Contacts of the helix formed by residues 314 - 337 (chain A) in PDB entry 1HK2
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 ASP 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A SER* 3.0 11.8 + - - +
313A LYS* 1.3 85.5 + - - +
315A VAL* 1.3 54.4 + - - +
316A CYS 3.4 2.7 - - - -
317A LYS* 3.3 38.7 + - + +
318A ASN* 2.7 57.5 + - - +
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Residues in contact with VAL 315 (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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308A ASP 4.1 9.2 - - - +
309A PHE 4.0 22.7 - - - +
310A VAL 4.2 0.9 - - - +
312A SER* 3.3 17.4 + - - +
313A LYS 3.2 2.2 - - - -
314A ASP* 1.3 76.7 - - - +
316A CYS* 1.3 58.3 + - - +
318A ASN* 4.4 0.2 - - - +
319A TYR* 3.1 25.5 + - - +
326A PHE* 3.8 14.4 - - + -
353A TYR* 3.6 20.6 - - - +
357A LEU* 3.7 25.8 - - + -
370A TYR* 3.2 30.5 - - + +
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Residues in contact with CYS 316 (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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313A LYS 4.6 3.5 + - - +
314A ASP 3.4 0.2 - - - -
315A VAL* 1.3 77.7 - - - +
317A LYS* 1.3 67.8 + - - +
319A TYR* 3.5 2.4 - - - +
320A ALA* 3.0 24.8 + - - +
361A CYS* 2.0 61.4 - - + +
366A PRO* 3.7 12.6 - - + -
370A TYR* 3.7 24.3 + - - -
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Residues in contact with LYS 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LYS 5.1 1.3 + - - +
314A ASP* 3.2 40.0 + - + +
316A CYS* 1.3 78.4 - - - +
318A ASN* 1.3 62.2 + - - +
320A ALA* 3.4 2.7 + - - +
321A GLU* 2.8 55.8 + - + +
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Residues in contact with ASN 318 (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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308A ASP 5.5 2.0 + - - -
312A SER* 5.2 1.0 + - - -
314A ASP* 2.7 42.2 + - - +
315A VAL* 4.0 0.4 - - - +
317A LYS* 1.3 82.6 - - - +
319A TYR* 1.3 61.2 + - - +
321A GLU* 4.2 5.5 - - - +
322A ALA* 2.8 35.1 + - + +
326A PHE* 3.4 38.2 - - + +
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Residues in contact with TYR 319 (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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315A VAL 3.1 18.1 + - - +
316A CYS* 3.5 8.3 - - - +
318A ASN* 1.3 76.7 - - - +
320A ALA* 1.3 61.7 + - + +
323A LYS* 2.6 61.1 + - + +
326A PHE* 4.2 4.6 - - + -
327A LEU* 4.3 24.0 - - + -
354A GLU* 3.8 23.1 + - + +
357A LEU* 4.1 24.2 - - + -
358A GLU* 2.9 42.1 + - - +
361A CYS* 4.3 17.9 - - + -
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Residues in contact with ALA 320 (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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316A CYS 3.0 15.5 + - - +
317A LYS* 3.8 3.4 - - - +
319A TYR* 1.3 82.4 - - + +
321A GLU* 1.3 67.5 + - + +
322A ALA 3.0 1.7 + - - -
323A LYS* 4.0 4.2 + - - +
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Residues in contact with GLU 321 (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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317A LYS* 2.8 47.6 + - + +
318A ASN* 4.1 5.2 - - - +
320A ALA* 1.3 76.8 - - + +
322A ALA* 1.3 61.3 + - + +
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Residues in contact with ALA 322 (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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318A ASN* 2.8 16.8 + - + +
320A ALA 4.0 0.7 - - - -
321A GLU* 1.3 79.9 - - + +
323A LYS* 1.3 67.5 + - - +
324A ASP 3.2 2.9 - - - -
325A VAL* 2.9 23.0 + - + -
326A PHE* 2.8 18.8 + - + +
