Contacts of the helix formed by residues 318 - 340 (chain C) in PDB entry 1L0N
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 ARG 318 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C LEU 5.9 0.2 + - - -
103C TYR 5.2 0.4 + - - -
105C GLY 5.8 0.2 - - - +
107C TYR* 4.7 2.8 + - - -
308C HIS* 3.6 20.4 + - - -
310C SER* 3.3 30.6 + - - -
312C GLN* 3.6 16.8 + - + +
313C ARG 3.3 23.8 + - - -
314C SER 2.7 24.1 + - - +
315C MET* 2.6 39.3 + - - +
316C MET 3.4 1.2 + - - -
317C PHE* 1.3 77.0 - - - +
319C PRO* 1.3 65.9 - - - +
320C LEU 3.5 0.9 - - - -
321C SER* 3.2 28.7 + - - -
322C GLN* 3.0 25.3 + - - +
366C MET 5.8 0.6 + - - -
370C GLY* 5.1 2.4 - - - -
373C GLU* 3.3 28.4 + - - +
20F TYR* 3.7 4.0 - - - +
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Residues in contact with PRO 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C PHE 3.6 9.6 - - - +
318C ARG* 1.3 83.8 - - - +
320C LEU* 1.3 70.3 + - + +
322C GLN* 3.0 15.7 + - - +
323C CYS* 3.2 17.5 + - - -
19F TRP* 5.5 5.6 - - + -
20F TYR* 3.9 20.0 - - + +
23F ALA* 3.6 31.4 - - + -
24F ALA* 3.9 6.3 - - - +
47G ARG* 3.4 35.5 - - + +
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Residues in contact with LEU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C PRO* 1.3 82.0 - - + +
321C SER* 1.3 63.6 + - - +
323C CYS* 3.2 11.3 + - - +
324C LEU* 3.1 27.0 + - + +
369C ALA* 4.5 13.2 - - + +
372C ILE* 4.0 33.2 - - + -
373C GLU* 3.1 21.1 + - + +
376C LEU* 5.0 4.5 - - + -
19F TRP* 4.5 24.9 - - + -
20F TYR* 4.5 7.2 - - + -
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Residues in contact with SER 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C MET* 3.6 15.9 - - - +
318C ARG* 3.2 33.1 + - - -
319C PRO 3.1 0.6 - - - -
320C LEU* 1.3 73.9 - - - +
322C GLN* 1.3 65.1 + - - +
324C LEU* 3.4 8.4 + - - +
325C PHE* 2.8 23.6 + - - +
366C MET* 4.6 7.0 + - - +
369C ALA* 4.0 11.6 - - - +
370C GLY 4.5 2.4 + - - -
373C GLU* 2.9 27.7 + - - -
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Residues in contact with GLN 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C TYR* 3.3 32.3 + - + +
315C MET* 3.9 13.6 - - + +
316C MET* 4.3 6.6 - - - +
318C ARG 3.0 14.4 + - - +
319C PRO* 3.0 11.1 + - - +
321C SER* 1.3 76.7 - - - +
323C CYS* 1.4 52.1 + - - +
325C PHE* 2.9 10.2 + - - +
326C TRP* 2.8 48.1 + - + +
44G CYS* 5.3 8.9 - - - +
47G ARG* 2.7 54.8 + - + +
48G VAL* 5.4 1.6 - - - +
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Residues in contact with CYS 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C PRO* 3.6 14.4 - - - -
320C LEU* 3.2 11.1 + - - +
322C GLN* 1.4 76.9 - - - +
324C LEU* 1.3 60.9 + - + +
326C TRP* 3.1 2.8 + - - +
327C ALA* 2.8 29.7 + - - +
46G LEU 4.2 6.1 - - - -
47G ARG* 4.0 35.7 - - - +
51G PRO* 3.9 8.3 - - + +
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Residues in contact with LEU 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C LEU* 3.1 11.7 + - + +
321C SER* 3.7 8.5 - - - +
323C CYS* 1.3 79.1 - - + +
325C PHE* 1.3 63.0 + - - +
327C ALA* 3.2 8.5 + - + +
328C LEU* 3.0 19.9 + - - +
361C LEU* 3.9 22.1 - - + +
365C LEU* 3.4 44.4 - - + +
366C MET* 4.0 17.0 - - + +
369C ALA* 3.6 20.4 - - + -
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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
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99C GLY* 3.9 21.3 - - - -
102C LEU* 4.6 13.2 - - + -
103C TYR* 3.6 44.9 - + + -
