Contacts of the helix formed by residues 283 - 303 (chain A) in PDB entry 2QLU
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 THR 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ILE 5.6 1.3 - - - +
282A ILE* 1.3 75.6 - - - +
284A TRP* 1.3 61.0 + - - +
285A ASN* 3.6 8.3 + - - +
286A GLU* 2.9 42.5 + - - +
287A LEU* 2.8 29.1 + - - +
400A CYS* 4.0 1.3 - - - -
401A LYS* 5.1 7.0 - - + +
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Residues in contact with TRP 284 (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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283A THR* 1.3 73.7 - - - +
285A ASN* 1.3 80.5 + - - +
287A LEU* 3.3 9.9 + - + +
288A CYS* 3.0 48.1 + - - +
400A CYS* 3.9 16.0 - - - -
401A LYS 4.8 6.7 + - - +
447A HIS* 3.6 23.3 - + + +
449A GLY* 3.2 45.1 - - - -
450A LEU* 3.8 22.0 - - + -
453A LEU* 5.6 4.3 - - + -
481A ILE* 3.7 24.0 - - + -
482A ARG* 4.4 10.8 + - - +
484A SER 6.1 0.2 - - - -
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Residues in contact with ASN 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A THR* 3.2 7.8 + - - +
284A TRP* 1.3 95.8 + - - +
286A GLU* 1.3 56.5 + - + +
288A CYS* 3.6 5.1 + - - +
289A HIS* 3.0 28.2 + - - +
482A ARG* 4.7 11.6 + - - +
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Residues in contact with GLU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A TYR* 4.4 6.2 + - - -
281A ILE 4.6 1.2 - - - +
282A ILE* 3.3 17.0 - - + +
283A THR* 2.9 46.5 + - - +
285A ASN* 1.3 73.6 - - + +
287A LEU* 1.4 61.7 + - - +
289A HIS* 3.0 7.4 + - - +
290A VAL* 2.8 35.3 + - - +
333A LEU* 3.6 33.4 - - + +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ILE* 3.7 16.2 - - + +
283A THR 2.8 12.5 + - - +
284A TRP* 3.5 14.6 - - + +
286A GLU* 1.4 76.3 - - - +
288A CYS* 1.3 70.6 + - - +
290A VAL* 4.0 2.8 - - - +
291A ALA* 2.7 39.9 + - + +
396A LEU* 4.0 14.7 - - + +
397A VAL* 4.0 20.4 - - + +
400A CYS* 3.8 26.2 - - + -
450A LEU* 3.8 21.8 - - + -
453A LEU* 4.0 17.5 - - + -
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Residues in contact with CYS 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A TRP* 3.0 49.1 + - - +
285A ASN* 3.7 3.6 - - - +
287A LEU* 1.3 85.8 - - - +
289A HIS* 1.3 58.0 + - - +
292A GLU* 2.9 32.7 + - - +
453A LEU* 6.4 1.1 - - - -
478A VAL* 3.6 13.6 - - + +
481A ILE* 5.5 0.9 - - - -
482A ARG* 3.0 46.7 + - + -
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Residues in contact with HIS 289 (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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285A ASN 3.0 18.6 + - - +
286A GLU* 3.0 6.3 + - - +
288A CYS* 1.3 76.0 - - - +
290A VAL* 1.3 53.1 + - - +
292A GLU* 4.1 1.5 - - - +
293A THR* 2.7 61.7 + - + +
332A ASP* 3.3 24.2 + - - +
333A LEU* 3.6 19.7 - - + -
334A THR* 3.1 28.2 + - + -
482A ARG* 4.3 11.1 + - - +
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU* 4.2 18.8 - - + -
282A ILE* 5.5 3.4 - - + -
286A GLU* 2.8 24.6 + - + +
287A LEU 4.0 2.2 - - - +
289A HIS* 1.3 71.0 - - - +
291A ALA* 1.3 58.4 + - - +
293A THR* 3.7 5.6 + - - -
294A MET* 2.9 30.0 + - + +
327A VAL* 5.0 0.9 - - + -
