Contacts of the helix formed by residues 289 - 311 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ARG* 4.3 28.7 - - + +
94A TYR* 4.1 17.7 - - - +
95A ALA* 4.0 18.4 - - + -
288A ILE* 1.3 76.2 - - - +
290A ASP* 1.3 66.0 + - - +
291A ASP* 4.0 6.7 - - - +
292A ASN* 2.9 38.1 + - - +
293A LEU* 2.9 18.9 + - - +
602A SO4 3.2 25.1 - - - +
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Residues in contact with ASP 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 5.7 0.2 - - - -
166A LYS* 3.7 31.6 + - + +
285A LYS* 5.7 2.4 - - - -
288A ILE 3.8 1.1 + - - +
289A VAL* 1.3 70.3 - - - +
291A ASP* 1.3 61.5 + - - +
293A LEU* 3.0 11.4 + - - +
294A TYR* 2.9 61.2 + - + +
602A SO4 2.6 33.9 + - - +
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Residues in contact with ASP 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ALA* 4.5 6.1 - - + -
164A GLU* 3.7 10.4 - - - +
165A TYR* 3.9 13.1 + - - -
166A LYS 5.4 0.6 + - - +
289A VAL* 3.1 6.3 - - + +
290A ASP* 1.3 79.6 - - - +
292A ASN* 1.3 63.3 + - - +
295A PRO* 3.4 19.5 - - - +
602A SO4 3.9 11.8 + - - -
1C G 4.9 1.4 + - - -
32C A 2.8 47.5 + - + +
33C C 3.3 38.7 + - - +
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Residues in contact with ASN 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TYR 5.2 0.6 + - - -
95A ALA* 3.9 14.4 + - - +
288A ILE* 3.9 17.0 - - + +
289A VAL* 2.9 29.1 + - + +
291A ASP* 1.3 81.1 - - - +
293A LEU* 1.3 64.8 + - - +
294A TYR 3.4 0.3 + - - -
295A PRO* 3.7 5.9 - - - +
296A GLN* 3.2 23.1 + - - +
403A ASN* 4.9 2.6 - - - +
1C G 3.2 37.0 + - - +
32C A 3.8 13.5 - - - -
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LYS* 3.9 36.1 - - + -
286A PRO* 4.3 15.7 - - + +
288A ILE* 3.7 22.2 - - + +
289A VAL 2.9 12.7 + - - +
290A ASP* 3.5 19.3 - - - +
292A ASN* 1.3 77.4 - - - +
294A TYR* 1.3 62.5 + - + +
296A GLN* 3.1 9.2 + - - +
297A LEU* 3.0 46.3 + - + +
322A ALA* 4.3 14.6 - - + -
327A CYS* 4.3 2.2 - - - -
404A VAL* 4.2 13.2 - - + -
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Residues in contact with TYR 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 4.3 16.4 - - + +
166A LYS* 3.3 49.3 + - + -
290A ASP* 2.9 54.8 + - + +
293A LEU* 1.3 77.9 - - + +
295A PRO* 1.3 71.6 - - + +
297A LEU* 3.1 11.3 + - + +
298A GLU* 2.9 33.4 + - - +
320A PHE* 3.5 34.5 - + + -
321A LYS* 6.3 0.2 - - - -
322A ALA* 3.9 25.1 + - + +
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Residues in contact with PRO 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 3.6 33.0 - - + -
168A ARG* 5.2 0.9 - - - +
291A ASP 3.4 23.8 - - - +
292A ASN 3.7 4.9 - - - +
294A TYR* 1.3 94.6 - - + +
296A GLN* 1.3 50.6 + - - +
298A GLU* 3.3 16.9 - - - +
299A ARG* 2.7 32.4 + - - +
1C G 5.3 0.7 - - - +
2C G 3.4 40.9 + - - +
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Residues in contact with GLN 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ILE* 4.5 2.2 - - - +
292A ASN* 3.2 13.0 + - - +
293A LEU 3.1 8.0 + - - +
294A TYR 3.1 0.8 - - - -
295A PRO* 1.3 76.5 - - - +
297A LEU* 1.3 56.1 + - - +
299A ARG* 3.1 8.0 + - - +
300A ALA* 2.8 33.8 + - - +