315C MET* 3.9 15.5 - - + -
321C SER 2.8 15.0 + - - +
322C GLN* 2.9 7.4 + - - +
324C LEU* 1.3 74.5 - - - +
326C TRP* 1.3 107.5 + + - +
328C LEU* 2.7 32.5 + - + +
329C VAL* 3.1 19.5 + - + +
366C MET* 4.2 12.1 - - + +
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Residues in contact with TRP 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TRP* 5.7 12.3 - + - -
103C TYR* 4.4 14.3 - + - -
322C GLN* 2.8 37.8 + - + +
323C CYS 3.1 0.8 + - - +
325C PHE* 1.3 103.3 - + - +
327C ALA* 1.3 56.6 + - - +
329C VAL* 3.4 20.3 + - + +
330C ALA* 2.8 30.3 + - - +
47G ARG 3.3 29.6 - - - +
48G VAL* 3.5 32.9 - - + +
51G PRO* 3.6 14.0 - - + +
52G PHE* 3.7 27.1 - + + -
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Residues in contact with ALA 327 (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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323C CYS 2.8 13.8 + - - +
324C LEU* 3.5 14.4 - - + +
325C PHE 3.2 0.2 - - - -
326C TRP* 1.3 75.9 - - - +
328C LEU* 1.4 53.3 + - - +
330C ALA* 3.7 2.9 - - - +
331C ASP* 2.7 36.0 + - - +
357C LEU* 4.9 4.7 - - + +
361C LEU* 3.8 15.3 - - + +
51G PRO* 3.7 15.4 - - + +
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Residues in contact with LEU 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LEU* 4.2 23.3 - - + -
324C LEU 3.0 10.3 + - - +
325C PHE* 2.7 25.7 + - + +
327C ALA* 1.4 66.9 - - - +
329C VAL* 1.3 62.0 + - + +
331C ASP* 3.2 4.5 + - + +
332C LEU* 2.8 37.5 + - + +
358C TYR* 3.8 34.3 - - + +
361C LEU* 3.6 19.0 - - + +
362C ILE* 4.0 28.9 - - + -
366C MET* 4.7 7.9 - - + -
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Residues in contact with VAL 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C GLY* 6.5 0.2 - - - -
325C PHE* 3.1 24.7 + - + +
326C TRP* 3.8 29.6 - - + +
328C LEU* 1.3 77.7 - - + +
330C ALA* 1.3 64.7 + - - +
332C LEU* 2.9 24.9 + - + +
333C LEU* 3.1 19.0 + - + +
52G PHE* 3.8 23.1 - - + -
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Residues in contact with ALA 330 (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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326C TRP 2.8 22.7 + - - +
327C ALA* 3.7 4.3 - - - +
329C VAL* 1.3 71.5 - - - +
331C ASP* 1.3 62.1 + - - +
333C LEU* 3.0 17.2 + - - +
334C THR* 3.2 14.6 + - - -
51G PRO* 3.4 35.2 - - + +
52G PHE* 4.1 17.7 - - + +
55G PHE* 4.3 8.2 - - + +
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Residues in contact with ASP 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 ALA 2.7 22.7 + - - +
328C LEU* 3.2 9.1 + - + +
330C ALA* 1.3 75.0 - - - +
332C LEU* 1.3 57.5 + - - +
334C THR* 3.4 7.2 + - - -
335C LEU* 3.0 29.0 + - - +
354C ALA* 3.0 41.1 - - - +
357C LEU* 3.5 23.8 - - + +
358C TYR* 3.2 23.9 + - - +
361C LEU* 4.9 0.6 - - + +
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Residues in contact with LEU 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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276C PHE* 3.8 28.8 - - + +
328C LEU* 2.8 27.0 + - + +
329C VAL* 2.9 18.5 + - + +
331C ASP* 1.3 73.3 - - - +
333C LEU* 1.3 66.0 + - + +
335C LEU* 3.8 9.5 - - + +
336C THR* 3.2 28.9 + - + +
358C TYR* 3.6 34.8 - - + -
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Residues in contact with LEU 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C VAL* 3.1 20.3 + - + +
330C ALA 3.0 9.4 + - - +
332C LEU* 1.3 76.4 - - + +
334C THR* 1.3 56.5 + - - +
336C THR* 2.9 13.2 + - + +
