Contacts of the helix formed by residues 319 - 342 (chain N) in PDB entry 1KYO
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 LYS 319 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309N ASP* 4.3 6.7 + - - -
311N SER* 2.6 42.2 + - - -
313N VAL* 3.2 23.7 + - + -
315N GLY 3.2 27.8 + - - +
316N ASN* 3.2 8.5 + - - +
317N THR 3.6 0.4 + - - -
318N PHE* 1.3 81.7 - - - +
320N VAL* 1.3 65.0 + - - +
321N LEU 3.5 0.2 - - - -
322N SER* 3.6 17.6 + - - +
323N LYS* 2.9 30.2 + - - +
371N SER* 5.2 1.6 - - - -
374N GLU* 3.2 32.5 + - - +
378N PHE* 4.7 11.4 - - + -
32R PHE* 4.4 3.1 - - - -
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Residues in contact with VAL 320 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319N LYS* 1.3 72.4 - - - +
321N LEU* 1.3 71.0 + - + +
323N LYS* 4.5 0.4 - - + -
324N PHE* 3.2 20.0 + - + +
32R PHE* 3.6 30.1 - - + +
35R LEU* 3.4 48.7 - - + +
36R ALA* 4.0 3.1 - - - +
58S TYR* 3.2 36.6 - - + +
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Residues in contact with LEU 321 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320N VAL* 1.3 85.0 - - + +
322N SER* 1.3 61.0 + - - +
324N PHE* 3.7 4.5 - - - +
325N PHE* 3.1 41.9 + - + +
370N ILE* 3.8 31.9 - - + -
373N ILE* 5.7 9.0 - - + -
374N GLU* 3.2 12.2 + - + +
377N LEU* 4.5 12.8 - - + -
32R PHE* 3.9 24.2 - - + -
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Residues in contact with SER 322 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316N ASN* 3.5 24.6 + - - -
319N LYS* 3.6 17.0 + - - +
320N VAL 3.2 0.6 - - - -
321N LEU* 1.3 74.1 - - - +
323N LYS* 1.3 66.4 + - - +
324N PHE 3.1 1.9 + - - -
325N PHE* 3.1 4.3 + - - +
326N PHE* 2.8 26.5 + - - +
362N TYR* 5.2 1.0 + - - -
370N ILE* 4.0 8.5 - - - +
371N SER* 5.2 2.6 + - - -
374N GLU* 2.7 27.5 + - - -
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Residues in contact with LYS 323 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102N TYR* 3.6 15.3 - - - +
316N ASN* 3.0 27.6 - - + +
317N THR* 3.0 24.2 + - - +
318N PHE* 5.0 0.4 - - - +
319N LYS 2.9 23.6 + - - +
320N VAL* 4.5 3.8 - - - +
322N SER* 1.3 74.9 - - - +
324N PHE* 1.3 63.6 + - - +
326N PHE* 3.4 6.3 + - - +
327N PHE* 2.9 34.6 + - + -
35R LEU 5.4 3.2 + - - -
36R ALA* 5.0 4.4 + - - +
55S GLN* 2.9 42.3 + - - +
58S TYR* 3.9 29.8 + - + -
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Residues in contact with PHE 324 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320N VAL* 3.2 15.5 + - + +
321N LEU* 3.7 6.7 - - - +
322N SER 3.1 0.4 - - - -
323N LYS* 1.3 83.0 - - - +
325N PHE* 1.3 91.9 + + - +
326N PHE 3.0 0.3 + - - -
327N PHE* 3.1 12.0 + - - +
328N ILE* 3.1 40.0 + - + +
57S LEU 5.3 0.7 - - - -
58S TYR* 3.9 20.1 - + + -
61S ILE* 4.0 33.7 - - + -
62S PRO* 4.0 14.4 - - + +
65S ILE* 4.6 7.0 - - + -
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Residues in contact with PHE 325 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321N LEU* 3.1 34.9 + - + +
322N SER* 3.1 5.4 + - - +
324N PHE* 1.3 103.2 - + - +
326N PHE* 1.3 63.9 + - - +
328N ILE* 3.5 18.8 + - + +
329N PHE* 3.1 15.9 + - - +
362N TYR* 3.7 16.4 - - + -
366N ILE* 3.8 37.6 - - + +
370N ILE* 4.0 28.7 - - + -
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Residues in contact with PHE 326 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98N ALA* 4.0 19.1 - - + -
101N LEU* 4.0 15.7 - - + -
102N TYR* 3.5 51.1 - + + -
316N ASN* 3.9 13.9 - - - +
