Contacts of the helix formed by residues 289 - 311 (chain B) in PDB entry 3OUY
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 VAL 289 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ARG* 3.8 32.6 - - + +
94B TYR* 4.1 24.2 - - - +
95B ALA* 3.7 22.2 - - + +
288B ILE* 1.3 76.0 - - - +
290B ASP* 1.3 65.0 - - - +
291B ASP* 3.9 9.2 - - - +
292B ASN* 3.1 33.1 + - - +
293B LEU* 3.0 17.2 + - - +
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Residues in contact with ASP 290 (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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164B GLU* 6.4 1.1 - - + -
166B LYS* 4.1 20.5 + - + +
285B LYS* 5.2 8.3 + - - -
288B ILE 3.7 1.6 + - - +
289B VAL* 1.3 73.3 - - - +
291B ASP* 1.3 62.7 + - - +
293B LEU* 2.8 29.9 + - - +
294B TYR* 3.0 47.8 + - + +
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Residues in contact with ASP 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ALA* 4.3 4.4 + - + -
164B GLU* 3.5 17.5 - - - +
165B TYR* 3.6 9.4 + - - -
166B LYS 6.2 0.2 - - - +
289B VAL* 3.2 10.8 - - - +
290B ASP* 1.3 80.2 + - - +
292B ASN* 1.3 60.1 + - - +
295B PRO* 3.5 18.8 - - - +
1D G 4.7 1.2 + - - +
32D A 2.7 58.8 + - + +
33D C 3.2 27.5 + - - +
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Residues in contact with ASN 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TYR 5.4 0.2 + - - -
95B ALA* 4.2 13.0 + - - +
288B ILE* 4.0 20.8 - - + +
289B VAL* 3.1 30.3 + - - +
291B ASP* 1.3 78.9 - - - +
293B LEU* 1.3 63.3 + - - +
295B PRO* 3.6 5.6 - - - +
296B GLN* 3.3 13.0 - - - +
403B ASN* 5.9 0.2 - - - +
1D G 3.1 52.4 + - - +
32D A 3.8 13.7 - - - +
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LYS* 4.2 18.8 - - + -
286B PRO* 4.1 12.6 - - + -
288B ILE* 3.7 27.1 - - + +
289B VAL 3.0 12.5 + - - +
290B ASP* 2.8 20.7 + - - +
292B ASN* 1.3 71.6 - - - +
294B TYR* 1.3 64.5 + - + +
296B GLN* 3.0 9.6 + - + +
297B LEU* 2.8 55.2 + - + -
322B ALA* 3.9 20.4 - - + -
327B CYS* 4.4 0.7 - - - -
404B VAL* 3.9 18.8 - - + -
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Residues in contact with TYR 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B TYR* 4.1 17.0 - - + +
166B LYS* 3.4 62.1 + - + +
290B ASP* 3.0 49.6 + - + +
293B LEU* 1.3 73.2 - - + +
295B PRO* 1.3 74.4 - - + +
297B LEU* 3.0 16.2 + - + +
298B GLU* 2.8 29.1 + - - +
320B PHE* 3.7 30.2 - + + -
321B LYS* 5.8 0.2 - - - -
322B ALA* 4.4 25.5 + - + +
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Residues in contact with PRO 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B TYR* 3.4 38.8 - - + -
168B ARG* 5.1 1.6 - - - +
291B ASP 3.5 19.5 - - - +
292B ASN 3.6 5.8 - - - +
294B TYR* 1.3 91.0 - - + +
296B GLN* 1.3 57.1 + - - +
298B GLU* 3.1 17.6 - - + +
299B ARG* 2.9 28.2 + - - +
1D G 5.1 0.9 - - - +
2D G 3.4 40.0 + - - +
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Residues in contact with GLN 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ILE* 4.1 4.6 - - - +
292B ASN 3.3 13.0 + - - +
293B LEU* 3.0 13.8 + - - +
295B PRO* 1.3 80.3 - - - +
297B LEU* 1.3 53.8 + - - +
299B ARG* 3.2 8.3 + - - +
300B ALA* 2.8 28.4 + - - +
400B LEU 4.0 0.5 - - - +
401B GLY* 4.4 1.6 - - - -
402B LYS 3.6 3.3 + - - -
403B ASN* 2.8 54.6 + - - +
404B VAL* 3.0 29.8 + - + +
