Contacts of the helix formed by residues 340 - 364 (chain C) in PDB entry 1QK1
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 SER 340 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C THR* 3.5 26.2 + - - +
105C ASP* 3.5 28.2 + - - +
284C THR* 4.1 0.4 - - - -
339C LYS* 1.3 76.3 - - - +
341C GLU* 1.3 65.7 + - - +
342C VAL* 3.4 5.0 + - - +
343C GLU* 2.9 39.7 + - - +
344C LEU* 3.0 21.0 + - - +
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Residues in contact with GLU 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C THR* 3.3 19.1 + - - +
105C ASP 2.9 42.1 + - - +
106C LEU* 3.3 25.5 - - + +
130C ARG* 4.6 3.3 + - - -
245C PHE* 4.1 7.9 - - + -
248C PHE* 5.9 0.2 - - - -
274C TYR* 4.5 7.8 - - - -
284C THR* 3.5 34.8 - - + +
286C LEU* 3.8 24.9 - - + +
340C SER* 1.3 72.0 - - - +
342C VAL* 1.3 60.6 + - - +
344C LEU* 3.3 6.5 + - - +
345C VAL* 3.0 28.9 + - - +
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Residues in contact with VAL 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ASP* 3.2 34.2 + - - +
107C ASP 3.5 25.6 - - - +
110C LYS* 4.0 26.5 - - + +
111C ILE* 3.8 13.3 - - + +
245C PHE* 4.2 15.3 - - + -
340C SER* 3.1 7.7 + - - +
341C GLU* 1.3 77.7 - - - +
343C GLU* 1.3 65.8 + - + +
346C GLN* 3.1 24.5 + - + +
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Residues in contact with GLU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C THR* 5.9 2.1 - - - +
338C GLY 4.7 0.2 - - - +
339C LYS* 3.5 14.4 - - + -
340C SER* 2.9 44.5 + - - +
342C VAL* 1.3 81.7 - - + +
344C LEU* 1.3 56.7 + - - +
346C GLN* 3.6 5.9 + - - +
347C LEU* 3.0 30.1 + - - +
376C HIS* 4.7 7.6 - - - -
377C THR* 3.3 29.2 - - + +
378C LYS 5.7 0.5 + - - -
379C HIS* 5.5 3.6 - - - +
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Residues in contact with LEU 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C THR* 3.4 27.1 - - + +
286C LEU* 3.9 15.9 - - + -
333C ASN* 4.1 15.7 - - + +
335C ASP* 3.7 38.4 - - + +
336C ARG* 4.2 4.0 - - - +
339C LYS* 3.8 33.2 - - + +
340C SER 3.0 20.2 + - - +
341C GLU* 3.8 4.0 - - - +
343C GLU* 1.3 74.8 - - - +
345C VAL* 1.3 65.7 + - - +
347C LEU* 3.3 11.8 + - + +
348C VAL* 3.0 28.0 + - - +
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Residues in contact with VAL 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ILE* 4.2 11.9 - - + -
126C VAL* 4.9 2.5 - - + -
241C MET* 4.2 17.3 - - + -
245C PHE* 3.6 39.9 - - + -
286C LEU* 4.4 7.0 - - + -
288C ALA* 4.2 19.1 - - + -
341C GLU 3.0 20.5 + - - +
342C VAL 4.1 2.9 - - - +
344C LEU* 1.3 72.6 - - - +
346C GLN* 1.3 61.5 + - - +
348C VAL* 3.0 8.3 + - + +
349C ILE* 2.9 44.8 + - + +
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Residues in contact with GLN 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LYS 4.3 2.8 - - - +
111C ILE* 3.7 12.8 - - + +
112C ARG* 3.2 48.8 + - - +
113C SER* 5.4 0.8 - - - -
342C VAL* 3.1 21.2 + - + +
343C GLU* 3.7 6.5 - - - +
345C VAL* 1.3 76.8 - - - +
347C LEU* 1.3 58.5 + - - +
349C ILE* 3.2 9.0 + - - +
350C ASP* 2.9 65.9 + - - +
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Residues in contact with LEU 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C LEU 3.6 20.7 - - - +
311C ARG* 3.9 23.3 - - + +
312C LEU* 4.2 9.3 - - + +
333C ASN* 4.6 6.5 - - + -
335C ASP* 4.5 3.4 - - - +
339C LYS* 3.9 30.5 - - + +
343C GLU 3.0 19.3 + - - +
344C LEU* 3.5 11.4 - - + +
346C GLN* 1.3 78.4 - - - +
348C VAL* 1.3 59.9 + - + +
350C ASP* 3.9 5.9 - - - +
351C GLY* 3.0 24.8 + - - -
374C VAL* 4.6 12.8 - - + -
