Contacts of the helix formed by residues 285 - 306 (chain D) in PDB entry 3OLJ
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 SER 285 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D LYS 3.8 1.2 + - - -
284D PRO* 1.3 77.3 - - - +
286D GLU* 1.3 64.6 + - - +
287D GLU* 3.6 12.0 + - - +
288D ARG* 3.1 23.0 + - - +
289D VAL* 3.1 21.1 + - - +
337D PHE* 4.5 0.4 - - - -
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Residues in contact with GLU 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D SER* 1.3 72.7 - - - +
287D GLU* 1.3 57.2 + - - +
289D VAL* 3.3 1.4 + - - +
290D ARG* 2.8 54.2 + - + +
332D MET* 4.7 0.5 - - - +
337D PHE* 3.5 45.5 - - + +
338D SER* 2.8 40.7 + - - +
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Residues in contact with GLU 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D SER* 3.0 11.1 + - - +
286D GLU* 1.3 80.1 - - - +
288D ARG* 1.3 59.5 + - - +
290D ARG* 3.4 11.4 + - - +
291D GLU* 3.0 34.7 + - - +
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Residues in contact with ARG 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D TRP* 3.5 25.5 - - - -
216D ASP* 5.8 1.0 + - - -
219D ALA* 5.7 1.0 - - - +
223D GLU* 2.6 30.6 + - - +
284D PRO* 4.1 13.5 - - + -
285D SER* 3.1 23.9 + - - +
287D GLU* 1.3 79.0 - - - +
289D VAL* 1.3 63.1 + - - +
291D GLU* 2.8 48.0 + - - +
292D ILE* 3.1 42.8 + - + +
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Residues in contact with VAL 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D VAL* 4.2 14.8 - - + -
277D PHE* 4.3 0.4 - - + -
284D PRO* 3.9 25.6 - - + -
285D SER 3.1 13.4 + - - +
286D GLU 3.7 6.1 - - - +
288D ARG* 1.3 73.5 - - - +
290D ARG* 1.3 56.1 + - - +
292D ILE* 3.0 9.8 + - + +
293D ILE* 2.8 40.3 + - + +
332D MET* 3.6 23.6 - - + -
335D LEU* 4.2 11.0 - - + -
337D PHE* 3.7 30.3 - - + -
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Residues in contact with ARG 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D GLU* 2.8 41.6 + - + +
287D GLU* 3.5 9.2 - - - +
289D VAL* 1.3 71.6 - - - +
291D GLU* 1.3 57.4 + - - +
293D ILE* 4.0 2.6 - - - +
294D ILE* 2.8 51.7 + - + +
332D MET* 3.7 22.0 - - + -
338D SER* 5.0 2.6 + - - +
339D LYS 4.2 5.7 + - - -
340D VAL* 3.7 42.9 + - + +
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Residues in contact with GLU 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D GLU* 3.0 17.4 + - + +
288D ARG* 2.8 47.5 + - - +
290D ARG* 1.3 77.5 - - - +
292D ILE* 1.3 62.3 + - - +
294D ILE* 4.1 5.8 - - - +
295D ASN* 3.1 24.6 + - - +
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Residues in contact with ILE 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D TRP* 3.8 27.8 - - + -
213D TRP* 3.9 26.9 - - + -
223D GLU* 4.3 19.5 - - + +
226D VAL* 4.1 19.7 - - + -
227D ALA* 4.2 6.3 - - - -
284D PRO* 6.0 0.4 - - + -
288D ARG* 3.1 47.9 + - + +
289D VAL* 3.0 10.8 + - + +
291D GLU* 1.3 76.6 - - - +
293D ILE* 1.3 66.8 + - + +
295D ASN* 3.4 5.8 + - - +
296D ALA* 3.1 20.8 + - - +
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Residues in contact with ILE 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D VAL* 4.0 16.2 - - + -
230D ALA* 3.9 19.3 - - + -
234D ILE* 3.8 14.4 - - + -
289D VAL* 2.8 28.1 + - + +
290D ARG* 4.0 2.5 - - - +
292D ILE* 1.3 70.6 - - + +
294D ILE* 1.3 60.2 + - - +
296D ALA* 3.2 5.2 + - - +
297D VAL* 3.0 27.9 + - + +
328D ALA* 3.8 19.1 - - + +
331D LEU* 3.7 27.1 - - + -
332D MET* 3.8 31.6 - - + -
335D LEU* 5.0 1.1 - - + -
340D VAL* 5.1 5.8 - - + -
341D PHE* 5.4 0.2 - - + -
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Residues in contact with ILE 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ARG* 2.8 45.1 + - + +
291D GLU* 4.1 5.2 - - - +
293D ILE* 1.3 68.3 - - + +
295D ASN* 1.3 67.5 + - - +
297D VAL* 3.2 8.1 + - - +
298D ARG* 3.1 44.3 + - + +
340D VAL* 3.9 31.9 - - + -
341D PHE* 4.1 13.2 - - + -
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Residues in contact with ASN 295 (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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209D TRP* 2.8 31.6 - - - +
213D TRP* 6.2 0.6 - - - -
291D GLU* 3.1 19.3 + - + +
292D ILE* 3.5 6.7 - - - +
294D ILE* 1.3 79.1 - - - +
296D ALA* 1.3 60.9 + - - +
298D ARG* 3.3 7.6 + - - +
299D ILE* 3.2 31.5 + - - +
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Residues in contact with ALA 296 (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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209D TRP* 4.2 9.4 - - + -
230D ALA* 4.0 24.7 - - + -
234D ILE* 4.0 9.4 - - + -
235D PHE* 3.4 29.2 - - + -
292D ILE 3.1 13.6 + - - +
293D ILE 3.5 8.3 - - - +
294D ILE 3.2 0.2 - - - -
295D ASN* 1.3 72.9 - - - +
297D VAL* 1.3 61.1 + - - +
299D ILE* 3.3 2.3 + - - -
300D GLU* 2.9 27.2 + - - +