1D G 3.0 37.6 + - - +
2D G 3.8 10.8 - - - +
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B PHE* 3.9 11.4 - - + -
293B LEU* 2.8 38.3 + - + +
294B TYR* 3.5 28.7 - - + +
296B GLN* 1.3 73.1 - - - +
298B GLU* 1.3 60.9 + - - +
300B ALA* 3.2 5.1 + - + +
301B SER* 2.9 31.6 + - - -
320B PHE* 4.1 21.5 - - + -
321B LYS 4.8 4.7 - - - +
322B ALA* 4.4 9.0 - - + -
327B CYS* 3.9 20.4 - - + -
329B LEU* 4.1 12.9 - - + +
404B VAL* 3.7 22.2 - - + -
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B TYR* 4.5 5.7 - - - +
168B ARG* 2.8 45.3 + - - -
294B TYR* 2.8 14.8 + - + +
295B PRO* 3.1 16.7 - - - +
297B LEU* 1.3 74.9 - - - +
299B ARG* 1.3 64.4 + - - +
301B SER* 3.3 3.0 - - - -
302B ARG* 3.0 25.3 + - - +
320B PHE* 3.6 28.9 - - + -
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Residues in contact with ARG 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B PRO 2.9 13.6 + - - +
296B GLN* 3.3 11.9 - - - +
298B GLU* 1.3 74.4 - - - +
300B ALA* 1.3 66.6 + - - +
302B ARG* 3.2 13.2 + - - +
303B LYS* 3.1 29.7 + - + +
398B HIS 5.0 0.6 + - - -
399B THR* 2.5 45.1 + - - +
401B GLY* 3.8 20.6 - - - +
603B SO4 2.8 42.6 + - - -
2D G 4.0 12.7 + - - +
3D A 3.1 32.6 + - - +
23D U 5.7 0.8 + - - -
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B GLN 2.8 15.0 + - - +
297B LEU* 3.2 8.7 + - + +
299B ARG* 1.3 74.0 - - - +
301B SER* 1.3 63.0 + - - +
303B LYS* 3.4 2.4 + - - +
304B ILE* 3.2 31.7 + - + +
329B LEU* 3.8 17.7 - - + -
400B LEU* 3.5 38.4 - - + +
404B VAL* 4.5 6.7 - - + -
408B ILE* 5.2 2.0 - - + -
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Residues in contact with SER 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LEU 2.9 17.7 + - - -
298B GLU* 3.3 7.9 - - - -
300B ALA* 1.3 78.5 - - - +
302B ARG* 1.3 56.0 + - - -
304B ILE 3.5 0.3 + - - -
305B PHE* 3.0 28.7 + - - +
318B SER* 3.3 26.8 - - - -
319B ALA 4.0 8.5 + - - -
320B PHE* 4.0 14.6 - - - -
329B LEU* 4.4 8.4 - - - +
331B PHE* 3.5 19.1 - - - -
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Residues in contact with ARG 302 (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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298B GLU 3.0 15.1 + - - +
299B ARG* 3.2 13.2 + - - +
301B SER* 1.3 78.3 - - - +
303B LYS* 1.3 68.2 + - - +
305B PHE* 3.3 10.0 + - + +
306B GLU* 2.8 71.2 + - + +
318B SER* 5.5 0.4 - - - -
603B SO4 2.7 32.9 + - - -
3D A 4.3 15.6 + - - -
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Residues in contact with LYS 303 (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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299B ARG* 3.1 26.2 + - + +
301B SER 3.3 0.2 - - - -
302B ARG* 1.3 84.9 - - - +
304B ILE* 1.3 59.1 + - - +
306B GLU* 3.4 11.7 + - - +
307B PHE* 2.8 28.1 + - - +
310B ARG* 4.5 2.6 + - - +
392B TYR* 3.5 14.6 + - - +
399B THR* 3.8 30.1 - - - +
400B LEU* 3.6 15.9 - - + -
603B SO4 3.5 34.4 + - - +
22D A 2.5 45.3 + - - -
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Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B VAL* 4.5 9.6 - - + -
300B ALA 3.2 18.9 + - - +
301B SER 3.8 0.4 - - - +
303B LYS* 1.3 73.2 - - - +
305B PHE* 1.3 66.1 + - - +
307B PHE* 3.1 4.3 + - + +
308B LEU* 2.9 35.8 + - + +
329B LEU* 3.7 24.9 - - + -
331B PHE* 3.6 27.1 - - + -
389B VAL* 3.7 27.6 - - + -
