Contacts of the helix formed by residues 319 - 342 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309C ASP* 4.5 4.9 + - - -
311C SER* 3.2 37.5 + - - -
313C VAL* 3.6 19.1 - - + -
315C GLY 2.8 34.1 - - - +
316C ASN* 3.1 9.1 + - - +
318C PHE* 1.3 79.8 - - - +
320C VAL* 1.3 62.2 + - - +
322C SER* 3.4 21.0 + - - +
323C LYS* 3.2 30.0 + - - +
371C SER* 4.9 4.8 - - - +
374C GLU* 3.3 31.3 + - + +
378C PHE* 4.5 12.8 - - + -
32G PHE* 4.4 2.7 - - - -
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Residues in contact with VAL 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C LYS* 1.3 68.9 - - - +
321C LEU* 1.3 77.0 + - + +
322C SER 3.1 2.0 + - - -
323C LYS* 3.2 15.0 + - - +
324C PHE* 3.2 11.1 + - + +
374C GLU* 3.4 3.4 + - - -
32G PHE* 3.7 27.9 - - + +
35G LEU* 3.9 42.2 - - + +
36G ALA* 4.2 4.5 - - - +
58H TYR* 3.3 37.1 - - + +
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Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C VAL* 1.3 91.3 - - + +
322C SER* 1.3 62.4 + - - +
324C PHE* 3.5 5.9 + - - +
325C PHE* 3.0 37.0 + - + -
370C ILE* 3.6 28.7 - - + -
373C ILE* 4.2 25.6 - - + -
374C GLU* 3.2 18.1 + - + +
377C LEU* 4.5 9.2 - - + -
32G PHE* 4.3 7.2 - - + -
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Residues in contact with SER 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C ASN* 3.3 22.8 + - - -
319C LYS* 3.4 23.8 + - - +
320C VAL 3.1 0.4 - - - -
321C LEU* 1.3 78.1 - - - +
323C LYS* 1.3 53.4 + - - +
325C PHE* 3.2 3.2 + - - +
326C PHE* 2.7 38.0 + - - +
362C TYR* 4.9 1.7 + - - -
370C ILE* 4.1 8.4 - - - +
371C SER* 5.5 0.9 + - - -
374C GLU* 2.6 28.5 + - - -
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Residues in contact with LYS 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C TYR* 3.3 31.6 - - + +
316C ASN* 3.3 13.4 - - + +
317C THR* 3.1 26.6 + - - +
318C PHE* 5.2 0.8 - - - +
319C LYS 3.2 15.1 + - - +
320C VAL* 3.2 7.9 + - - +
322C SER* 1.3 77.8 - - - +
324C PHE* 1.3 57.6 + - - +
326C PHE* 3.3 6.5 + - - +
327C PHE* 2.9 39.9 + - + -
35G LEU 5.6 3.2 + - - -
36G ALA 5.0 4.4 + - - -
55H GLN* 2.7 39.9 + - - +
58H TYR* 3.8 28.5 + - + -
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Residues in contact with PHE 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C VAL* 3.2 9.4 + - + +
321C LEU* 3.6 9.6 - - - +
322C SER 3.2 0.4 - - - -
323C LYS* 1.3 78.1 - - - +
325C PHE* 1.3 86.4 + + - +
327C PHE* 3.0 7.8 + - - +
328C ILE* 3.0 49.5 + - + +
57H LEU 5.2 0.2 - - - -
58H TYR* 3.9 22.2 - + + -
61H ILE* 3.6 37.0 - - + -
62H PRO* 3.9 16.1 - - + +
65H ILE* 4.5 7.0 - - + -
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Residues in contact with PHE 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C LEU* 3.0 34.4 + - + +
322C SER* 3.9 3.4 - - - +
324C PHE* 1.3 95.8 - + - +
326C PHE* 1.3 66.1 + - - +
328C ILE* 3.1 18.8 + - + +
329C PHE 3.0 18.0 + - - -
362C TYR* 3.5 12.9 - - + -
366C ILE* 3.8 45.3 - - + -
370C ILE* 4.1 28.7 - - + -
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Residues in contact with PHE 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ALA* 4.1 14.4 - - + -
101C LEU* 4.0 18.4 - - + -
102C TYR* 3.7 46.7 - + + -
316C ASN* 4.0 17.0 - - - +
322C SER 2.7 21.8 + - - +
323C LYS* 3.3 4.3 - - - +
325C PHE* 1.3 71.6 - - - +
327C PHE* 1.3 92.1 + + - +
329C PHE* 3.0 9.2 + + - +
330C VAL* 3.0 48.4 + - + +
