Contacts of the helix formed by residues 284 - 305 (chain D) in PDB entry 2OIB
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 284 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282D PRO 3.6 4.6 + - - -
283D LEU* 1.3 75.7 - - - +
285D TRP* 1.3 58.9 + - - +
286D HIS* 3.6 7.4 + - - +
287D MET* 3.1 36.8 + - - +
288D ARG* 2.9 26.5 + - - +
418D MET* 4.8 4.3 - - - +
419D ASN* 6.0 0.2 - - - -
420D ASP* 3.6 17.5 - - - -
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Residues in contact with TRP 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D SER* 1.3 69.9 - - - +
286D HIS* 1.3 58.2 + - - +
288D ARG* 3.1 14.8 + - + +
289D CYS* 2.9 51.4 + - - -
380D ILE* 4.5 0.7 - - + -
381D ILE* 4.1 25.8 - - + -
418D MET* 3.7 31.6 - - + -
420D ASP* 2.8 35.8 + - - +
421D ALA* 3.8 10.3 - - + -
422D ASP* 4.4 3.6 - - - -
425D SER* 2.7 29.5 + - - -
426D VAL* 3.6 42.6 - - + +
429D MET* 3.6 32.1 - - + -
457D MET* 4.8 0.2 - - - -
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Residues in contact with HIS 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B THR* 5.3 12.4 + - + +
247B GLU* 2.8 38.4 + - - -
249B LEU* 3.5 23.1 - - + +
263B VAL* 4.7 6.1 - - + -
284D SER* 3.7 5.8 - - - +
285D TRP* 1.3 79.7 - - - +
287D MET* 1.3 65.7 + - + +
289D CYS* 3.5 6.3 + - - +
290D LYS* 3.4 21.4 + - + +
420D ASP* 3.0 16.8 + - - +
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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
----------------------------------------------------------
247B GLU* 6.0 1.3 - - - +
282D PRO 5.0 2.2 - - - +
283D LEU* 3.4 31.4 - - + -
284D SER* 3.1 38.0 + - - +
286D HIS* 1.3 82.2 - - + +
288D ARG* 1.3 56.7 + - - +
290D LYS* 3.3 8.5 + - - +
291D ILE* 3.0 37.1 + - + +
323D PHE* 3.5 42.3 - - + +
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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
----------------------------------------------------------
270D LEU* 6.0 0.4 - - + -
274D LEU* 3.8 18.6 + - + +
282D PRO* 4.7 3.2 - - - +
283D LEU* 2.9 49.2 + - + +
284D SER 2.9 10.7 + - - +
285D TRP* 3.1 15.0 + - + +
287D MET* 1.3 73.7 - - - +
289D CYS* 1.3 58.5 + - - +
291D ILE* 3.4 8.5 + - + +
292D ALA* 2.9 30.5 + - - +
380D ILE* 2.8 58.9 + - + +
383D GLY 4.2 0.6 - - - +
415D ASP* 2.8 40.2 + - - +
417D LYS* 4.0 6.3 + - - +
418D MET* 3.5 30.5 - - - +
429D MET* 4.6 0.9 - - - -
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Residues in contact with CYS 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D TRP* 2.9 57.3 + - - +
286D HIS* 3.9 6.7 - - - +
288D ARG* 1.3 73.6 - - - +
290D LYS* 1.3 63.3 + - - +
292D ALA* 3.5 1.6 + - - +
293D GLN* 3.0 33.4 + - - +
425D SER* 5.0 2.5 - - - -
429D MET* 4.2 7.0 - - - -
457D MET* 4.0 23.2 - - + +
458D THR* 4.7 9.2 - - - +
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Residues in contact with LYS 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B GLN* 4.0 22.1 - - - +
247B GLU* 6.1 0.7 - - - +
286D HIS* 3.4 12.7 + - + +
287D MET* 3.3 10.2 + - - +
288D ARG 3.3 0.2 - - - -
289D CYS* 1.3 75.3 - - - +
291D ILE* 1.3 61.1 + - - +
293D GLN* 3.4 12.9 + - - +
294D GLY* 2.9 26.7 + - - -
322D ALA* 2.9 32.6 + - - +
323D PHE* 4.0 11.9 - - + +
324D THR* 3.3 28.1 + - - +
325D ALA* 5.1 1.1 + - - +
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Residues in contact with ILE 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D LEU* 4.0 31.9 - - + -
