Contacts of the helix formed by residues 283 - 304 (chain A) in PDB entry 2HBH
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ASP 4.7 0.9 - - - +
282A LEU* 1.3 76.6 - - - +
284A ALA* 1.3 66.1 + - - +
285A GLU* 3.0 15.8 + - - +
286A ASP* 3.3 28.7 + - - +
287A GLN* 3.1 19.5 + - - +
375A GLN* 5.4 1.6 - - - +
376A ASP* 5.8 4.3 - - + -
379A ARG* 6.3 0.4 - - - +
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LEU 3.7 1.4 + - - -
283A THR* 1.3 73.2 - - - +
285A GLU* 1.3 68.3 + - - +
287A GLN* 3.5 15.3 + - - +
288A ILE* 2.9 33.0 + - + +
691B HIS* 4.1 24.5 - - + +
694B LEU* 4.7 3.9 - - + +
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Residues in contact with GLU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A THR* 3.0 13.2 - - - +
284A ALA* 1.3 88.1 + - - +
286A ASP* 1.3 59.4 + - - +
288A ILE* 3.1 11.5 + - + +
289A ALA* 2.8 28.7 + - - +
373A GLY 5.7 0.9 - - - -
375A GLN* 5.9 5.8 - - + +
691B HIS* 3.9 21.0 + - - -
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Residues in contact with ASP 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LEU* 4.3 13.2 - - + +
283A THR* 3.1 22.2 + - - +
285A GLU* 1.3 74.8 - - - +
287A GLN* 1.3 61.3 + - - +
289A ALA* 3.6 3.3 - - - +
290A LEU* 2.8 37.5 + - - +
373A GLY 4.3 0.9 - - - +
374A VAL* 3.3 8.3 - - - +
375A GLN* 2.5 35.2 + - - +
376A ASP* 3.1 30.9 + - - +
380A ILE* 4.1 16.2 - - + -
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Residues in contact with GLN 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LYS* 5.7 0.3 - - - +
279A PHE* 3.6 55.1 + - + +
280A ARG* 3.9 16.7 + - - +
282A LEU* 2.8 28.7 + - + -
283A THR 3.1 15.5 + - - +
284A ALA* 3.6 14.1 - - - +
286A ASP* 1.3 76.1 - - - +
288A ILE* 1.3 59.2 + - - +
290A LEU* 3.5 0.8 + - - -
291A LEU* 2.8 35.7 + - - +
694B LEU* 3.7 28.4 - - + +
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Residues in contact with ILE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ALA 2.9 16.6 - - - +
285A GLU* 3.1 11.6 + - + +
287A GLN* 1.3 74.7 - - - +
289A ALA* 1.3 56.9 + - - +
291A LEU* 4.2 4.9 - - - -
292A LYS* 2.7 46.7 + - + +
687B HIS* 3.8 24.2 - - + +
690B LEU* 3.7 27.8 - - + -
691B HIS* 3.5 42.2 - - + +
694B LEU* 4.0 16.6 - - + -
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLU 2.8 18.4 + - - +
286A ASP* 3.1 7.8 + - - +
288A ILE* 1.3 75.3 - - - +
290A LEU* 1.3 60.4 + - - +
292A LYS* 4.1 4.1 - - - +
293A SER* 2.6 33.4 + - - -
372A PRO 4.3 4.5 - - - +
373A GLY* 3.7 33.9 - - - +
374A VAL* 3.9 10.8 - - + +
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PHE* 4.0 7.2 - - + -
282A LEU* 3.4 33.0 - - + -
286A ASP 2.8 20.9 + - - +
287A GLN 3.8 2.7 - - - +
289A ALA* 1.3 70.0 - - - +
291A LEU* 1.3 58.9 + - - +
293A SER* 4.2 0.5 - - - -
294A SER* 2.6 41.0 + - - -
366A LEU* 3.6 20.2 - - + +
367A LEU* 3.8 18.2 - - + -
368A SER 3.3 26.5 - - - +
371A ARG* 4.2 6.7 - - + -
374A VAL* 3.8 16.6 - - + -
380A ILE* 3.9 17.7 - - + -
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ILE* 5.2 4.0 - - + +
269A VAL* 3.9 28.5 - - + -
270A ILE* 4.0 25.1 - - + -
273A ALA* 3.9 12.3 - - + -
279A PHE* 3.3 27.1 - - + -