392B TYR* 3.9 25.1 - - + -
393B ALA* 5.9 3.1 - - + -
400B LEU* 4.4 14.1 - - + -
408B ILE* 5.9 0.2 - - + -
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Residues in contact with PHE 305 (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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343A ARG* 5.3 4.3 - - - -
370A GLU* 6.1 1.8 - - - -
301B SER 3.0 15.6 + - - +
302B ARG* 3.4 13.2 - - + +
304B ILE* 1.3 74.3 - - - +
306B GLU* 1.3 66.9 + - + +
308B LEU* 3.0 21.1 + - - +
309B GLU* 3.0 37.5 + - - +
315B PRO* 3.3 42.3 - - + +
316B LEU 4.2 6.7 - - - -
317B ARG* 3.8 25.4 - - - -
318B SER* 3.2 19.5 - - - +
331B PHE* 4.0 5.1 - + + -
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ARG* 2.8 60.3 + - + +
303B LYS* 3.7 13.6 + - + +
305B PHE* 1.3 79.5 - - + +
307B PHE* 1.3 62.5 + - - +
309B GLU* 3.1 24.9 + - + +
310B ARG* 3.1 34.3 + - - +
603B SO4 4.8 0.2 + - - -
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Residues in contact with PHE 307 (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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303B LYS 2.8 14.8 + - - +
304B ILE* 3.2 12.3 - - + +
306B GLU* 1.3 75.4 - - - +
308B LEU* 1.3 72.9 + - + +
310B ARG* 3.2 33.5 - - - +
311B GLU* 2.9 68.5 + - + +
313B PHE* 5.2 1.6 - + - -
382B PHE* 3.9 12.1 - + - -
388B GLY* 3.6 36.1 - - - -
389B VAL* 4.0 4.7 - - - -
392B TYR* 3.5 41.1 - + + -
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Residues in contact with LEU 308 (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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279B PHE* 4.5 5.4 - - + -
304B ILE* 2.9 35.8 + - + +
305B PHE* 3.3 8.3 - - - +
307B PHE* 1.3 87.0 - - + +
309B GLU* 1.3 59.1 + - - +
311B GLU* 3.6 3.8 - - - -
312B ASN 3.1 5.0 + - - -
313B PHE* 2.8 41.4 + - + +
314B MET 3.8 0.3 + - - -
315B PRO* 3.9 13.9 - - + -
331B PHE* 4.0 25.4 - - + -
333B CYS* 3.9 16.4 - - - -
385B PRO* 3.8 36.6 - - + +
389B VAL* 5.2 1.8 - - + -
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Residues in contact with GLU 309 (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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305B PHE* 3.0 31.8 + - - +
306B GLU* 3.1 35.4 + - + +
307B PHE 3.1 0.2 - - - -
308B LEU* 1.3 74.2 - - - +
310B ARG* 1.3 60.1 + - + +
311B GLU 3.1 3.8 - - - -
312B ASN* 3.1 23.6 + - - -
314B MET* 4.7 2.1 + - - +
315B PRO* 3.6 21.1 - - + +
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Residues in contact with ARG 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LYS* 4.5 2.6 + - - +
306B GLU* 3.1 16.6 + - - +
307B PHE* 3.2 59.1 + - - +
309B GLU* 1.3 79.3 - - + +
311B GLU* 1.3 65.0 + - + +
312B ASN* 3.2 9.9 - - - +
392B TYR* 3.6 13.7 - - - -
396B HIS* 5.4 0.2 - - - -
20D C 4.8 6.0 + - - -
21D C 3.4 59.2 + - - -
22D A 4.6 4.0 + - - -
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Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B PHE* 2.9 43.8 + - + +
308B LEU* 3.9 7.0 - - - +
309B GLU 3.1 0.2 - - - -
310B ARG* 1.3 85.4 + - - +
312B ASN* 1.3 69.3 + - - +
313B PHE* 3.5 16.4 + - + -
338B ILE* 4.7 5.7 - - - +
380B ARG* 4.8 14.8 + - - +
382B PHE* 3.5 35.9 - - + -
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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