337C TRP* 2.7 34.7 + - - +
52G PHE* 4.0 26.0 - - + -
55G PHE* 3.8 36.3 - - + -
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Residues in contact with THR 334 (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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330C ALA 3.2 12.6 + - - -
331C ASP* 3.4 16.3 + - - +
333C LEU* 1.3 76.5 - - - +
335C LEU* 1.3 54.9 + - - +
337C TRP* 3.3 18.4 + - + +
338C ILE* 2.7 40.3 + - + +
350C ILE* 3.8 24.2 - - + -
354C ALA* 4.3 9.9 - - + -
55G PHE* 3.2 24.7 - - + +
58G VAL* 4.7 5.6 - - + -
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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
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275C LEU 3.5 0.5 - - - +
276C PHE* 3.8 18.2 - - + +
279C ALA* 3.2 23.1 - - + +
280C ILE* 4.0 23.8 - - + -
331C ASP* 3.0 21.4 + - - +
332C LEU* 3.8 22.9 - - + +
333C LEU 3.1 0.2 - - - -
334C THR* 1.3 80.7 - - - +
336C THR* 1.3 57.0 + - - +
338C ILE* 4.6 0.9 - - + -
339C GLY 2.8 24.8 + - - -
351C GLY* 4.4 5.8 - - - +
354C ALA* 3.7 24.5 - - + -
355C SER* 3.8 19.1 - - - +
358C TYR* 4.2 16.2 - - + -
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Residues in contact with THR 336 (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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272C TRP* 4.4 15.7 - - + +
275C LEU* 3.8 25.1 - - - +
276C PHE* 3.6 24.9 - - + +
332C LEU* 3.2 15.7 + - + +
333C LEU* 2.9 20.4 + - + +
335C LEU* 1.3 70.9 - - - +
337C TRP* 1.3 67.4 + - - +
339C GLY* 3.2 0.9 + - - -
340C GLY* 2.9 20.6 + - - -
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Residues in contact with TRP 337 (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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333C LEU 2.7 18.6 + - - +
334C THR* 3.7 26.7 - - + -
336C THR* 1.3 77.0 + - - +
338C ILE* 1.3 71.1 + - + +
340C GLY* 3.0 9.2 + - - -
341C GLN* 3.3 33.8 + - + +
347C TYR* 3.7 25.1 - + - -
350C ILE* 3.2 31.2 - - + -
55G PHE* 4.0 13.5 - + + -
58G VAL* 3.7 14.8 - - + -
59G TYR* 3.3 63.6 - + - -
62G GLY* 4.3 4.5 - - - -
63G THR* 4.3 5.5 + - - -
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Residues in contact with ILE 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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279C ALA* 4.1 13.0 - - + +
282C ARG* 3.0 13.6 + - + +
334C THR* 2.7 25.5 + - + +
335C LEU* 3.7 3.8 - - + +
337C TRP* 1.3 78.8 - - + +
339C GLY* 1.3 55.9 + - - +
341C GLN* 2.7 30.8 + - - +
347C TYR* 3.6 45.5 - - + +
350C ILE* 3.6 34.5 - - + -
351C GLY* 3.8 23.1 - - - -
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Residues in contact with GLY 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C LYS* 4.3 2.3 - - - +
275C LEU* 3.4 24.9 - - - +
278C TYR* 3.2 20.8 - - - -
279C ALA* 3.9 7.9 - - - -
282C ARG* 2.7 21.5 + - - -
335C LEU 2.8 21.3 + - - -
336C THR 3.2 1.3 + - - -
338C ILE* 1.3 73.1 - - - +
340C GLY* 1.3 56.8 + - - +
341C GLN 3.4 0.3 + - - -
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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
----------------------------------------------------------
269C LYS* 4.3 23.6 + - - +
275C LEU* 3.9 15.9 - - - +
336C THR 2.9 12.4 + - - -
337C TRP 3.0 4.4 + - - -
338C ILE 3.0 0.2 + - - -
339C GLY* 1.3 76.3 - - - +
341C GLN* 1.3 72.1 + - - +
342C PRO* 4.7 0.2 - - - +
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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