - - + -
276A GLU* 3.1 26.9 - - + +
277A SER* 3.4 14.1 - - - +
279A ILE* 1.3 78.4 - - - +
281A ASP* 1.3 60.3 + - - +
283A VAL* 3.8 10.3 - - + +
284A ALA* 2.9 31.5 + - - +
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Residues in contact with ASP 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLU* 4.4 19.9 - - - +
245A ILE* 5.2 5.5 - - - +
249A LYS* 3.3 28.9 + - - +
277A SER 3.2 18.9 + - - +
278A ALA* 3.6 10.1 - - - +
279A ILE 3.2 0.6 - - - -
280A LEU* 1.3 78.8 - - - +
282A ARG* 1.3 60.3 + - + +
284A ALA* 4.0 1.8 - - - +
285A ASP* 3.1 25.3 + - - +
304A PHE* 5.5 6.8 - - - -
355A ARG* 5.8 0.9 + - - -
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Residues in contact with ARG 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LEU* 4.2 17.4 - - + +
271A GLN* 3.7 33.4 + - - +
273A PRO* 3.7 33.4 - - - +
278A ALA* 3.2 15.2 + - - +
279A ILE 3.2 5.1 + - - +
281A ASP* 1.3 78.1 - - + +
283A VAL* 1.3 54.0 + - - +
284A ALA 3.4 0.4 - - - -
285A ASP* 3.6 10.2 - - + +
286A GLY* 2.7 30.1 + - - -
292A LEU* 6.6 0.2 - - - -
301A GLN* 4.1 13.6 + - - +
303A VAL* 3.4 48.8 - - + +
312A THR* 5.3 2.6 + - - +
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A LEU* 3.6 24.5 - - + -
261A LEU* 3.7 29.8 - - + +
264A LEU* 4.2 14.8 - - + -
265A LEU* 3.7 27.6 - - + -
279A ILE 3.0 21.9 + - - +
280A LEU* 4.0 7.0 - - - +
282A ARG* 1.3 76.5 - - - +
284A ALA* 1.3 57.7 - - - +
286A GLY* 3.2 1.2 + - - -
287A MET* 2.9 39.5 + - + +
333A TRP* 4.5 7.5 - - + -
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ILE* 3.7 27.8 - - + -
248A ILE* 4.1 22.9 - - + -
249A LYS* 3.8 11.4 - - + +
252A LEU* 4.7 1.3 - - + +
280A LEU 2.9 19.7 + - - +
281A ASP 4.0 2.2 - - - +
283A VAL* 1.3 74.8 - - - +
285A ASP* 1.3 63.9 + - - +
287A MET* 3.6 2.1 + - - +
288A VAL* 3.2 32.0 + - - +
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Residues in contact with ASP 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ILE* 5.1 3.0 - - - +
281A ASP* 3.1 20.9 + - - +
282A ARG* 3.6 10.2 - - - +
284A ALA* 1.3 75.3 - - - +
286A GLY* 1.3 64.7 + - - +
289A PHE* 3.2 34.5 + - - +
290A GLY 3.6 2.4 + - - +
292A LEU* 3.9 16.1 - - - +
304A PHE* 4.9 4.1 + - + +
309A TYR* 2.7 39.1 + - - -
330A ARG* 5.4 0.4 - - - -
355A ARG* 2.7 22.7 + - - +
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Residues in contact with GLY 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ARG 2.7 21.0 + - - -
283A VAL 3.2 2.6 + - - -
285A ASP* 1.3 75.7 - - - +
287A MET* 1.3 56.4 + - - +
290A GLY* 2.9 40.6 + - - -
291A ALA* 5.0 0.2 - - - -
292A LEU* 6.4 0.2 - - - -
333A TRP* 3.2 28.7 - - - +
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Residues in contact with MET 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A ILE* 3.2 35.2 - - + -
252A LEU* 3.7 26.5 - - + -
264A LEU* 5.9 3.1 - - - -
283A VAL* 2.9 29.0 + - + +
284A ALA* 4.1 2.0 - - - +
286A GLY* 1.3 75.1 - - - +
288A VAL* 1.3 65.7 + - + +
290A GLY 4.7 0.5 + - - -
332A GLU* 4.7 7.4 - - - +
333A TRP* 3.4 38.5 - - + +
335A THR* 5.2 5.2 - - - -
345A LEU* 5.8 8.7 - - + -
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Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A GLN* 5.6 0.4 - - + +
244A LEU* 4.6 17.9 - - + -
245A ILE* 4.4 11.9 - - + -
248A ILE* 3.4 34.1 - - + -
284A ALA 3.2 18.4 + - - +
287A MET* 1.3 79.0 - - + +
289A PHE* 1.3 94.7 + - + +
332A GLU* 5.7 0.5 - - - +
350A VAL* 6.3 2.9 - - + -
351A LYS 4.9 8.0 - - - +
352A LYS* 5.7 0.9 - - - -
353A GLN* 4.3 15.0 + - + +
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Residues in contact with PHE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A GLN* 3.6 33.4 - - + -
245A ILE* 3.8 13.5 - - + -
285A ASP* 3.2 27.7 + - - +
287A MET 4.8 0.4 - - - -
288A VAL* 1.3 101.5 - - + +
290A GLY* 1.3 58.0 + - - +
309A TYR* 4.2 2.7 - - - -
330A ARG* 3.3 32.7 + - - +
332A GLU* 4.8 9.2 - - - +
353A GLN* 3.4 22.5 - - + +
354A ASP* 3.5 5.8 - - - -
355A ARG* 3.3 53.2 - - - -
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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