283D LEU* 3.9 32.8 - - + -
287D MET* 3.0 29.7 + - + +
288D ARG* 3.7 6.7 - - - +
290D LYS* 1.3 74.3 - - - +
292D ALA* 1.3 66.3 + - - +
294D GLY 3.3 0.7 + - - -
295D ALA* 2.9 23.8 + - + +
317D ILE* 4.5 2.2 - - + -
319D LEU* 3.7 21.1 - - + -
323D PHE* 3.5 23.8 - - + +
325D ALA* 3.4 18.1 - - + +
380D ILE* 4.5 4.5 - - + -
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Residues in contact with ALA 292 (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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288D ARG 2.9 18.0 + - - +
289D CYS 3.7 3.4 - - - +
291D ILE* 1.3 77.7 - - - +
293D GLN* 1.3 61.8 + - + +
295D ALA* 4.6 2.9 - - - -
296D ALA* 3.1 19.8 + - - +
373D PHE* 3.6 10.4 - - - -
377D LEU* 3.9 20.9 - - + -
380D ILE* 4.3 11.2 - - + +
429D MET* 3.7 23.6 - - + -
454D LEU* 3.7 10.0 - - + +
457D MET* 5.1 0.2 - - + -
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Residues in contact with GLN 293 (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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289D CYS 3.0 19.4 + - - +
290D LYS* 3.8 11.5 - - - +
292D ALA* 1.3 74.0 - - - +
294D GLY* 1.3 59.4 + - - +
296D ALA* 3.3 7.3 + - - +
297D ASN* 2.9 40.7 + - - +
454D LEU* 3.0 36.7 + - + +
455D GLN* 3.9 11.4 - - + +
457D MET* 4.5 3.1 - - + +
458D THR* 2.6 37.2 + - - +
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Residues in contact with GLY 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D ASN* 3.2 35.8 - - - +
290D LYS 2.9 13.9 + - - -
291D ILE 3.7 2.9 - - - -
293D GLN* 1.3 74.3 - - - +
295D ALA* 1.3 65.1 + - - +
297D ASN* 3.0 5.9 + - - +
298D GLY 3.0 20.1 + - - -
325D ALA* 3.9 5.4 - - - -
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Residues in contact with ALA 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D ASN* 5.3 0.2 - - - -
291D ILE* 2.9 22.5 + - + +
292D ALA* 3.8 1.8 - - - +
294D GLY* 1.3 68.8 - - - +
296D ALA* 1.3 62.7 + - - +
298D GLY* 3.3 2.3 + - - -
299D ILE* 3.0 30.4 + - - +
317D ILE* 4.2 15.3 - - + -
325D ALA* 3.5 9.1 - - + +
327D ILE* 3.9 21.5 - - + +
373D PHE* 3.6 22.9 - - + -
376D VAL* 5.6 0.2 - - + -
380D ILE* 6.2 0.7 - - + -
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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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292D ALA 3.1 14.7 + - - +
293D GLN* 3.6 8.5 - - - +
294D GLY 3.3 0.2 - - - -
295D ALA* 1.3 77.1 - - - +
297D ASN* 1.3 58.2 + - - +
299D ILE* 3.5 1.0 + - - -
300D ASN* 2.8 30.8 + - - +
373D PHE* 3.9 12.4 - - + -
447D ILE* 3.6 16.8 - - + +
450D VAL* 4.5 0.7 - - + -
451D GLN* 4.4 18.3 - - - +
454D LEU* 3.7 21.1 - - + -
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Residues in contact with ASN 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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242D HIS* 3.8 13.9 + - + +
244D ASN* 3.4 16.1 + - - +
293D GLN* 2.9 28.7 + - - +
294D GLY* 3.0 8.5 + - - +
296D ALA* 1.3 75.7 - - - +
298D GLY* 1.3 57.8 + - - +
300D ASN* 3.4 3.1 + - - +
301D PHE* 2.9 27.9 + - - +
451D GLN* 2.7 40.7 + - - +
455D GLN* 4.7 5.8 + - - +
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Residues in contact with GLY 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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242D HIS* 4.1 4.5 - - - -
244D ASN* 3.7 27.5 - - - +
245D LEU* 3.7 11.7 - - - +
294D GLY 3.0 10.1 + - - -
