Contacts of the helix formed by residues 344 - 364 (chain C) in PDB entry 2FYU
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 GLU 344 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342C PRO* 3.0 30.5 + - - +
343C VAL* 1.3 77.4 - - - +
345C HIS* 1.3 68.9 + - - +
346C PRO* 3.8 2.2 - - - -
347C TYR* 3.1 18.8 + - - +
348C ILE* 3.2 17.6 + - - +
157E TYR* 5.6 4.0 - - - +
66G PHE* 4.4 16.1 - - + -
70G LYS* 3.4 37.9 + - - +
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Residues in contact with HIS 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C GLU* 1.3 75.8 - - - +
346C PRO* 1.4 85.0 - - + +
348C ILE* 3.8 10.2 + - - +
349C THR* 4.0 13.1 + - + +
61G TRP* 5.4 3.8 - + - -
65G GLU* 3.2 34.7 + - + +
66G PHE* 5.1 1.4 - - + -
69G SER* 3.7 23.8 + - - +
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Residues in contact with PRO 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C GLU 3.9 1.1 - - - +
345C HIS* 1.4 98.5 - - + +
347C TYR* 1.3 71.6 + - + +
348C ILE 3.2 0.5 + - - -
349C THR* 3.2 22.6 + - - +
350C ILE* 3.2 17.5 + - + +
61G TRP* 3.9 27.1 - - + -
62G GLY* 3.4 28.5 - - - +
65G GLU* 4.2 8.3 - - + -
66G PHE* 3.7 28.7 - - + +
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Residues in contact with TYR 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C TRP* 3.5 26.6 - + - -
338C ILE* 3.7 37.5 - - + +
341C GLN* 3.2 41.0 + - + -
342C PRO* 3.7 25.1 - - + +
343C VAL* 5.8 0.4 - - - -
344C GLU 3.1 9.6 + - - +
346C PRO* 1.3 79.6 - - + +
348C ILE* 1.4 52.8 + - - +
350C ILE* 4.5 0.9 - - + -
351C GLY* 2.8 33.4 + - - -
62G GLY 3.6 14.4 - - - -
63G THR* 3.6 21.0 + - - +
66G PHE* 3.4 45.2 - + + -
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Residues in contact with ILE 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C ARG 6.0 1.8 - - - +
283C SER* 5.3 1.3 + - - -
343C VAL* 3.5 37.0 - - + +
344C GLU* 3.2 23.7 + - - +
345C HIS* 4.3 6.3 - - - +
346C PRO 3.2 0.6 + - - -
347C TYR* 1.4 74.1 - - - +
349C THR* 1.3 61.7 + - + +
351C GLY* 3.6 1.3 - - - -
352C GLN* 2.9 51.2 + - + +
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Residues in contact with THR 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C HIS* 4.0 10.5 + - + +
346C PRO* 3.2 13.4 + - - +
348C ILE* 1.3 78.9 - - + +
350C ILE* 1.3 61.5 + - - +
352C GLN* 3.4 21.7 + - - +
353C LEU* 3.0 37.6 + - - +
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Residues in contact with ILE 350 (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 THR* 3.7 20.6 - - + -
337C TRP* 3.6 30.1 - - + -
338C ILE* 3.7 20.0 - - + -
346C PRO* 3.2 19.3 + - + +
347C TYR* 4.0 3.8 - - - +
349C THR* 1.3 80.0 - - - +
351C GLY* 1.3 60.2 + - - +
352C GLN 3.3 0.2 - - - -
353C LEU* 3.7 14.4 - - + +
354C ALA* 2.9 30.7 + - + +
58G VAL* 3.8 17.3 - - + -
61G TRP* 4.5 19.3 - - + -
62G GLY* 6.3 0.7 - - - -
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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
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283C SER* 3.1 9.9 + - - -
335C LEU* 4.1 3.8 - - - +
338C ILE* 3.8 22.9 - - - -
347C TYR 2.8 19.8 + - - -
348C ILE 3.6 1.8 - - - -
350C ILE* 1.3 77.1 - - - +
352C GLN* 1.3 51.7 + - - +
354C ALA* 4.0 4.0 - - - +
355C SER* 2.7 36.2 + - - -
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Residues in contact with GLN 352 (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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283C SER* 3.4 37.3 + - - +
285C PRO* 4.7 8.3 - - - +
348C ILE* 2.9 28.9 + - + +
349C THR* 3.4 32.6 - - - +
351C GLY* 1.3 74.5 - - - +
353C LEU* 1.3 57.7 + - + +
355C SER* 3.4 2.8 + - - -
356C VAL* 3.0 35.7 + - + +
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Residues in contact with LEU 353 (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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349C THR* 3.0 26.8 + - - +
350C ILE* 3.8 14.1 - - + +
351C GLY 3.4 0.2 - - - -
352C GLN* 1.3 72.6 - - + +
354C ALA* 1.3 59.3 - - - +
356C VAL* 3.5 9.3 + - + +
357C LEU* 3.0 30.5 + - - +
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Residues in contact with ALA 354 (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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331C ASP* 2.9 40.3 - - - +
334C THR* 4.5 17.9 - - + -
335C LEU* 3.7 25.4 - - + +
338C ILE* 5.9 0.2 - - + -
350C ILE* 2.9 19.2 + - + +
351C GLY* 4.0 2.5 - - - +
353C LEU* 1.3 73.0 - - - +
355C SER* 1.3 52.1 + - - +