287A GLN 2.8 25.3 + - - +
288A ILE* 3.6 7.0 - - - +
290A LEU* 1.3 73.1 - - - +
292A LYS* 1.3 68.0 + - - +
294A SER* 4.2 2.0 - - - -
295A ALA* 2.8 36.4 + - + +
366A LEU* 4.4 5.4 - - + -
447A VAL* 4.9 1.3 - - + -
690B LEU* 5.0 12.3 - - + -
694B LEU* 4.7 10.1 - - + -
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Residues in contact with LYS 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 ILE* 2.7 29.5 + - + +
289A ALA* 4.1 4.5 - - - +
291A LEU* 1.3 75.5 - - - +
293A SER* 1.3 62.2 + - - +
294A SER 3.7 0.2 + - - -
295A ALA* 4.0 7.3 + - - +
296A ILE 5.2 0.3 + - - -
446A GLU 3.5 9.3 + - - +
447A VAL* 3.4 35.1 - - - +
448A PHE* 4.7 6.4 - - - -
449A GLY 3.2 23.5 + - - -
450A SER 4.7 0.2 - - - -
451A GLU 3.2 15.0 + - - +
687B HIS* 2.8 42.9 + - + +
690B LEU* 3.8 16.4 - - + -
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Residues in contact with SER 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ALA* 2.6 24.8 + - - -
290A LEU 4.2 0.2 - - - -
292A LYS* 1.3 78.5 - - - +
294A SER* 1.3 59.2 + - - +
296A ILE* 5.1 1.2 + - - +
371A ARG* 3.6 29.3 + - - +
372A PRO* 3.5 28.0 + - - +
420A ASN* 2.9 28.1 + - - +
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Residues in contact with SER 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU 2.6 22.7 + - - -
291A LEU 3.9 0.2 + - - -
293A SER* 1.3 75.5 - - - +
295A ALA* 1.3 67.8 + - - +
296A ILE 3.3 2.5 - - - -
297A GLU* 2.8 17.8 + - - +
298A ILE* 2.9 18.4 + - - +
365A CYS* 4.1 7.4 - - - -
366A LEU* 2.9 25.9 - - - +
371A ARG* 3.3 31.4 - - - +
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ILE* 4.8 12.8 - - + -
269A VAL* 4.7 10.1 - - + +
291A LEU* 2.8 25.6 + - + +
292A LYS 4.2 2.7 - - - +
293A SER 3.6 0.8 - - - -
294A SER* 1.3 77.6 + - - +
296A ILE* 1.3 64.0 + - - +
298A ILE* 3.2 7.8 + - - +
299A ILE* 3.0 29.0 + - + +
447A VAL* 3.8 24.2 - - + -
448A PHE* 4.4 5.2 - - + -
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Residues in contact with ILE 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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262A VAL* 6.1 0.9 - - + -
292A LYS 5.2 0.4 + - - -
293A SER 5.1 0.8 + - - +
294A SER 3.3 0.8 - - - -
295A ALA* 1.3 79.0 - - - +
297A GLU* 1.3 63.3 + - - +
299A ILE* 3.6 10.1 + - + +
300A MET* 2.9 54.7 + - + +
420A ASN* 3.7 41.7 - - - +
423A HIS* 3.3 44.6 - - + +
448A PHE* 3.9 21.3 - - + -
500A XE4 4.6 14.1 - - + -
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Residues in contact with GLU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A SER 2.8 8.1 + - - +
296A ILE* 1.3 75.4 - - + +
298A ILE* 1.3 68.4 + - - +
300A MET* 3.2 9.2 + - - +
301A LEU* 3.0 26.3 + - - +
365A CYS* 3.2 17.2 - - - -
371A ARG* 3.0 33.4 + - - -
413A LEU 4.8 0.5 - - - +
416A LEU* 3.4 36.0 - - + +
417A ARG* 3.1 19.4 + - - -
420A ASN* 2.7 39.8 + - + +
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Residues in contact with ILE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A VAL* 3.5 37.5 - - + -
272A PHE* 5.2 7.4 - - + -
294A SER* 2.9 21.6 + - - +
295A ALA 3.6 5.8 - - - +
297A GLU* 1.3 75.4 - - - +
299A ILE* 1.3 54.6 + - - +