329A LEU* 4.1 16.2 - - + -
333A LEU* 3.5 34.3 - - + +
335A ALA* 4.1 7.1 - - + +
396A LEU* 3.9 30.7 - - + -
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Residues in contact with ALA 291 (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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287A LEU* 2.7 30.6 + - + +
288A CYS 3.9 2.5 - - - +
290A VAL* 1.3 79.5 - - - +
292A GLU* 1.3 57.7 + - - +
294A MET* 3.8 3.6 - - - +
295A SER* 2.9 31.8 + - - -
393A LEU* 3.9 24.9 - - + +
396A LEU* 4.3 8.5 - - + +
453A LEU* 5.0 0.9 - - + -
478A VAL* 3.9 17.2 - - + +
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Residues in contact with GLU 292 (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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288A CYS 2.9 20.3 + - - +
289A HIS* 4.1 2.2 - - - +
291A ALA* 1.3 75.1 - - - +
293A THR* 1.3 61.6 + - + +
295A SER* 3.3 6.3 + - - -
296A ARG* 2.8 31.0 + - + +
475A GLU* 3.7 22.4 - - + +
478A VAL* 3.6 10.2 - - + +
479A SER* 3.4 38.0 + - - -
482A ARG* 3.3 28.7 + - - +
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Residues in contact with THR 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A GLU* 5.7 2.0 - - - +
243A ASN* 3.6 31.3 - - - +
289A HIS* 2.7 48.5 + - + +
290A VAL* 3.7 1.7 + - - -
292A GLU* 1.3 77.2 - - + +
294A MET* 1.3 59.8 + - - +
296A ARG* 3.7 10.8 - - - +
297A GLY* 3.0 23.6 + - - -
334A THR* 3.8 7.7 - - + -
335A ALA* 3.0 24.5 + - - +
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Residues in contact with MET 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU* 4.7 4.7 - - - -
290A VAL* 2.9 21.3 + - - +
291A ALA* 3.8 4.5 - - - +
293A THR* 1.3 79.4 + - - +
295A SER* 1.3 55.7 + - - +
297A GLY* 3.5 0.9 + - - -
298A LEU* 3.1 21.3 + - - +
322A PHE* 3.7 23.8 - - + -
327A VAL* 4.0 22.0 - - + -
335A ALA* 3.6 12.1 - - + -
337A LEU* 4.3 7.6 - - + +
389A MET* 3.1 27.1 - - + +
392A VAL* 3.5 31.4 - - + -
393A LEU* 3.7 30.3 - - + -
396A LEU* 4.1 9.2 - - + -
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ALA 2.9 18.9 + - - -
292A GLU* 3.3 3.5 + - - -
294A MET* 1.3 75.1 - - - +
296A ARG* 1.3 62.1 + - - +
298A LEU* 4.3 0.2 - - - -
299A SER* 2.7 33.3 + - - -
389A MET* 3.4 17.7 - - - +
471A ALA* 3.8 16.1 - - - +
474A VAL* 3.9 20.1 + - - +
475A GLU* 3.3 23.1 + - - -
478A VAL* 4.8 0.5 - - - +
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Residues in contact with ARG 296 (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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241A HIS* 3.6 25.2 + - + +
242A GLU* 2.9 32.1 + - - +
243A ASN* 3.1 18.4 + - - +
292A GLU* 2.8 21.1 + - + +
293A THR* 3.7 11.7 - - - +
295A SER* 1.3 78.4 + - - +
297A GLY* 1.4 51.1 + - - +
299A SER* 3.7 2.1 - - - -
300A TYR* 2.8 35.8 + - + +
475A GLU* 3.5 35.1 + - - +
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Residues in contact with GLY 297 (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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241A HIS* 4.3 5.4 - - - -
243A ASN* 3.6 30.3 - - - -
244A LEU* 3.4 13.7 - - - +
293A THR 3.0 12.4 + - - -
294A MET 4.0 1.1 - - - -
