Contacts of the helix formed by residues 364 - 377 (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 VAL 364 (chain C).
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Specific contacts
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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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Residues in contact with LEU 365 (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* 3.5 26.9 - - + +
357C LEU* 5.4 8.1 - - + -
360C LEU* 2.8 44.3 + - + +
361C LEU* 3.3 28.0 + - + +
364C VAL* 1.3 81.1 - - + +
366C MET* 1.3 60.0 + - - +
368C THR* 3.2 8.4 + - - -
369C ALA 3.0 23.9 + - - -
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Residues in contact with MET 366 (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* 4.2 20.0 - - + -
309C THR* 4.7 0.2 - - - +
315C MET* 3.8 30.7 - - + -
318C ARG* 5.7 0.7 + - - -
321C SER* 4.5 6.5 + - - +
324C LEU* 3.9 28.5 - - + +
325C PHE* 3.9 23.6 - - + +
328C LEU* 4.6 11.2 - - + -
361C LEU* 2.8 39.4 + - - +
362C ILE* 4.3 8.5 - - - +
365C LEU* 1.3 70.2 - - - +
367C PRO* 1.4 61.7 - - + +
369C ALA* 3.2 5.1 + - - +
370C GLY* 3.1 24.4 + - - -
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Residues in contact with PRO 367 (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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307C LEU* 3.4 32.8 - - + +
309C THR* 3.0 21.5 + - + +
362C ILE 3.2 26.2 - - - +
363C LEU 3.7 14.6 - - - +
364C VAL 3.4 13.2 - - - +
366C MET* 1.4 85.6 - - + +
368C THR* 1.3 58.4 + - - -
371C THR* 3.0 22.0 + - - -
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Residues in contact with THR 368 (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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364C VAL* 2.7 31.4 + - - +
365C LEU* 3.2 9.3 + - - -
367C PRO* 1.3 74.3 - - - +
369C ALA* 1.3 59.3 + - - +
370C GLY 3.4 0.2 - - - -
371C THR* 3.3 6.6 + - - -
372C ILE* 3.0 47.1 + - + +
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Residues in contact with ALA 369 (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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320C LEU* 3.9 26.2 - - + +
321C SER* 4.0 13.5 - - - +
324C LEU* 3.6 27.8 - - + -
365C LEU 3.0 5.1 + - - -
366C MET* 3.2 9.4 + - - +
368C THR* 1.3 75.2 - - - +
370C GLY* 1.3 56.4 + - - +
372C ILE* 3.3 3.9 + - - +
373C GLU* 2.9 37.0 + - - +
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Residues in contact with GLY 370 (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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309C THR* 3.5 19.5 - - - +
310C SER* 4.2 13.7 - - - -
318C ARG* 4.7 2.0 - - - -
321C SER* 4.2 2.2 + - - -
366C MET 3.1 11.0 + - - -
368C THR 3.4 0.2 - - - -
369C ALA* 1.3 74.5 - - - +
371C THR* 1.3 56.0 + - - +
373C GLU* 3.4 13.5 + - - +
374C ASN* 3.0 36.5 + - - +
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Residues in contact with THR 371 (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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309C THR* 3.2 16.5 + - - +
367C PRO 3.0 15.9 + - - -
368C THR* 3.3 11.5 + - - -
370C GLY* 1.3 71.5 - - - +
372C ILE* 1.3 60.4 + - + +
374C ASN* 3.4 12.4 + - + +
375C LYS* 3.1 51.6 + - + +
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Residues in contact with ILE 372 (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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320C LEU* 4.2 18.8 - - + -
368C THR* 3.0 39.6 + - + +
369C ALA* 3.7 4.3 - - - +
371C THR* 1.3 74.6 - - + +
373C GLU* 1.3 52.0 + - - +
375C LYS* 3.1 10.4 + - + +
376C LEU* 2.8 53.3 + - + +
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Residues in contact with GLU 373 (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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312C GLN* 5.6 2.9 - - - +
318C ARG* 3.2 35.1 - - - +
320C LEU* 3.2 24.0 + - + +
321C SER* 2.8 40.4 + - - -
369C ALA 2.9 25.6 + - - +
370C GLY* 3.4 5.9 - - - +
372C ILE* 1.3 72.5 - - - +
374C ASN* 1.3 56.4 + - - +
376C LEU* 3.5 6.4 + - - +
377C LEU* 3.1 34.4 + - - +
20F TYR* 3.2 32.1 + - + +
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Residues in contact with ASN 374 (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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309C THR 2.9 28.1 + - - -
310C SER* 3.6 4.2 + - - -
311C LYS* 3.1 37.7 + - - +
312C GLN* 4.9 2.8 + - - -
370C GLY 3.0 20.8 + - - +
371C THR* 3.4 13.1 - - + +
372C ILE 3.3 0.4 - - - -
373C GLU* 1.3 72.9 - - - +
375C LYS* 1.3 61.9 + - - +
377C LEU* 3.2 8.7 + - - -
379C TRP* 2.9 52.1 + - + +
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Residues in contact with LYS 375 (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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371C THR* 3.1 36.8 + - + +
372C ILE* 3.4 11.7 - - + +
374C ASN* 1.3 72.5 - - - +
376C LEU* 1.3 59.0 + - + +
378C LYS* 3.0 21.9 + - - +
379C TRP 4.5 11.2 - - - +
17F ARG* 4.2 13.0 + - - +
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Residues in contact with LEU 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C LEU* 4.4 8.1 - - + -
372C ILE* 2.8 38.4 + - + +
373C GLU* 3.6 6.3 - - - +
374C ASN 3.3 0.2 - - - -
375C LYS* 1.3 76.6 - - + +
377C LEU* 1.3 58.0 + - - +
378C LYS* 3.4 4.0 + - - +
16F ILE* 3.7 41.3 - - + +
17F ARG* 3.3 37.0 - - + +
19F TRP* 5.7 2.5 - - + -
20F TYR* 3.7 38.8 - - + -
83F TYR* 5.8 0.7 - - - -
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Residues in contact with LEU 377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C GLN* 3.9 20.6 - - - +
317C PHE 5.6 0.2 - - - +
373C GLU 3.1 13.5 + - - +
374C ASN 3.2 3.7 + - - +
376C LEU* 1.3 72.8 - - - +
378C LYS* 1.4 59.3 + - - +
379C TRP* 3.3 31.9 - - + -
17F ARG 5.7 0.9 - - - +
20F TYR* 3.6 31.9 - - + -
21F TYR* 4.2 20.4 - - + -
24F ALA* 5.4 0.2 - - + -
26F PHE* 3.9 27.6 - - + -
33F ARG* 2.8 43.1 + - + -
83F TYR* 6.4 0.9 - - + -
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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
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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