322N SER 2.8 16.4 + - - +
323N LYS* 3.4 5.4 - - - +
325N PHE* 1.3 76.9 - - - +
327N PHE* 1.3 81.3 + + - +
329N PHE* 2.7 28.1 + + - +
330N VAL* 2.9 36.7 + - + +
362N TYR* 3.9 21.5 + + - +
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Residues in contact with PHE 327 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102N TYR* 4.3 14.1 - + - -
323N LYS* 2.9 28.0 - - + -
324N PHE 3.1 4.6 + - - +
326N PHE* 1.3 101.8 - + - +
328N ILE* 1.3 67.0 + - - +
330N VAL* 4.1 10.3 - - + +
331N PHE* 2.9 39.6 + + + -
55S GLN* 5.1 7.6 - - - -
58S TYR* 3.5 31.0 - - + +
59S VAL* 4.0 35.7 - - + -
62S PRO* 3.9 10.8 - - + -
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Residues in contact with ILE 328 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324N PHE* 3.1 46.3 + - + +
325N PHE* 3.5 23.8 - - + +
326N PHE 3.1 0.2 - - - -
327N PHE* 1.3 76.7 - - - +
329N PHE* 1.3 58.3 + - - +
332N ASN* 3.0 28.6 + - - +
358N ILE* 4.8 11.4 - - + -
366N ILE* 6.0 2.9 - - + -
62S PRO* 3.8 23.9 - - + +
65S ILE* 4.4 11.9 - - + -
66S TYR* 3.6 26.3 - - + +
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Residues in contact with PHE 329 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101N LEU* 4.5 17.9 - - + -
325N PHE 3.1 12.0 + - - +
326N PHE* 2.7 16.4 + + - +
328N ILE* 1.3 76.7 - - - +
330N VAL* 1.3 67.5 + - + -
332N ASN* 3.2 7.6 + - - +
333N PHE* 2.9 38.8 + + + +
358N ILE* 5.6 3.6 - - + -
359N TYR* 3.7 43.3 - + - -
362N TYR* 3.5 37.5 - + + -
363N PHE* 3.6 32.8 - + - -
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Residues in contact with VAL 330 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98N ALA* 5.7 4.3 - - + -
326N PHE* 2.9 50.5 + - + +
327N PHE* 3.1 15.7 + - + +
329N PHE* 1.3 82.5 - - + +
331N PHE* 1.3 75.6 + - + +
333N PHE* 3.0 18.3 + - + +
334N VAL* 3.1 23.3 + - + +
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Residues in contact with PHE 331 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327N PHE* 2.9 40.6 + + + +
330N VAL* 1.3 78.5 - - + +
332N ASN* 1.3 55.8 + - - +
334N VAL* 2.9 17.8 + - + +
335N LEU* 2.8 34.8 + - - +
59S VAL* 3.6 39.0 - - + -
62S PRO* 3.9 3.6 - - + -
63S ALA* 3.6 36.1 - - + -
66S TYR* 3.9 27.1 - - + +
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Residues in contact with ASN 332 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328N ILE 3.0 22.2 + - - +
329N PHE* 3.3 8.3 - - - +
331N PHE* 1.3 75.2 - - - +
333N PHE* 1.3 52.9 + - - +
335N LEU* 3.1 4.5 + - - +
336N LEU* 2.8 36.6 + - - +
355N ALA* 3.1 39.7 - - - +
358N ILE* 3.5 23.7 - - + +
359N TYR* 3.6 11.8 + - - +
66S TYR* 2.6 38.1 + - - +
69S TRP* 4.6 0.6 - - - -
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Residues in contact with PHE 333 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94N PHE* 4.4 29.6 - + - -
277N PRO* 3.5 39.2 - - + +
278N PHE* 4.2 22.7 - + - -
281N ILE* 6.1 0.2 - - + -
329N PHE* 2.9 23.3 + + + +
330N VAL* 3.0 16.1 + - + +
332N ASN* 1.3 78.8 - - - +
334N VAL* 1.3 58.2 + - + +
336N LEU* 3.2 11.7 - - + +
337N GLY 3.0 21.8 + - - -
359N TYR* 3.9 34.1 - + + -
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Residues in contact with VAL 334 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330N VAL* 3.1 23.6 - - + +
331N PHE* 2.9 23.5 + - + +
333N PHE* 1.3 79.5 - - + +
335N LEU* 1.3 59.7 + - - +
337N GLY* 3.1 3.7 + - - -
338N GLN* 2.8 28.6 + - + +