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Residues in contact with LYS 323 (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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209A ARG* 5.0 6.1 - - - +
319A TYR* 2.6 55.0 + - + +
320A ALA 4.0 3.4 + - - +
322A ALA* 1.3 70.0 - - - +
324A ASP* 1.3 75.4 + - + +
326A PHE* 4.3 1.1 - - - -
327A LEU* 2.7 39.8 + - + +
354A GLU* 5.9 1.3 - - - +
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Residues in contact with ASP 324 (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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209A ARG* 2.6 46.3 + - - -
322A ALA 3.0 1.8 + - - -
323A LYS* 1.3 84.1 - - + +
325A VAL* 1.3 64.5 + - + +
327A LEU* 4.1 3.0 - - - +
328A GLY* 3.1 18.9 + - - -
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Residues in contact with VAL 325 (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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228A PHE* 4.4 14.1 - - + -
322A ALA* 2.9 23.2 + - + +
324A ASP* 1.3 72.9 - - + +
326A PHE* 1.3 63.7 + - - +
328A GLY* 2.9 3.4 + - - -
329A MET* 2.8 45.9 + - + +
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Residues in contact with PHE 326 (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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308A ASP* 4.2 11.9 - - + -
309A PHE* 3.5 30.2 - + - -
315A VAL* 3.8 23.3 - - + -
318A ASN* 3.4 42.4 - - + +
319A TYR* 4.2 12.3 - - - -
322A ALA* 2.8 16.4 + - + +
323A LYS* 3.8 2.9 - - - +
325A VAL* 1.3 78.7 - - - +
327A LEU* 1.3 67.9 + - + +
329A MET* 3.1 14.4 - - + +
330A PHE* 3.0 24.9 + - - +
353A TYR* 3.7 26.7 - + - -
357A LEU* 4.0 6.1 - - + -
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Residues in contact with LEU 327 (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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319A TYR* 4.3 16.8 - - + -
323A LYS* 2.7 28.5 + - + +
324A ASP* 4.4 4.3 - - - +
326A PHE* 1.3 84.8 - - + +
328A GLY* 1.3 64.6 + - - +
330A PHE* 3.2 6.6 + - + +
331A LEU* 3.1 21.5 + - - +
350A ALA* 5.3 5.7 - - + +
353A TYR* 4.0 27.4 - - + -
354A GLU* 3.5 45.5 - - + +
357A LEU* 4.5 2.0 - - + -
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Residues in contact with GLY 328 (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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216A VAL* 4.2 5.9 - - - +
228A PHE* 3.5 19.0 - - - -
324A ASP 3.1 14.1 + - - -
325A VAL 2.9 7.5 + - - -
327A LEU* 1.3 75.4 - - - +
329A MET* 1.3 58.1 + - - +
331A LEU* 3.4 7.7 + - - +
332A TYR* 2.9 30.0 + - - +
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Residues in contact with MET 329 (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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228A PHE* 3.7 34.1 - - + -
309A PHE* 4.1 14.4 - - + -
325A VAL* 2.8 28.0 + - + +
326A PHE* 3.1 15.5 - - + +
328A GLY* 1.3 74.9 - - - +
330A PHE* 1.3 59.8 + - - +
332A TYR* 3.5 9.1 - - - +
333A GLU* 2.8 42.0 + - + +
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Residues in contact with PHE 330 (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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305A LEU* 5.2 1.8 - - + -
309A PHE* 3.6 42.8 - + + -
326A PHE 3.0 12.9 + - - +
327A LEU* 3.2 13.7 + - + +
329A MET* 1.3 75.4 - - - +
331A LEU* 1.3 70.0 + - + +
333A GLU* 3.8 1.2 - - - +
334A TYR* 2.9 62.7 + + + +
349A LEU* 4.4 2.7 - - + -
350A ALA* 4.0 25.6 - - + -
353A TYR* 3.6 52.3 - + + -
374A PHE* 5.0 6.5 - + - -
377A PHE* 4.0 9.2 - + - -