362C TYR* 3.6 24.1 - + - +
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Residues in contact with PHE 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C TYR* 4.5 13.5 - + - -
323C LYS* 2.9 30.3 + - + -
324C PHE 3.5 4.9 - - - +
326C PHE* 1.3 99.9 - + - +
328C ILE* 1.3 63.2 + - - +
329C PHE 3.1 1.6 - - - -
330C VAL* 3.9 10.5 - - + +
331C PHE* 3.1 51.2 + + - +
55H GLN* 5.6 4.7 - - - -
58H TYR* 3.2 32.3 - - + +
59H VAL* 3.8 28.0 - - + -
62H PRO* 3.8 7.8 - - + +
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Residues in contact with ILE 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C PHE* 3.0 44.8 + - + +
325C PHE* 3.3 26.0 - - + +
327C PHE* 1.3 77.1 - - - +
329C PHE* 1.3 59.5 + - - +
332C ASN* 3.0 29.3 + - - +
358C ILE* 4.4 15.0 - - + -
362C TYR* 6.2 0.7 - - + -
366C ILE* 5.5 4.3 - - + -
62H PRO* 4.0 22.0 - - + -
65H ILE* 4.5 11.0 - - + -
66H TYR* 3.7 28.1 - - + +
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Residues in contact with PHE 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C LEU* 4.0 24.0 - - + -
302C LEU* 5.9 0.4 - - + -
325C PHE 3.0 11.1 + - - +
326C PHE* 3.0 12.8 + + - +
328C ILE* 1.3 77.1 - - - +
330C VAL* 1.3 76.9 + - + +
332C ASN* 3.3 7.6 + - - +
333C PHE* 3.0 29.2 + + + +
358C ILE* 5.5 2.2 - - + -
359C TYR* 3.7 37.7 - + - -
362C TYR* 3.5 40.8 - + + -
363C PHE* 3.6 37.2 - + - -
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Residues in contact with VAL 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ALA* 5.5 7.2 - - + -
326C PHE* 3.0 48.1 + - + +
327C PHE* 4.1 12.8 - - + +
328C ILE 3.5 0.2 - - - -
329C PHE* 1.3 83.3 - - + +
331C PHE* 1.3 74.5 + - + +
333C PHE* 3.0 22.8 + - + +
334C VAL* 3.1 15.4 + - + +
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Residues in contact with PHE 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C PHE* 3.1 44.7 + + - +
330C VAL* 1.3 81.6 - - + +
332C ASN* 1.3 55.6 + - - +
334C VAL* 2.8 20.3 + - + +
335C LEU* 2.7 36.2 + - - +
59H VAL* 3.9 26.9 - - + -
62H PRO* 4.1 1.8 - - + -
63H ALA* 3.8 35.2 - - + -
66H TYR* 4.0 25.5 - - + +
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Residues in contact with ASN 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C ILE 3.0 22.4 + - - +
329C PHE* 3.4 6.5 - - - +
330C VAL 3.3 0.2 - - - -
331C PHE* 1.3 76.8 - - - +
333C PHE* 1.3 57.1 + - - +
335C LEU* 3.7 1.3 - - - +
336C LEU* 2.9 30.5 + - - +
355C ALA* 3.1 47.7 + - - +
358C ILE* 3.4 19.7 - - + +
359C TYR* 3.4 13.5 + - - +
66H TYR* 3.0 35.2 + - - +
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Residues in contact with PHE 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C PHE* 4.1 39.0 - + + -
277C PRO* 3.5 37.3 - - + +
278C PHE* 4.3 21.3 - + - -
281C ILE* 6.5 0.2 - - + -
329C PHE* 3.0 20.4 + + + +
330C VAL* 3.0 16.8 + - + +
332C ASN* 1.3 77.4 + - - +
334C VAL* 1.3 65.9 + - + +
336C LEU* 3.1 11.4 + - + +
337C GLY 3.1 16.5 + - - -
359C TYR* 4.0 28.0 - + + -
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Residues in contact with VAL 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C PRO* 5.9 0.4 - - - -
330C VAL* 3.1 19.8 + - + +
331C PHE* 2.8 22.9 + - + +
333C PHE* 1.3 83.3 - - + +
335C LEU* 1.3 56.8 + - - +
337C GLY* 3.0 3.6 + - - +
338C GLN* 2.8 29.2 + - + +
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Residues in contact with LEU 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C PHE 2.7 17.8 + - - +