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Residues in contact with VAL 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C PHE* 4.9 1.6 - - + -
241C MET* 4.4 20.0 - - + -
288C ALA* 3.5 32.8 - - + +
289C GLY* 4.7 4.0 - - - -
312C LEU* 4.2 11.4 - - + +
331C ILE 5.2 1.6 - - - +
333C ASN* 3.6 28.3 - - + +
344C LEU 3.0 17.5 + - - +
345C VAL* 3.0 9.2 + - - +
347C LEU* 1.3 76.0 - - - +
349C ILE* 1.3 62.5 + - - +
352C VAL* 2.8 45.2 + - + +
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Residues in contact with ILE 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ILE* 3.8 23.1 - - + -
112C ARG 4.1 4.0 - - - +
113C SER* 4.1 2.7 - - - +
114C GLY* 3.7 35.4 - - - +
116C PHE* 3.7 23.1 - - + -
241C MET* 4.0 12.8 - - + -
242C LYS 5.2 0.4 - - - +
345C VAL* 2.9 28.7 + - + +
346C GLN* 3.5 21.5 - - - +
348C VAL* 1.3 78.2 - - + +
350C ASP* 1.3 64.0 + - - +
353C ASN* 3.1 39.1 + - - +
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Residues in contact with ASP 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C SER* 5.9 0.7 - - - -
310C LEU* 5.7 0.9 - - - -
346C GLN* 2.9 45.1 + - - +
347C LEU* 4.0 6.4 - - - +
349C ILE* 1.3 79.8 - - - +
351C GLY* 1.3 62.9 + - - +
353C ASN* 3.4 7.2 + - - +
354C TYR* 3.1 23.0 + - - +
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Residues in contact with GLY 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C LEU* 3.7 20.1 - - - +
312C LEU* 4.0 18.8 - - - -
347C LEU 3.0 18.3 + - - -
348C VAL 3.8 0.7 - - - -
350C ASP* 1.3 78.5 - - - +
352C VAL* 1.3 60.8 + - - +
354C TYR* 3.3 3.7 + - - +
355C LEU* 3.1 27.5 + - - +
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Residues in contact with VAL 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C PHE* 3.7 31.4 - - + -
121C VAL* 4.3 4.7 - - + -
290C VAL* 3.9 21.8 - - + -
292C ILE* 4.0 21.8 - - + -
312C LEU* 4.9 1.3 - - + -
331C ILE* 4.6 17.5 - - + -
348C VAL* 2.8 36.6 + - + +
351C GLY* 1.3 70.3 - - - +
353C ASN* 1.3 65.9 + - - +
355C LEU* 3.1 9.2 + - + +
356C ILE* 2.9 27.0 + - + +
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Residues in contact with ASN 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C SER* 3.8 21.4 + - - -
115C TYR 5.0 2.5 + - - +
116C PHE* 3.5 20.9 - - - -
117C ASP 5.5 0.3 + - - -
349C ILE* 3.1 30.6 + - - +
350C ASP* 3.8 8.0 + - - +
352C VAL* 1.3 76.6 - - - +
354C TYR* 1.3 58.5 + - - +
356C ILE* 3.2 13.2 + - - +
357C ASP* 2.9 30.5 + - - +
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Residues in contact with TYR 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ILE* 4.3 3.8 - - + -
310C LEU* 4.1 23.1 - - + -
350C ASP 3.1 13.2 + - - +
351C GLY* 3.5 9.6 - - - +
352C VAL 3.2 0.2 - - - -
353C ASN* 1.3 75.4 - - - +
355C LEU* 1.3 68.9 + - + +
357C ASP* 3.6 9.6 - - + +
358C CYS* 2.9 42.9 + - - -
369C ARG* 2.6 42.3 + - - +
371C PRO* 3.8 35.4 - - + +
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Residues in contact with LEU 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C ILE* 4.8 4.0 - - + -
294C LEU* 4.2 26.7 - - + -
297C LEU* 3.7 21.3 - - + +
303C PHE* 4.8 0.9 - - + -
306C ILE* 4.0 16.6 - - + -
307C LEU* 4.2 22.9 - - + -
310C LEU* 3.5 21.3 - - + -
312C LEU* 4.2 11.4 - - + -
331C ILE* 4.3 13.5 - - + -
351C GLY 3.1 20.3 + - - +
352C VAL* 3.4 13.9 - - + +
354C TYR* 1.3 76.9 - - + +
356C ILE* 1.3 59.3 + - - +
358C CYS* 3.0 5.2 + - - +
359C GLU* 2.9 26.5 + - - +
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Residues in contact with ILE 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C PHE* 4.4 1.1 - - + -