295D ALA 3.3 3.1 + - - -
297D ASN* 1.3 75.5 - - - +
299D ILE* 1.3 64.1 + - - +
301D PHE* 3.3 4.2 + - - +
302D LEU* 3.1 26.6 + - - +
327D ILE* 4.3 2.7 - - - -
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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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295D ALA 3.0 19.9 + - - +
296D ALA 3.9 3.4 - - - +
298D GLY* 1.3 72.6 - - - +
300D ASN* 1.3 62.1 - - - +
302D LEU* 3.1 12.3 + - + +
303D HIS* 2.9 55.7 + - + +
309D HIS* 6.3 0.2 - - + -
312D ILE* 4.1 31.0 - - + -
327D ILE* 4.3 9.0 - - + -
369D ASP* 4.5 10.1 - - + +
370D ILE* 5.1 1.1 - - + -
373D PHE* 3.9 39.7 - - + -
447D ILE* 3.8 14.4 - - + -
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Residues in contact with ASN 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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296D ALA 2.8 19.3 + - - +
297D ASN 3.6 4.6 + - - +
299D ILE* 1.3 75.7 - - - +
301D PHE* 1.3 56.8 + - - +
303D HIS* 3.4 1.0 + - - +
304D GLU* 2.8 65.1 + - - +
447D ILE* 3.4 27.5 - - + +
448D LYS* 3.4 24.1 + - - +
451D GLN* 3.3 31.2 + - - +
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Residues in contact with PHE 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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239D LYS 4.8 1.8 - - - -
240D CYS* 3.7 31.2 - - + -
241D GLN 3.3 26.9 - - - -
242D HIS* 3.6 28.3 - + + +
245D LEU* 3.7 18.2 - - + -
297D ASN 2.9 14.3 + - - +
298D GLY 3.5 8.1 - - - +
299D ILE 3.3 0.2 - - - -
300D ASN* 1.3 77.5 - - - +
302D LEU* 1.3 59.0 + - - +
304D GLU* 3.2 14.2 + - - +
305D ASN* 2.9 63.2 + - - -
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Residues in contact with LEU 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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236D VAL* 4.6 2.2 - - + -
240D CYS* 4.1 18.4 - - + -
245D LEU* 4.0 15.9 - - + -
298D GLY 3.1 19.2 + - - +
299D ILE* 3.1 16.6 + - + +
301D PHE* 1.3 76.8 - - - +
303D HIS* 1.3 54.9 + - + +
305D ASN* 3.1 14.0 + - - -
306D HIS 3.1 0.2 + - - -
307D HIS* 2.8 55.6 + - + +
309D HIS* 4.2 23.8 - - + -
327D ILE* 4.5 4.7 - - + -
330D PHE* 3.9 35.9 - - + -
369D ASP* 6.0 0.2 - - - +
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Residues in contact with HIS 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D ILE* 2.9 30.6 + - + +
302D LEU* 1.3 74.2 - - + +
304D GLU* 1.3 65.3 + - - +
306D HIS* 3.0 19.1 + - - +
307D HIS 3.3 19.3 - - - +
366D PRO* 3.3 44.1 + - + +
369D ASP* 2.8 32.6 + - + +
370D ILE* 4.1 9.5 - - + +
447D ILE* 3.6 26.2 + - + +
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Residues in contact with GLU 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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300D ASN* 2.8 47.3 + - - +
301D PHE* 3.4 17.6 - - - +
303D HIS* 1.3 76.5 - - - +
305D ASN* 1.3 64.3 + - - +
306D HIS* 3.5 15.6 + - - -
447D ILE* 5.6 0.2 - - - +
448D LYS* 3.9 13.9 + - + +
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Residues in contact with ASN 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D LYS* 4.4 8.8 - - - +
240D CYS* 4.2 9.8 - - - -
301D PHE* 2.9 62.1 + - - +
302D LEU 3.1 6.2 + - - +
304D GLU* 1.3 83.6 + - - +
306D HIS* 1.3 63.3 + - - +
307D HIS* 2.7 35.2 + - + +
337D GLU* 4.6 4.5 - - - +
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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