332C ASN 3.8 2.7 - - - +
334C VAL* 1.3 74.6 - - - +
336C LEU* 1.3 57.6 + - - +
338C GLN* 3.3 7.5 + - + -
339C ILE* 2.9 56.5 + - + +
351C MET* 4.2 11.2 - - + +
355C ALA* 3.8 27.4 - - + -
66H TYR* 3.8 26.2 - - + +
69H TRP* 4.4 17.3 - - + -
70H TRP* 3.9 29.6 - - + -
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Residues in contact with LEU 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C PRO* 3.9 20.4 - - + +
280C ALA* 3.0 32.9 - - + +
281C ILE* 4.0 24.0 - - + -
332C ASN* 2.9 15.3 + - - +
333C PHE* 3.1 15.9 - - + +
335C LEU* 1.3 78.7 - - - +
337C GLY* 1.3 58.7 + - - +
339C ILE* 3.2 4.9 + - + +
340C GLY 3.1 7.1 + - - -
352C GLY* 3.9 17.0 - - - +
355C ALA* 3.4 36.8 - - + +
356C THR* 4.0 7.6 - - - +
359C TYR* 4.3 18.2 - - + -
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Residues in contact with GLY 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C LEU* 3.8 16.6 - - - +
277C PRO* 3.7 29.8 - - - +
333C PHE 3.1 6.8 + - - -
334C VAL* 3.0 6.9 + - - -
336C LEU* 1.3 74.3 - - - +
338C GLN* 1.3 65.7 + - - +
340C GLY 3.3 8.1 + - - -
341C ALA* 3.3 9.7 + - - +
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Residues in contact with GLN 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334C VAL* 2.8 16.8 + - + +
335C LEU* 3.3 15.5 + - + +
337C GLY* 1.3 77.2 - - - +
339C ILE* 1.3 57.6 + - - +
341C ALA* 3.2 21.7 + - - +
342C CYS* 2.9 24.1 - - - -
70H TRP* 3.5 49.9 + - + +
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Residues in contact with ILE 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C ALA* 4.5 7.2 - - + +
283C ARG* 3.2 13.8 + - - +
284C SER* 5.5 1.6 - - - +
335C LEU* 2.9 51.6 + - + +
336C LEU* 3.3 10.3 - - - +
337C GLY 3.1 0.2 - - - -
338C GLN* 1.3 72.1 - - - +
340C GLY* 1.3 66.3 + - - +
341C ALA 3.0 1.6 - - - -
342C CYS* 3.0 19.2 + - - +
343C HIS 5.0 0.3 - - - +
348C TYR* 3.9 24.5 - - + +
349C VAL* 6.0 0.2 - - - -
351C MET* 4.0 25.8 - - + -
352C GLY* 4.0 17.5 - - - -
70H TRP* 4.0 15.7 - - + -
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Residues in contact with GLY 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C VAL* 4.8 2.6 - - - +
276C LEU* 3.7 12.5 - - - +
279C TYR* 3.3 32.2 - - - -
280C ALA* 3.7 18.1 - - - +
283C ARG* 3.4 12.5 + - - -
336C LEU 3.1 8.5 + - - -
337C GLY 3.3 4.4 + - - -
339C ILE* 1.3 79.6 - - - +
341C ALA* 1.3 58.7 + - - +
342C CYS 3.7 0.7 - - - +
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Residues in contact with ALA 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C VAL* 4.8 16.2 - - + +
276C LEU* 4.0 17.5 - - + +
337C GLY 3.3 9.3 + - - +
338C GLN* 3.2 24.0 + - - +
339C ILE 3.0 0.4 - - - -
340C GLY* 1.3 76.8 - - - +
342C CYS* 1.3 60.7 + - - +
343C HIS* 5.4 1.7 - - - -
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Residues in contact with CYS 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C ARG* 2.6 32.8 + - - -
338C GLN* 2.9 26.0 - - - -
339C ILE* 3.0 10.9 + - - +
340C GLY 3.7 0.9 - - - +
341C ALA* 1.3 78.6 - - - +
343C HIS* 1.3 62.7 + - + +
348C TYR* 3.7 25.8 - - + -
70H TRP* 3.2 32.8 - - - -
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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
------------------------------------------------------------
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