117C ASP* 4.1 26.7 - - + +
120C TYR* 4.2 22.2 - - + -
121C VAL* 4.3 11.9 - - + -
292C ILE* 4.0 14.6 - - + -
294C LEU* 4.8 2.0 - - + -
352C VAL* 2.9 29.9 + - + +
353C ASN* 3.4 19.5 - - - +
355C LEU* 1.3 77.4 - - - +
357C ASP* 1.3 61.4 + - - +
359C GLU* 3.3 7.4 + - - +
360C ARG* 3.1 51.6 + - - +
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Residues in contact with ASP 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C ASN 2.9 16.7 + - - +
354C TYR* 3.6 13.7 - - + +
355C LEU 3.2 0.2 - - - -
356C ILE* 1.3 77.5 - - - +
358C CYS* 1.3 66.2 + - - +
360C ARG* 3.5 20.2 + - - +
361C ARG* 3.1 39.9 + - - +
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Residues in contact with CYS 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C LEU* 3.9 20.0 - - + -
306C ILE* 4.8 9.2 - - - -
354C TYR* 2.9 52.2 + - - +
355C LEU* 3.0 8.0 + - - +
357C ASP* 1.3 79.2 - - - +
359C GLU* 1.3 63.5 + - - +
361C ARG* 3.1 3.1 + - - -
362C LEU* 3.0 23.7 + - - +
368C ILE* 3.4 36.8 - - + +
369C ARG 4.8 1.6 - - - -
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Residues in contact with GLU 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C TYR* 3.5 29.6 - - + -
294C LEU* 3.8 17.7 - - + -
295C PRO* 3.2 17.5 - - - +
296C LEU* 2.8 34.3 + - - +
297C LEU* 2.7 33.7 + - - +
355C LEU 2.9 12.4 + - - +
356C ILE* 3.6 9.2 - - - +
357C ASP 3.3 0.2 - - - -
358C CYS* 1.3 76.7 - - - +
360C ARG* 1.3 57.2 + - - +
362C LEU* 3.1 7.3 + - - +
363C GLU* 2.9 36.1 + - - +
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Residues in contact with ARG 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ASP* 3.1 29.3 + - - +
120C TYR* 3.8 21.3 - - + +
356C ILE* 3.1 30.0 + - - +
357C ASP* 3.8 21.6 + - - +
359C GLU* 1.3 73.4 - - - +
361C ARG* 1.3 66.6 + - - +
363C GLU* 3.2 21.0 + - - +
364C ARG* 3.3 33.3 + - - +
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Residues in contact with ARG 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C ASP* 3.1 30.9 + - - +
358C CYS* 3.1 2.2 + - - +
360C ARG* 1.3 75.8 - - + +
362C LEU* 1.3 62.6 + - - +
364C ARG* 3.3 30.6 + - - +
366C GLN* 2.8 60.2 + - + +
367C ASP 2.8 24.4 + - - +
368C ILE* 3.4 29.8 - - + +
369C ARG* 6.1 2.5 - - - +
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Residues in contact with LEU 362 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C LEU* 3.6 23.0 - - + +
297C LEU* 3.7 42.6 - - + +
300C ASP* 5.0 12.3 - - + +
302C ARG* 5.1 2.7 - - - +
358C CYS 3.0 17.0 + - - +
359C GLU* 3.5 6.5 - - - +
361C ARG* 1.3 74.0 - - - +
363C GLU* 1.3 67.4 + - - +
365C GLY* 3.2 12.1 + - - -
366C GLN 3.9 16.2 - - - +
367C ASP* 5.1 1.1 - - - +
368C ILE* 4.0 23.3 - - + +
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Residues in contact with GLU 363 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ARG* 3.8 19.6 + - - -
120C TYR* 2.8 37.3 + - - -
295C PRO* 5.9 1.0 - - - +
296C LEU* 3.4 18.7 - - + +
359C GLU* 2.9 27.4 + - + +
360C ARG* 3.2 16.5 + - - +
362C LEU* 1.3 77.8 - - - +
364C ARG* 1.3 57.0 + - + +
365C GLY 3.6 1.7 + - - -
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Residues in contact with ARG 364 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C ARG* 3.4 38.1 + - - +
361C ARG* 3.7 25.3 - - - +
362C LEU 3.2 0.6 - - - -
363C GLU* 1.3 79.8 - - + +
365C GLY* 1.3 56.4 + - - +
366C GLN* 2.4 45.2 + - + +
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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