Contacts of the helix formed by residues 363 - 383 (chain F) in PDB entry 3FKS
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 363 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F ILE* 3.9 23.8 - - + -
146F PRO* 4.5 14.6 - - + -
357F LEU* 3.6 20.2 - - + +
358F LEU* 4.5 5.8 - - + -
359F ASP 3.1 23.1 - - - +
362F VAL* 1.3 78.3 - - + +
364F GLY* 1.3 59.6 + - - +
367F HIS* 3.0 55.0 + - + +
368F TYR* 4.3 6.7 - - + +
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Residues in contact with GLY 364 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360F ALA* 3.2 21.7 + - - -
361F ALA 4.3 1.7 + - - -
362F VAL 3.4 3.2 - - - +
363F VAL* 1.3 83.7 - - - +
365F GLN* 1.3 67.4 + - - -
366F GLU 3.2 3.3 + - - -
368F TYR* 3.2 14.2 + - - +
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Residues in contact with GLN 365 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360F ALA* 3.2 28.9 + - + +
364F GLY* 1.3 72.1 - - - -
366F GLU* 1.3 57.6 + - - +
368F TYR* 3.5 10.2 + - - +
369F ASP* 2.9 65.2 + - - +
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Residues in contact with GLU 366 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364F GLY 3.2 1.0 - - - -
365F GLN* 1.3 76.9 - - - +
367F HIS* 1.3 58.6 + - - +
369F ASP* 3.1 8.7 + - + +
370F VAL* 2.8 43.4 + - + +
438F VAL* 4.5 12.8 - - + +
439F ALA* 5.9 2.0 - - - -
442F LYS* 3.1 36.4 + - - +
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Residues in contact with HIS 367 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142F ASP 3.2 22.8 + - - -
143F LEU* 3.1 34.6 + - + +
146F PRO* 4.5 2.8 - - - +
358F LEU* 4.8 2.9 - - + -
363F VAL* 3.0 47.5 + - + +
364F GLY 3.4 1.8 + - - -
366F GLU* 1.3 78.0 - - - +
368F TYR* 1.3 57.8 + - - +
370F VAL* 3.8 1.2 - - - +
371F ALA* 2.9 26.6 + - + +
434F LEU* 3.7 22.2 - - + +
438F VAL* 3.5 35.9 - - + +
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Residues in contact with TYR 368 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C ARG* 4.4 25.5 + - - -
433C ASN* 5.5 7.3 + - - -
358F LEU* 3.7 45.3 - - + -
359F ASP* 4.5 4.9 - - - -
360F ALA* 4.0 22.9 - - + +
363F VAL* 4.3 1.8 - - + +
364F GLY 3.2 14.0 + - - +
365F GLN* 3.7 11.9 - - - +
366F GLU 3.2 0.4 - - - -
367F HIS* 1.3 78.1 - - - +
369F ASP* 1.3 68.5 + - - +
371F ALA* 3.8 3.0 - - - +
372F SER* 2.7 56.1 + - - -
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Residues in contact with ASP 369 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365F GLN* 2.9 54.1 + - - +
366F GLU* 3.1 8.8 + - + +
368F TYR* 1.3 83.8 - - - +
370F VAL* 1.3 57.5 + - + +
372F SER* 3.7 4.6 - - - -
373F LYS* 3.0 45.8 + - - +
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Residues in contact with VAL 370 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F LEU* 4.0 16.6 - - + -
366F GLU* 2.8 22.4 + - + +
367F HIS 3.8 3.4 - - - +
369F ASP* 1.3 74.4 - - + +
371F ALA* 1.3 67.0 + - - +
373F LYS* 3.0 13.9 + - - +
374F VAL* 3.0 22.4 + - + +
438F VAL* 3.9 28.3 - - + +
441F PHE* 4.3 8.7 - - + -
442F LYS* 3.7 45.8 - - + +
445F LEU* 4.1 4.8 - - + +
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Residues in contact with ALA 371 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F LEU* 3.4 36.1 - - + +
144F LEU* 3.8 7.9 - - + +
358F LEU* 3.9 18.4 - - + -
367F HIS 2.9 18.6 + - - +
368F TYR 3.9 2.5 - - - +
370F VAL* 1.3 76.5 - - - +
372F SER* 1.3 61.3 + - - +
374F VAL* 3.2 9.7 + - - +
375F GLN* 3.1 26.0 + - - +
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Residues in contact with SER 372 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C ARG* 5.2 9.7 + - - -
358F LEU* 5.7 0.9 - - - +
368F TYR* 2.7 53.3 + - - -
369F ASP* 3.7 6.1 - - - -
370F VAL 3.1 0.2 - - - -
371F ALA* 1.3 72.5 - - - +
373F LYS* 1.3 58.2 + - - +
374F VAL 3.0 4.5 - - - -
375F GLN* 3.0 16.7 + - - +
376F GLU* 2.8 39.1 + - - +
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Residues in contact with LYS 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369F ASP* 3.0 33.1 + - - +
370F VAL* 3.0 9.3 + - - +
372F SER* 1.3 76.2 - - - +
374F VAL* 1.3 56.8 + - - +
376F GLU* 4.0 19.9 - - - +
377F THR* 2.8 25.6 + - - -
442F LYS* 5.4 12.3 - - - +
445F LEU* 3.5 33.2 - - + +
446F GLU* 5.6 6.5 + - - +
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Residues in contact with VAL 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F LEU* 4.3 19.7 - - + -
144F LEU* 3.9 20.9 - - + -
370F VAL 3.0 14.3 + - - +
371F ALA* 3.3 9.9 - - - +
372F SER 3.0 0.4 - - - -