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Residues in contact with LEU 331 (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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213A ALA* 2.9 46.9 - - + +
216A VAL* 3.9 13.0 - - + -
217A ALA* 3.9 13.5 - - + +
327A LEU 3.1 9.7 + - - +
328A GLY* 3.6 10.5 - - - +
329A MET 3.3 0.2 - - - -
330A PHE* 1.3 81.9 - - + +
332A TYR* 1.3 66.8 + - - +
334A TYR* 3.6 2.8 - - + +
335A ALA* 2.8 28.4 + - - +
346A LEU* 4.0 18.8 - - + +
347A LEU* 4.1 11.9 - - + -
350A ALA* 3.6 28.9 - - + -
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Residues in contact with TYR 332 (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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216A VAL* 4.2 3.7 - - + +
220A SER* 3.2 33.9 - - - +
223A PHE 5.0 2.7 - - - -
226A ALA 2.4 30.1 + - - -
227A GLU* 3.7 2.8 - - - -
228A PHE* 3.4 54.3 + + + -
231A VAL* 4.3 10.5 - - + -
328A GLY 2.9 18.9 + - - +
329A MET* 3.5 7.9 - - - +
331A LEU* 1.3 75.7 - - - +
333A GLU* 1.3 90.3 + - + +
336A ARG* 3.1 57.6 + - + +
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Residues in contact with GLU 333 (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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303A PRO* 6.5 0.2 - - - -
305A LEU* 3.3 19.5 - - + -
309A PHE* 4.0 17.5 - - + -
329A MET* 2.8 31.8 + - + +
330A PHE 3.8 1.8 - - - +
332A TYR* 1.3 94.3 - - + +
334A TYR* 1.3 64.8 + - - +
336A ARG* 3.1 36.1 + - - +
337A ARG* 2.8 44.1 + - - +
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Residues in contact with TYR 334 (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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305A LEU* 3.8 23.1 - - + +
330A PHE* 2.9 48.4 + + + +
331A LEU* 3.7 4.0 - - + +
333A GLU* 1.3 72.9 - - - +
335A ALA* 1.3 64.9 - - - +
337A ARG* 3.2 15.2 + - - +
338A HIS* 3.2 50.1 + + - +
341A TYR* 3.9 9.4 + + - -
346A LEU* 3.5 20.4 - - + -
349A LEU* 3.9 22.7 - - + +
374A PHE* 4.2 17.8 - + - -
377A PHE* 3.6 35.5 - + - +
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Residues in contact with ALA 335 (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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217A ALA* 3.6 24.2 - - + +
220A SER* 3.6 18.8 - - - -
221A GLN* 3.5 11.5 - - + +
331A LEU* 2.8 20.9 + - + +
334A TYR* 1.3 72.6 - - - +
336A ARG* 1.3 64.1 + - - +
338A HIS 2.9 20.8 + - - -
339A PRO 4.0 0.2 - - - -
346A LEU* 3.7 25.0 - - + +
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Residues in contact with ARG 336 (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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220A SER* 3.1 25.0 + - - +
221A GLN* 4.6 0.6 - - - +
224A PRO* 2.5 41.9 + - + +
225A LYS 4.4 4.8 + - - -
226A ALA 4.2 1.6 + - - -
298A MET* 3.6 20.2 - - - +
299A PRO* 4.4 7.5 - - - +
302A LEU* 3.9 32.7 - - + +
332A TYR* 3.1 46.2 + - + +
333A GLU* 3.1 46.0 + - - +
335A ALA* 1.3 78.1 - - - +
337A ARG* 1.3 61.9 + - + +
338A HIS 3.6 0.3 + - - -
339A PRO* 4.1 5.5 - - - +
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Residues in contact with ARG 337 (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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298A MET* 3.5 24.6 - - - +
302A LEU* 3.7 33.4 + - + +
303A PRO* 2.4 38.9 + - - +
304A SER* 4.1 1.4 - - - +
305A LEU* 3.3 37.3 - - + +
333A GLU* 2.8 46.7 + - - +
334A TYR 3.4 6.3 - - - +
335A ALA 3.1 0.4 - - - -
336A ARG* 1.3 85.9 - - + +
338A HIS* 1.3 73.2 + - + +
339A PRO* 3.5 6.6 - - - +
340A ASP* 4.4 0.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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