296A ARG* 1.4 73.7 - - - +
298A LEU* 1.3 57.4 + - - +
300A TYR* 3.2 1.6 + - - +
301A LEU* 2.8 24.4 + - - +
337A LEU* 3.8 9.6 - - - -
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A MET 3.1 6.4 + - - +
295A SER 3.9 0.9 - - - +
297A GLY* 1.3 71.6 - - - +
299A SER* 1.4 67.0 + - - +
300A TYR 3.0 0.9 - - - -
301A LEU* 3.2 10.4 + - + +
302A HIS* 2.9 55.9 + - + +
319A HIS* 4.7 0.9 - - + -
322A PHE* 3.9 21.5 - - + -
337A LEU* 3.6 14.4 - - + +
385A ASP* 4.1 16.2 - - + +
386A MET* 3.7 27.4 - - - -
389A MET* 3.1 46.2 - - + -
471A ALA* 3.7 2.7 - - + -
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Residues in contact with SER 299 (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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295A SER 2.7 21.7 + - - -
296A ARG 3.7 3.8 - - - -
298A LEU* 1.4 69.9 - - - +
300A TYR* 1.3 65.1 + - - +
302A HIS* 3.4 5.4 + - - +
303A GLU* 3.0 27.2 + - - +
471A ALA* 3.0 22.4 - - - +
472A GLY* 3.5 24.0 + - - +
475A GLU* 4.4 7.9 + - - -
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Residues in contact with TYR 300 (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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238A GLY* 2.5 34.5 + - - -
239A MET* 4.9 0.2 - - - -
240A LYS 5.0 1.1 + - - -
241A HIS* 3.4 50.0 - + + +
244A LEU* 4.0 15.0 - - + -
296A ARG* 2.8 19.6 + - + +
297A GLY 3.6 3.6 - - - +
298A LEU 3.0 0.2 - - - -
299A SER* 1.3 81.3 - - - +
301A LEU* 1.3 62.3 + - - +
303A GLU* 3.1 27.7 + - - +
305A VAL* 4.2 20.9 - - + +
308A CYS* 4.6 3.6 - - - -
314A LYS* 3.1 36.1 + - + +
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Residues in contact with LEU 301 (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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239A MET* 4.4 5.8 - - + -
244A LEU* 4.1 22.4 - - + -
297A GLY 2.8 16.7 + - - +
298A LEU* 3.4 19.3 - - + +
300A TYR* 1.3 74.4 - - - +
302A HIS* 1.4 57.6 + - + +
314A LYS* 2.7 23.2 + - - +
317A ILE* 3.0 66.3 + - + +
319A HIS* 3.9 40.4 - - + +
337A LEU* 4.6 1.6 - - + -
340A PHE* 4.2 17.9 - - + -
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Residues in contact with HIS 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 2.9 39.0 + - + +
299A SER* 3.6 8.5 - - - +
301A LEU* 1.4 75.3 - - + +
303A GLU* 1.3 57.1 + - - +
304A ASP 3.6 0.3 + - - -
316A SER* 2.8 26.4 + - - -
317A ILE 3.3 19.7 - - - +
378A ARG* 4.6 2.6 + - - -
382A LEU* 3.6 49.5 - - + +
385A ASP* 2.8 41.4 + - + +
386A MET* 4.2 7.6 - - + +
470A SER* 6.0 0.4 - - - -
471A ALA* 4.2 12.1 + - + +
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Residues in contact with GLU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A SER* 3.0 18.0 + - - +
300A TYR* 3.1 29.9 + - + +
302A HIS* 1.3 75.1 - - - +
304A ASP* 1.3 73.3 - - - +
305A VAL* 3.7 21.8 + - + +
314A LYS* 2.7 30.7 + - - +
315A PRO 3.7 0.9 - - - +
316A SER* 4.0 1.8 - - - -
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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
------------------------------------------------------------
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