400A LEU 3.8 4.0 - - - +
401A GLY* 4.0 6.1 - - - -
402A LYS 3.7 1.4 + - - -
403A ASN* 2.8 56.0 + - - +
404A VAL* 3.2 19.2 + - + +
1C G 2.6 39.5 + - - +
2C G 3.7 15.7 - - - +
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PHE* 3.8 28.7 - - + -
293A LEU* 3.0 31.8 + - + +
294A TYR* 3.1 17.0 + - + +
296A GLN* 1.3 73.4 - - - +
298A GLU* 1.3 58.9 + - - +
300A ALA* 3.3 5.3 + - - +
301A SER* 2.9 31.4 + - - -
320A PHE* 3.9 32.4 - - + -
321A LYS 4.9 1.1 - - - +
322A ALA* 4.3 15.9 - - + +
327A CYS* 4.1 20.0 - - + -
328A TYR 5.5 0.2 - - - +
329A LEU* 3.9 12.8 - - + +
404A VAL* 4.1 10.5 - - + -
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 5.0 3.6 - - - +
168A ARG* 2.4 50.2 + - - -
294A TYR* 2.9 13.2 + - - +
295A PRO* 3.3 18.1 - - - +
297A LEU* 1.3 72.5 - - - +
299A ARG* 1.3 66.2 + - - +
301A SER* 3.3 4.0 + - - -
302A ARG* 3.1 25.4 + - - +
320A PHE* 3.6 27.3 - - + -
2C G 5.5 0.3 + - - -
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Residues in contact with ARG 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A PRO 2.7 19.1 + - - +
296A GLN* 3.1 12.7 + - - +
298A GLU* 1.3 74.1 - - - +
300A ALA* 1.3 64.3 + - - +
302A ARG* 3.3 17.2 + - - +
303A LYS* 2.9 27.5 + - + +
399A THR* 2.6 57.6 + - - +
400A LEU 4.3 0.2 - - - -
401A GLY* 3.8 17.3 - - - +
601A SO4 2.6 42.9 + - - -
2C G 4.6 9.2 - - - +
3C A 2.9 33.2 + - - +
23C U 5.2 1.6 + - - -
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PHE* 5.7 0.2 - - + -
296A GLN 2.8 15.6 + - - +
297A LEU* 3.5 8.3 - - + +
299A ARG* 1.3 72.1 - - - +
301A SER* 1.3 64.9 + - - +
303A LYS* 3.1 1.0 + - - +
304A ILE* 3.0 28.6 + - - +
329A LEU* 3.3 28.9 - - + -
400A LEU* 3.9 28.2 + - + +
404A VAL* 4.2 9.6 - - + -
408A ILE* 5.0 0.7 - - + -
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Residues in contact with SER 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU 2.9 17.2 + - - -
298A GLU* 3.6 6.3 - - - -
299A ARG 3.2 0.4 - - - -
300A ALA* 1.3 75.3 - - - +
302A ARG* 1.3 53.8 + - - +
304A ILE 3.4 0.2 + - - -
305A PHE* 2.8 37.5 + - - +
318A SER* 4.1 18.4 + - - -
319A ALA 3.9 13.3 + - - -
320A PHE* 3.5 22.5 - - - +
329A LEU* 4.4 6.5 - - - +
331A PHE* 3.6 14.3 - - - -
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Residues in contact with ARG 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A GLU 3.1 15.5 + - - +
299A ARG* 3.6 17.9 - - - +
301A SER* 1.3 78.5 - - - +
303A LYS* 1.3 82.2 + - - +
305A PHE* 2.9 8.9 + - + +
306A GLU* 2.7 62.2 + - + +
601A SO4 2.8 32.3 + - - -
3C A 3.7 24.5 + - - -
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Residues in contact with LYS 303 (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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299A ARG* 2.9 37.8 + - + +
300A ALA 3.1 0.4 + - - +
302A ARG* 1.3 101.7 - - - +
304A ILE* 1.3 61.1 + - - +
306A GLU* 3.5 16.7 + - - +
307A PHE* 3.3 16.3 + - - +
310A ARG* 4.8 1.4 + - - +
392A TYR* 3.6 14.6 + - - +
399A THR* 4.0 17.2 + - + +
400A LEU* 3.6 20.2 - - + -
601A SO4 2.7 30.0 + - - +
22C A 2.9 41.7 + - - -
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL* 4.3 12.8 - - + -
