Contacts of the helix formed by residues 275 - 289 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D LYS* 6.2 3.4 - - - -
273D PRO 3.7 1.0 + - - -
274D SER* 1.3 75.9 + - - +
276D GLU* 1.3 64.5 + - - -
277D SER* 3.6 3.1 - - - -
278D ALA* 4.1 5.8 - - - -
279D ILE* 3.2 31.1 + - - +
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Residues in contact with GLU 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LYS* 6.3 0.2 - - - +
30D LYS* 4.4 16.3 + - - -
253D LYS* 3.6 31.8 + - - +
258D THR* 4.5 21.7 + - + +
261D LEU* 5.9 1.1 - - + +
275D GLY* 1.3 68.9 - - - +
277D SER* 1.3 67.1 + - - +
279D ILE* 3.1 17.6 + - - +
280D LEU* 3.1 17.4 + - + +
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Residues in contact with SER 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LYS* 3.8 27.3 - - - +
249D LYS* 4.0 8.5 + - - -
253D LYS* 4.9 4.2 - - - +
275D GLY* 5.1 1.2 - - - -
276D GLU* 1.3 79.6 + - - +
278D ALA* 1.3 65.3 + - - +
280D LEU* 3.4 15.1 - - - +
281D ASP* 3.2 23.8 + - - +
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Residues in contact with ALA 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D PRO* 3.8 14.0 - - + +
274D SER 4.2 19.1 - - - +
275D GLY* 3.9 3.7 + - - +
276D GLU 3.2 1.0 - - - -
277D SER* 1.3 80.9 + - - +
279D ILE* 1.3 65.0 + - - +
281D ASP* 3.6 8.0 - - - +
282D ARG* 3.2 31.6 + - + +
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Residues in contact with ILE 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D THR* 3.8 26.2 - - + +
261D LEU* 3.5 41.7 - - + +
262D LYS* 3.9 21.3 - - + +
265D LEU* 4.1 4.9 - - + +
272D VAL* 4.4 2.0 - - + -
273D PRO* 3.5 35.7 - - + +
275D GLY 3.2 22.1 + - - +
276D GLU* 3.1 9.7 + - - +
278D ALA* 1.3 76.9 - - - +
280D LEU* 1.3 59.1 + - - +
282D ARG* 3.2 5.9 + - - +
283D VAL* 3.0 28.8 + - - +
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Residues in contact with LEU 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D TRP* 6.0 0.7 - - + -
249D LYS* 3.2 56.8 - - + +
250D ASP* 5.0 0.4 - - - -
252D LEU* 5.0 4.9 - - + +
253D LYS* 3.6 39.3 - - + +
261D LEU* 4.3 20.9 - - + -
276D GLU* 3.1 26.0 - - + +
277D SER* 3.4 14.8 - - - +
279D ILE* 1.3 78.1 - - - +
281D ASP* 1.3 60.0 + - - +
283D VAL* 3.8 10.4 - - + +
284D ALA* 2.9 31.2 + - - +
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Residues in contact with ASP 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D GLU* 4.3 20.6 - - - +
245D ILE* 5.2 5.0 - - - +
249D LYS* 3.3 28.2 + - - +
277D SER 3.2 18.7 + - - +
278D ALA* 3.6 11.3 - - - +
279D ILE 3.2 0.8 - - - -
280D LEU* 1.3 78.6 - - - +
282D ARG* 1.3 58.3 + - + +
284D ALA* 4.0 1.4 - - - +
285D ASP* 3.1 25.8 + - - +
304D PHE* 5.5 6.6 - - - -
355D ARG* 5.8 1.0 + - - -
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Residues in contact with ARG 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D LEU* 4.2 18.4 - - + +
271D GLN* 3.7 31.7 + - - +
273D PRO* 3.7 33.3 - - + +
278D ALA* 3.2 15.4 + - - +
279D ILE 3.2 4.7 + - - +
281D ASP* 1.3 80.1 - - + +
283D VAL* 1.3 55.3 + - - +
284D ALA 3.4 0.2 - - - -
285D ASP* 3.6 10.1 - - + +
286D GLY* 2.7 30.8 + - - -
292D LEU* 6.6 0.2 - - - -
301D GLN* 4.1 13.6 + - - +
302D LEU 5.9 0.2 - - - -