357C LEU* 3.2 2.4 + - - -
358C TYR* 2.9 20.1 + - - +
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Residues in contact with SER 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C ILE* 3.5 29.1 - - - +
283C SER* 2.9 22.9 + - - -
284C ILE* 6.0 3.1 - - - -
335C LEU* 3.5 7.6 - - - +
351C GLY 2.7 23.7 + - - -
352C GLN 3.5 5.4 - - - -
353C LEU 3.3 0.2 - - - -
354C ALA* 1.3 73.6 - - - +
356C VAL* 1.3 64.2 + - - +
358C TYR* 3.5 3.0 + - - +
359C PHE* 3.2 31.6 + - - -
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Residues in contact with VAL 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C GLN* 3.0 20.7 + - + +
353C LEU* 3.5 10.5 + - + +
355C SER* 1.3 72.9 - - - +
357C LEU* 1.3 51.9 + - - +
359C PHE* 3.1 11.7 + - - +
360C LEU* 2.7 49.7 + - + +
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Residues in contact with LEU 357 (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* 4.6 5.4 - - + +
331C ASP* 3.4 26.9 - - + +
353C LEU 3.0 18.4 + - - +
354C ALA* 3.2 4.9 + - - +
356C VAL* 1.3 72.5 - - - +
358C TYR* 1.3 57.2 + - - +
360C LEU* 4.1 12.8 - - + -
361C LEU* 2.8 55.3 + - + +
365C LEU* 5.4 11.0 - - + -
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Residues in contact with TYR 358 (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* 4.6 5.8 - + - -
280C ILE* 3.8 15.0 - - + -
297C SER* 2.5 46.4 + - - -
300C ILE* 3.7 9.3 - - + +
301C LEU* 5.7 3.6 - - - +
328C LEU* 3.8 20.6 - - + +
331C ASP* 3.2 15.1 + - - +
332C LEU* 3.6 36.5 - - + +
335C LEU* 4.1 9.9 - - + -
354C ALA 2.9 11.4 + - - +
355C SER* 3.5 9.9 - - - +
357C LEU* 1.3 73.8 - - - +
359C PHE* 1.3 79.9 + + - +
361C LEU* 3.8 2.4 - - - +
362C ILE* 3.4 47.1 + - + +
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Residues in contact with PHE 359 (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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280C ILE* 3.9 17.9 - - + -
293C ALA* 3.6 29.8 - - + -
296C PHE* 3.6 32.5 - + + -
297C SER* 3.9 16.6 - - - -
300C ILE* 3.7 21.3 - - + -
355C SER* 3.2 24.4 + - - -
356C VAL* 3.1 8.2 + - - +
358C TYR* 1.3 91.8 - + - +
360C LEU* 1.3 60.3 + - - +
363C LEU* 3.0 39.3 + - + +
364C VAL* 5.0 0.5 - - - +
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Residues in contact with LEU 360 (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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356C VAL* 2.7 33.3 + - + +
357C LEU* 3.3 15.5 + - + +
359C PHE* 1.3 72.3 - - - +
361C LEU* 1.3 54.0 + - - +
364C VAL* 3.2 31.8 + - + +
365C LEU* 2.8 57.9 + - + +
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Residues in contact with LEU 361 (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 LEU* 3.7 41.7 - - + +
327C ALA* 3.7 29.2 - - + +
328C LEU* 3.8 22.7 - - + +
331C ASP* 4.5 2.0 - - + -
357C LEU* 2.8 43.1 + - + +
358C TYR 3.5 4.2 + - - +
360C LEU* 1.3 69.8 - - - +
362C ILE* 1.3 61.6 + - - +
365C LEU* 3.3 26.8 + - + +
366C MET* 2.8 38.6 + - - +
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Residues in contact with ILE 362 (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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102C LEU* 5.9 0.2 - - + -
300C ILE* 3.8 30.7 - - + -
304C ILE* 3.8 35.7 - - + -
307C LEU* 3.7 13.7 - - + +
328C LEU* 3.8 22.9 - - + -
358C TYR* 3.4 56.5 + - + +
359C PHE 4.5 0.2 - - - +
361C LEU* 1.3 77.3 - - - +
363C LEU* 1.3 59.2 + - - +
366C MET* 4.3 9.5 - - - +
367C PRO* 3.2 22.7 - - - +
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Residues in contact with LEU 363 (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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296C PHE* 4.5 24.2 - - + -
300C ILE* 3.8 26.7 - - + -
303C LEU* 4.6 9.2 - - + -
307C LEU* 4.1 31.2 - - + +
359C PHE* 3.0 23.1 + - + +
362C ILE* 1.3 77.3 - - - +
364C VAL* 1.3 67.1 + - + +
367C PRO* 3.7 10.1 - - - +
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Residues in contact with VAL 364 (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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360C LEU* 3.2 32.1 + - + +
362C ILE 3.4 0.8 - - - -
363C LEU* 1.3 89.9 - - + +
365C LEU* 1.3 68.3 + - + +
367C PRO* 3.4 6.7 - - - +
368C THR* 2.7 41.6 + - - +
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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
------------------------------------------------------------
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