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Residues in contact with LEU 335 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331N PHE 2.8 15.9 + - - +
332N ASN 3.3 7.6 - - - +
334N VAL* 1.3 68.9 - - - +
336N LEU* 1.3 62.3 + - - +
338N GLN* 3.0 6.9 + - + +
339N ILE* 2.8 51.8 + - + +
351N MET* 4.3 12.1 - - + +
355N ALA* 4.2 19.5 - - + -
66S TYR* 3.9 23.8 - - + +
69S TRP* 4.5 13.5 - - + -
70S TRP* 3.9 44.6 - - + +
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Residues in contact with LEU 336 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277N PRO* 4.1 18.4 - - + +
280N ALA* 3.2 17.7 - - + +
281N ILE* 3.8 27.1 - - + -
332N ASN* 2.8 14.2 + - - +
333N PHE* 3.2 17.3 - - + +
335N LEU* 1.3 77.7 - - - +
337N GLY* 1.3 63.7 + - - +
339N ILE* 3.2 4.5 + - + +
340N GLY 3.1 17.2 + - - -
352N GLY* 4.0 12.3 - - - +
355N ALA* 3.4 30.5 - - + +
356N THR* 4.0 11.4 - - - +
359N TYR* 4.1 25.6 - - + -
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Residues in contact with GLY 337 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276N LEU* 3.4 23.5 - - - +
277N PRO* 3.6 31.5 - - - +
333N PHE 3.0 11.5 + - - -
334N VAL* 3.1 5.5 + - - -
336N LEU* 1.3 76.3 - - - +
338N GLN* 1.3 58.5 + - - +
340N GLY 3.5 4.4 + - - -
341N ALA* 3.5 6.6 + - - +
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Residues in contact with GLN 338 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334N VAL* 2.8 14.6 + - + +
335N LEU* 3.0 14.3 + - + +
337N GLY* 1.3 74.1 - - - +
339N ILE* 1.3 66.2 + - - +
340N GLY 3.0 1.1 - - - -
341N ALA* 3.1 20.0 + - - +
342N CYS* 2.9 28.3 - - - -
70S TRP* 3.6 43.5 + - + +
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Residues in contact with ILE 339 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280N ALA* 4.6 7.9 - - + +
283N ARG* 3.3 14.9 + - - +
284N SER* 5.5 0.9 - - - +
335N LEU* 2.8 41.5 + - + +
336N LEU* 3.5 8.7 - - - +
338N GLN* 1.3 76.4 - - - +
340N GLY* 1.3 62.7 + - - +
342N CYS* 3.0 19.8 + - - +
348N TYR* 3.6 29.2 - - + +
349N VAL* 5.7 0.4 - - - -
351N MET* 4.1 20.2 - - + -
352N GLY* 4.1 18.8 - - - -
70S TRP* 3.9 24.5 - - + -
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Residues in contact with GLY 340 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270N VAL* 4.5 2.4 - - - +
276N LEU* 3.5 15.0 - - - +
279N TYR* 3.3 29.0 - - - -
280N ALA* 3.9 18.1 - - - +
283N ARG* 3.6 3.8 + - - -
336N LEU 3.1 9.5 + - - -
337N GLY 3.8 4.7 - - - -
338N GLN 3.0 1.4 - - - -
339N ILE* 1.3 78.9 - - - +
341N ALA* 1.3 57.8 + - - +
342N CYS 3.1 6.8 + - - +
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Residues in contact with ALA 341 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270N VAL* 4.2 18.5 - - + +
276N LEU* 3.6 22.1 - - + +
337N GLY 3.5 5.2 + - - +
338N GLN* 3.1 20.6 + - - +
340N GLY* 1.3 73.9 - - - +
342N CYS* 1.3 63.4 + - - +
343N HIS* 5.8 0.5 - - - -
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Residues in contact with CYS 342 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283N ARG* 3.2 20.6 + - - -
338N GLN* 2.9 31.4 - - - -
339N ILE* 3.0 13.9 + - - +
340N GLY 3.5 0.3 - - - +
341N ALA* 1.3 82.1 - - - +
343N HIS* 1.3 68.3 + - - +
348N TYR* 3.8 21.8 - - + -
70S TRP* 3.1 37.2 - - - -
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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) + - + + + + + -
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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