300A ALA 3.0 8.5 + - - +
303A LYS* 1.3 73.7 - - - +
305A PHE* 1.3 68.4 + - - +
307A PHE* 3.0 4.1 + - + +
308A LEU* 2.8 24.6 + - + +
329A LEU* 3.6 31.6 - - + -
331A PHE* 3.5 29.6 - - + -
389A VAL* 3.5 31.6 - - + -
392A TYR* 3.9 23.8 - - + -
393A ALA* 5.3 5.4 - - + -
400A LEU* 4.3 15.0 - - + -
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Residues in contact with PHE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A SER 2.8 20.5 + - - +
302A ARG* 3.3 11.4 - - + +
304A ILE* 1.3 78.1 - - - +
306A GLU* 1.3 61.0 + - + +
308A LEU* 3.1 7.6 + - - +
309A GLU* 3.0 53.7 + - - +
315A PRO* 3.6 41.8 - - + +
316A LEU 4.0 7.9 - - - -
317A ARG* 3.8 22.7 - - - -
318A SER* 3.6 23.6 - - - +
331A PHE* 4.0 8.7 - + + -
343B ARG* 6.3 0.9 - - - -
370B GLU* 5.9 3.8 - - - -
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Residues in contact with GLU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ARG* 2.7 53.8 + - + +
303A LYS* 3.9 19.8 + - - +
305A PHE* 1.3 74.6 - - + +
307A PHE* 1.3 57.2 + - - +
309A GLU* 3.3 25.6 - - - +
310A ARG* 3.0 41.6 + - - +
601A SO4 5.0 3.5 + - - -
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Residues in contact with PHE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LYS 3.3 12.6 + - - +
304A ILE* 3.0 12.9 + - - +
306A GLU* 1.3 75.5 - - - +
308A LEU* 1.3 76.7 + - + +
310A ARG* 3.1 24.3 + - - +
311A GLU* 3.0 61.5 + - + +
313A PHE* 5.0 0.7 - + - -
382A PHE* 3.8 16.8 - + - -
388A GLY* 3.4 40.4 - - - -
389A VAL* 4.1 11.9 - - + -
391A SER* 5.9 0.9 - - - -
392A TYR* 3.4 39.0 - + + -
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PHE* 3.9 18.6 - - + -
304A ILE* 2.8 23.3 + - + +
305A PHE* 3.5 7.4 - - - +
307A PHE* 1.3 79.6 - - + +
309A GLU* 1.3 59.3 + - - +
311A GLU 3.6 1.0 + - - -
312A ASN 3.3 2.6 + - - -
313A PHE* 2.9 41.8 + - + +
315A PRO* 3.9 15.7 - - + -
331A PHE* 3.9 27.6 - - + -
333A CYS* 3.9 11.9 - - - -
385A PRO* 3.6 30.7 - - + +
389A VAL* 3.8 20.4 - - + -
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Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A PHE* 3.0 48.2 + - + +
306A GLU* 3.3 32.6 - - - +
308A LEU* 1.3 77.0 - - - +
310A ARG* 1.3 56.1 + - - +
312A ASN* 2.9 25.5 + - - -
314A MET* 4.7 1.7 + - - +
315A PRO* 3.6 18.5 - - + +
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Residues in contact with ARG 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LYS* 4.8 1.4 + - - +
306A GLU* 3.0 37.2 + - - +
307A PHE* 3.5 23.9 - - - +
309A GLU* 1.3 76.0 - - + +
311A GLU* 1.3 73.7 + - + +
312A ASN* 3.2 11.2 + - - +
392A TYR* 3.9 15.0 - - - -
396A HIS* 5.2 0.2 - - - -
20C C 4.6 8.2 + - - -
21C C 3.1 58.6 + - - -
22C A 3.5 11.9 + - - -
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Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A PHE* 3.0 51.6 + - + +
310A ARG* 1.3 89.4 + - + +
312A ASN* 1.3 68.7 + - - +
313A PHE* 3.4 30.9 + - + -
338A ILE* 4.3 7.8 - - - +
380A ARG* 4.8 11.8 + - - +
382A PHE* 3.9 21.5 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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