303D VAL* 3.4 49.7 - - + +
312D THR* 5.3 2.4 + - - +
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Residues in contact with VAL 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252D LEU* 3.6 24.0 - - + -
261D LEU* 3.7 30.1 - - + +
264D LEU* 4.2 14.8 - - + -
265D LEU* 3.7 28.3 - - + -
279D ILE 3.0 21.9 + - - +
280D LEU* 4.0 7.2 - - - +
281D ASP 3.5 0.2 - - - -
282D ARG* 1.3 75.7 - - - +
284D ALA* 1.3 56.8 - - - +
286D GLY* 3.2 1.3 + - - +
287D MET* 2.9 39.0 + - + +
333D TRP* 4.5 7.5 - - + -
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Residues in contact with ALA 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D ILE* 3.7 27.6 - - + -
248D ILE* 4.1 22.4 - - + -
249D LYS* 3.8 12.3 - - + +
252D LEU* 4.7 1.5 - - + +
280D LEU 2.9 19.9 + - - +
281D ASP 4.0 2.0 - - - +
283D VAL* 1.3 75.1 - - - +
285D ASP* 1.3 62.9 + - - +
287D MET* 4.1 2.4 - - - -
288D VAL* 3.2 31.8 + - - +
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Residues in contact with ASP 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D ILE* 5.1 3.5 - - + +
281D ASP* 3.1 21.0 + - - +
282D ARG* 3.6 11.0 - - - +
283D VAL 3.3 0.2 - - - -
284D ALA* 1.3 75.2 - - - +
286D GLY* 1.3 63.3 + - - +
289D PHE* 3.2 34.7 + - - +
290D GLY 3.6 2.1 + - - +
292D LEU* 3.9 15.8 - - - +
304D PHE* 4.9 4.9 + - + +
309D TYR* 2.7 38.4 + - - -
330D ARG* 5.4 0.4 - - - -
355D ARG* 2.7 22.8 + - - +
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Residues in contact with GLY 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282D ARG 2.7 21.5 + - - -
283D VAL 3.2 2.4 + - - -
285D ASP* 1.3 75.7 - - - +
287D MET* 1.3 58.1 + - - +
290D GLY* 2.9 40.1 + - - -
291D ALA* 5.0 0.4 - - - -
333D TRP* 3.2 28.8 - - - +
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Residues in contact with MET 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D ILE* 3.2 35.7 - - + -
252D LEU* 3.7 27.1 - - + -
264D LEU* 5.9 3.4 - - - -
283D VAL* 2.9 28.2 + - + +
284D ALA* 4.1 2.2 - - - +
286D GLY* 1.3 74.2 - - - +
288D VAL* 1.3 65.1 + - + +
290D GLY 4.7 0.5 + - - -
332D GLU* 4.7 7.3 - - - +
333D TRP* 3.4 38.7 - - + +
335D THR* 5.2 5.4 - - - -
345D LEU* 5.8 8.7 - - + -
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Residues in contact with VAL 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D GLN* 5.6 0.4 - - + +
244D LEU* 4.6 17.7 - - + -
245D ILE* 4.4 13.0 - - + -
248D ILE* 3.4 33.4 - - + -
284D ALA 3.2 19.7 + - - +
287D MET* 1.3 81.1 - - + +
289D PHE* 1.3 93.3 + - + +
332D GLU* 5.7 0.5 - - - +
350D VAL* 6.3 3.8 - - + -
351D LYS 4.9 7.4 - - - +
352D LYS* 5.7 1.0 - - - -
353D GLN* 4.3 15.9 + - + +
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Residues in contact with PHE 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D GLN* 3.6 33.9 - - + -
245D ILE* 3.8 12.8 - - + -
285D ASP* 3.2 26.9 + - - +
287D MET 4.8 0.9 - - - -
288D VAL* 1.3 101.2 - - + +
290D GLY* 1.3 59.1 + - - +
309D TYR* 4.2 1.8 - - - -
330D ARG* 3.3 32.6 + - - +
332D GLU* 4.8 9.2 - - - +
353D GLN* 3.4 23.4 - - + +
354D ASP* 3.5 5.2 - - - -
355D ARG* 3.3 51.4 - - - -
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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