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Residues in contact with VAL 297 (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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234D ILE* 4.0 15.9 - - + -
293D ILE 3.0 18.8 + - - +
294D ILE 3.2 6.5 + - - +
296D ALA* 1.3 74.5 - - - +
298D ARG* 1.3 61.6 + - - +
300D GLU* 3.3 1.7 + - - +
301D GLN* 2.8 54.3 + - - +
324D ILE* 4.0 10.3 - - + +
325D GLU* 3.9 14.6 - - + -
328D ALA* 3.4 31.4 - - + -
341D PHE* 4.0 16.2 - - + -
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Residues in contact with ARG 298 (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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294D ILE* 3.1 31.7 + - + +
295D ASN* 3.7 9.4 - - - +
296D ALA 3.3 0.2 - - - -
297D VAL* 1.3 73.7 - - - +
299D ILE* 1.3 61.2 + - + +
301D GLN* 2.8 35.4 + - - +
302D GLU* 3.0 29.5 + - - +
325D GLU* 3.0 21.6 + - - -
341D PHE* 3.5 27.5 - - - -
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Residues in contact with ILE 299 (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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205D LYS* 4.1 28.7 - - + +
206D LYS* 3.5 37.5 - - + +
209D TRP* 3.4 38.6 - - + +
212D ARG* 5.8 0.9 - - - +
235D PHE* 4.0 7.2 - - + -
295D ASN* 3.2 24.8 + - - +
296D ALA 3.7 6.3 - - - +
298D ARG* 1.3 78.3 - - + +
300D GLU* 1.3 56.0 + - - +
302D GLU* 3.2 8.5 + - - +
303D PHE* 3.0 27.8 + - + +
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Residues in contact with GLU 300 (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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206D LYS* 2.7 32.4 + - - +
234D ILE* 3.4 24.7 - - + +
235D PHE* 3.2 12.5 - - + +
238D GLY* 3.0 27.5 + - - -
239D SER 4.0 1.7 + - - -
296D ALA 2.9 17.5 + - - +
297D VAL 3.7 3.6 - - - +
299D ILE* 1.3 76.5 - - - +
301D GLN* 1.3 58.3 + - - +
303D PHE* 3.2 5.8 + - - +
304D LEU* 3.0 47.0 + - + +
324D ILE* 3.7 20.9 - - + -
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Residues in contact with GLN 301 (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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297D VAL* 2.8 25.6 + - + +
298D ARG* 2.8 36.1 + - - +
300D GLU* 1.3 71.8 - - - +
302D GLU* 1.3 55.8 + - - +
304D LEU* 4.8 4.9 - - - -
305D THR* 2.5 37.8 + - - +
321D LYS* 2.9 61.6 + - + +
324D ILE* 4.2 7.4 - - + -
325D GLU* 3.1 27.7 + - - +
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Residues in contact with GLU 302 (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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202D CYS 5.5 1.0 - - - +
205D LYS* 3.8 33.5 - - + +
298D ARG 3.0 19.4 + - - +
299D ILE* 3.4 8.5 - - - +
301D GLN* 1.3 74.5 - - - +
303D PHE* 1.3 62.7 + - - +
305D THR* 4.0 3.8 - - - -
306D GLU* 2.8 67.7 + - - +
307D ALA* 3.2 18.0 + - - +
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Residues in contact with PHE 303 (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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130D VAL* 5.1 2.5 - - + -
133D PHE* 4.3 22.4 - + + -
202D CYS* 3.2 48.2 - - + +
203D VAL* 4.6 0.9 - - + -
206D LYS* 3.2 41.3 - - + -
239D SER* 3.8 17.0 - - - -
299D ILE* 3.0 13.5 + - + +
300D GLU 3.4 7.2 - - - +
302D GLU* 1.3 80.3 + - - +
304D LEU* 1.3 77.7 + - + +
307D ALA* 4.0 7.0 - - - -
308D LEU* 2.8 56.7 + - + +
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Residues in contact with LEU 304 (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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126D PHE* 5.3 3.1 - - + -
238D GLY* 3.5 31.2 - - - +
239D SER* 4.3 1.3 - - - +
242D SER* 4.6 2.0 - - - +
300D GLU* 3.0 40.1 + - + +
301D GLN* 4.2 3.8 - - - +
302D GLU 3.3 0.2 - - - -
303D PHE* 1.3 95.5 - - + +
305D THR* 1.3 62.3 + - + +
308D LEU 3.9 6.7 - - - +
310D VAL* 3.0 51.9 + - + +
320D MET* 3.7 19.5 - - + -
324D ILE* 3.5 18.4 - - + -
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Residues in contact with THR 305 (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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301D GLN 2.5 25.0 + - - +
302D GLU* 3.8 3.3 + - - -
304D LEU* 1.3 83.7 - - + +
306D GLU* 1.3 72.2 + - - +
309D PRO* 3.9 16.0 - - - +
310D VAL* 5.4 0.2 - - + -
317D CYS* 3.8 34.7 - - + +
320D MET* 5.7 0.4 - - + -
321D LYS* 3.7 39.1 + - + +
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Residues in contact with GLU 306 (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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302D GLU* 2.8 46.0 + - - +
305D THR* 1.3 85.8 + - - +
307D ALA* 1.3 64.5 + - - +
308D LEU 3.5 1.1 + - - -
309D PRO* 3.9 11.1 - - - +
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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
------------------------------------------------------------
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