373F LYS* 1.3 79.1 - - - +
375F GLN* 1.3 60.3 + - - +
377F THR* 3.5 4.2 + - - -
378F LEU* 3.1 46.8 + - + +
410F ILE* 4.0 19.6 - - + +
414F LEU* 5.1 2.0 - - + -
441F PHE* 4.4 16.8 - - + -
445F LEU* 4.2 13.5 - - + -
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Residues in contact with GLN 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C TYR* 3.7 33.2 - - + +
364C ARG* 3.8 19.9 + - - -
144F LEU* 3.8 26.2 + - + +
350F PRO 4.5 11.3 + - - +
351F LEU* 3.6 17.8 - - + +
353F SER 4.9 5.7 + - - -
354F LYS* 6.0 1.0 - - - +
358F LEU* 3.9 24.0 - - - +
371F ALA 3.1 14.2 + - - +
372F SER* 3.0 14.8 + - - +
374F VAL* 1.3 73.9 - - - +
376F GLU* 1.3 65.4 + - - +
378F LEU* 3.0 13.1 + - + -
379F GLN* 3.0 12.6 + - - +
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Residues in contact with GLU 376 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C TYR 3.2 18.8 + - - +
361C LYS* 3.7 19.7 - - - +
362C GLY* 3.5 19.2 - - - +
364C ARG* 5.3 3.9 + - - +
428C GLN* 5.6 0.5 + - - -
431C LYS* 4.2 8.0 + - - -
372F SER* 2.8 24.9 + - - +
373F LYS* 4.0 24.0 - - - +
375F GLN* 1.3 72.9 - - - +
377F THR* 1.3 60.1 + - - +
379F GLN* 3.8 3.5 + - - +
380F THR* 2.9 23.0 + - - -
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Residues in contact with THR 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373F LYS 2.8 23.0 + - - -
374F VAL* 3.5 5.7 + - - -
375F GLN 3.1 0.4 - - - -
376F GLU* 1.3 77.7 - - - +
378F LEU* 1.3 64.6 + - - +
379F GLN 3.2 0.4 - - - -
380F THR* 3.1 16.6 + - - -
381F TYR* 3.3 12.1 + - - +
403F THR* 3.6 38.4 - - + +
406F ARG* 5.0 4.9 - - + -
407F ALA* 3.8 15.7 - - + +
410F ILE* 5.5 4.0 - - + -
445F LEU* 4.0 12.5 - - + +
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Residues in contact with LEU 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F LEU* 5.2 0.2 - - + -
350F PRO* 3.7 35.2 - - + +
351F LEU* 3.5 18.5 - - + +
374F VAL* 3.1 38.3 + - + +
375F GLN* 3.0 6.6 + - - +
377F THR* 1.3 77.1 - - - +
379F GLN* 1.3 57.3 + - - +
381F TYR* 3.6 10.2 + - + +
382F LYS* 3.1 26.7 + - - +
407F ALA* 4.2 26.9 - - + +
410F ILE* 4.4 7.9 - - + -
411F GLN* 4.3 18.4 - - + -
414F LEU* 4.4 7.9 - - + -
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Residues in contact with GLN 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C GLU* 3.7 51.6 + - + +
360C TYR* 3.8 14.3 - - - +
361C LYS* 4.3 20.0 - - + +
351F LEU* 3.5 25.9 - - + +
375F GLN 3.0 14.5 + - - +
376F GLU 4.0 5.4 - - - +
377F THR 3.2 0.2 - - - -
378F LEU* 1.3 75.7 - - - +
380F THR* 1.3 61.4 + - - +
382F LYS* 3.5 24.1 + - - +
383F SER* 2.8 35.2 + - - +
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Residues in contact with THR 380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C LYS* 5.1 15.9 - - - +
376F GLU 2.9 17.8 + - - -
377F THR* 3.1 10.5 + - - -
379F GLN* 1.3 79.4 - - - +
381F TYR* 1.3 60.1 + - - +
383F SER* 3.6 5.0 + - - -
384F LEU* 3.3 42.1 + - + +
400F ASP* 5.2 6.7 - - - +
403F THR* 4.4 22.8 - - + +
404F VAL* 5.5 2.0 - - + -
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Residues in contact with TYR 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377F THR 3.3 2.6 + - - +
378F LEU* 3.6 11.6 + - + +
380F THR* 1.3 76.5 - - - +
382F LYS* 1.3 64.5 + - - +
384F LEU* 3.5 3.7 + - + -
385F GLN* 3.2 52.3 + - - +
388F ILE* 5.0 15.6 - - + +
404F VAL* 3.5 38.5 - - + +
407F ALA* 3.7 30.3 - - + -
408F ARG* 3.1 43.1 + - + +
411F GLN* 4.0 20.2 - - - -
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Residues in contact with LYS 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349F ASP* 5.0 9.5 + - - -
351F LEU* 3.6 32.1 - - + +
352F ASP* 6.0 1.8 - - - +
378F LEU 3.1 19.4 + - - +
379F GLN* 3.5 22.9 + - - +
381F TYR* 1.3 74.2 - - - +
383F SER* 1.3 57.0 + - - +
384F LEU 3.0 10.3 + - - -
385F GLN* 3.1 31.5 + - + +
386F ASP* 4.9 0.3 + - - -
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Residues in contact with SER 383 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C GLU* 3.8 23.6 + - - -
361C LYS* 5.3 9.7 + - - -
407C GLN* 5.4 2.4 + - - -
379F GLN* 2.8 24.2 + - - +
380F THR* 3.6 6.5 + - - -
381F TYR 3.5 0.2 - - - -
382F LYS* 1.3 71.0 - - - +
384F LEU* 1.3 68.5 + - - +
385F GLN 3.7 0.2 - - - -
386F ASP* 5.3 1.1 - - - +
387F ILE* 3.8 8.8 - - - +
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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) + - + + + + + -
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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