301A LEU* 3.1 5.8 + - + +
302A ARG* 2.8 38.0 + - + +
362A MET* 3.4 47.1 - - + +
365A CYS* 3.6 25.1 - - + -
366A LEU* 3.9 12.6 - - + +
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Residues in contact with ILE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A VAL* 3.8 32.5 - - + +
265A SER* 3.8 26.2 - - - -
266A ILE* 4.1 11.4 - - + -
269A VAL* 4.5 9.2 - - + -
295A ALA 3.0 16.6 + - - +
296A ILE* 3.6 17.7 - - + +
298A ILE* 1.3 77.3 - - - +
300A MET* 1.3 57.4 + - - +
302A ARG* 3.2 9.6 - - - +
303A SER* 2.9 32.7 + - - -
448A PHE* 5.1 1.3 - - + -
500A XE4 3.8 44.6 - - + -
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Residues in contact with MET 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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296A ILE* 2.9 47.3 + - + +
297A GLU* 3.2 7.8 + - - +
299A ILE* 1.3 76.5 - - - +
301A LEU* 1.3 59.8 + - - +
303A SER* 2.6 22.8 + - - -
304A ASN* 3.7 1.0 + - - +
337A LEU* 4.5 12.8 - - + -
341A LEU* 3.4 36.3 - - + -
344A PHE* 4.3 4.3 - - + -
345A GLN* 3.0 21.6 + - - +
416A LEU* 4.2 14.4 - - + -
419A LEU* 3.8 35.7 - - + +
420A ASN 5.0 0.7 - - - -
423A HIS* 6.2 0.2 - - + -
500A XE4 4.3 11.2 - - + -
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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
----------------------------------------------------------
297A GLU 3.0 14.4 + - - +
298A ILE* 3.1 10.1 + - + +
300A MET* 1.3 74.3 - - - +
302A ARG* 1.3 65.0 + - - +
304A ASN* 3.0 23.9 + - - +
344A PHE* 3.9 22.2 - - + -
348A LEU* 3.9 15.7 - - + +
358A HIS* 3.4 13.4 + - + +
361A LEU* 4.1 29.8 - - + +
362A MET* 3.8 37.9 - - + +
365A CYS* 4.1 10.1 - - + -
412A LYS* 5.7 1.1 - - + -
416A LEU* 3.8 20.2 - - + -
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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
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171A HIS* 4.8 4.9 + - + -
174A THR* 2.8 35.6 + - - -
175A TYR* 3.4 32.2 - - + +
264A TYR* 5.3 3.8 - - - -
265A SER* 4.2 9.5 + - - +
268A LYS* 3.3 28.7 - - - +
269A VAL* 4.2 13.2 - - - +
272A PHE* 5.9 1.2 - - - +
298A ILE* 2.8 30.0 + - + +
299A ILE* 3.2 17.5 - - - +
301A LEU* 1.3 73.0 - - - +
303A SER* 1.3 62.0 + - - +
305A GLN* 3.2 22.2 + - - +
358A HIS* 4.0 12.3 - - + -
362A MET* 3.8 16.1 - - - +
500A XE4 3.0 36.8 + - - +
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ILE 2.9 17.3 + - - -
300A MET* 2.6 25.7 + - - -
302A ARG* 1.3 75.6 - - - +
304A ASN* 1.3 59.3 + - - +
305A GLN 3.1 0.2 - - - -
306A SER* 2.8 28.8 + - - -
307A PHE 3.2 0.2 + - - -
314A TRP* 3.1 18.5 + - - -
345A GLN* 3.4 5.0 + - - -
500A XE4 3.2 45.9 - - - +
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Residues in contact with ASN 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A MET 4.5 0.2 - - - +
301A LEU 3.0 16.9 + - - +
303A SER* 1.3 81.1 + - - +
305A GLN* 1.3 57.2 + - - +
306A SER 2.9 0.2 + - - -
307A PHE* 2.8 22.5 + - - +
345A GLN* 2.9 48.3 + - - +
348A LEU* 3.6 26.2 - - + +
349A LYS* 3.0 43.8 + - - +
358A HIS* 4.8 7.1 - - - +
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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