Contacts of the helix formed by residues 364 - 384 (chain N) 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 GLY 364 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360N ALA 3.4 14.3 + - - -
361N ALA 4.6 0.8 - - - -
362N VAL 3.4 3.0 - - - -
363N VAL* 1.3 81.8 - - - +
365N GLN* 1.3 65.1 + - - -
366N GLU* 3.1 5.4 + - - -
367N HIS 3.2 3.9 + - - -
368N TYR* 3.1 21.0 + - - +
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Residues in contact with GLN 365 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360N ALA* 3.3 35.0 + - - +
364N GLY* 1.3 71.0 - - - -
366N GLU* 1.3 63.2 + - - +
368N TYR* 3.4 6.9 + - - +
369N ASP* 3.1 48.4 + - - +
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Residues in contact with GLU 366 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364N GLY* 3.1 2.6 - - - -
365N GLN* 1.3 81.1 - - - +
367N HIS* 1.3 64.0 + - - +
369N ASP* 3.4 6.1 + - - +
370N VAL* 3.2 25.6 + - - +
438N VAL* 4.6 10.7 - - + +
442N LYS* 2.7 38.5 + - - +
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Residues in contact with HIS 367 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142N ASP 2.9 23.1 + - - -
143N LEU* 2.9 47.3 - - + +
146N PRO* 5.7 2.4 - - + +
358N LEU* 4.8 5.1 - - + +
363N VAL* 3.6 41.8 + - + +
364N GLY 3.2 4.0 + - - +
366N GLU* 1.3 78.9 - - - +
368N TYR* 1.3 59.3 + - - +
370N VAL* 3.2 3.0 + - - +
371N ALA* 2.8 31.0 + - + +
434N LEU* 4.1 11.1 - - + +
438N VAL* 3.6 39.0 - - + +
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Residues in contact with TYR 368 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364K ARG* 5.6 5.7 + - - -
358N LEU* 3.3 32.3 - - + -
359N ASP* 3.6 12.8 - - - +
360N ALA* 3.3 30.3 - - + -
363N VAL* 4.4 3.3 - - + +
364N GLY 3.1 12.4 + - - +
365N GLN* 3.6 15.9 - - - +
366N GLU 3.2 0.2 - - - -
367N HIS* 1.3 77.4 + - - +
369N ASP* 1.3 68.0 + - - +
371N ALA* 3.3 3.5 + - - +
372N SER* 2.8 53.1 + - - -
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Residues in contact with ASP 369 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365N GLN* 3.1 38.1 + - - +
366N GLU* 3.4 6.4 + - - +
368N TYR* 1.3 85.7 - - - +
370N VAL* 1.3 59.1 + - + +
372N SER* 3.5 3.9 + - - -
373N LYS* 3.0 48.5 + - - +
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Residues in contact with VAL 370 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143N LEU* 4.4 9.6 - - + -
366N GLU* 3.2 17.0 - - + +
367N HIS* 3.2 8.0 + - - +
369N ASP* 1.3 78.3 - - + +
371N ALA* 1.3 57.2 + - - +
373N LYS* 3.4 4.4 + - + +
374N VAL* 3.0 33.1 + - + +
438N VAL* 4.1 12.3 - - + +
441N PHE* 3.7 30.7 - - + -
442N LYS* 3.8 41.5 - - + +
445N LEU* 4.1 10.7 - - + +
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Residues in contact with ALA 371 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143N LEU* 3.5 32.1 - - + +
144N LEU* 4.3 3.5 - - + +
358N LEU* 4.3 16.4 - - + -
367N HIS* 2.8 26.4 + - + +
368N TYR* 3.9 4.5 - - - +
370N VAL* 1.3 73.9 - - - +
372N SER* 1.3 61.7 + - - +
374N VAL* 3.5 7.6 + - - +
375N GLN* 3.1 31.6 + - - +
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Residues in contact with SER 372 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368N TYR* 2.8 48.4 + - - -
369N ASP* 3.8 6.7 - - - -
371N ALA* 1.3 76.2 - - - +
373N LYS* 1.3 60.0 + - - +
375N GLN* 4.0 8.3 + - - +
376N GLU* 3.0 33.8 + - - +
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Residues in contact with LYS 373 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369N ASP* 3.0 32.6 + - - +
370N VAL* 3.8 1.3 - - + +
372N SER* 1.3 74.8 - - - +
374N VAL* 1.3 61.9 + - - +
376N GLU* 3.3 10.3 + - - +
377N THR* 2.6 35.6 + - - +
445N LEU* 3.5 35.9 - - + +
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Residues in contact with VAL 374 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143N LEU* 4.1 12.3 - - + -
144N LEU* 3.9 21.8 - - + -
370N VAL* 3.0 24.5 + - + +
371N ALA 3.6 5.8 - - - +
372N SER 3.4 0.2 - - - -
373N LYS* 1.3 77.7 - - - +
375N GLN* 1.3 62.5 + - - +
377N THR* 3.2 6.0 + - - -
378N LEU* 3.1 31.9 + - + +
410N ILE* 4.0 25.9 - - + +
414N LEU* 5.4 1.3 - - + -
441N PHE* 3.8 29.4 - - + -
445N LEU* 4.6 10.1 - - + -
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Residues in contact with GLN 375 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144N LEU* 4.0 26.3 + - + +
350N PRO 4.0 18.6 + - - +
351N LEU* 4.2 13.9 + - + +
353N SER 4.5 6.3 + - - -
354N LYS* 5.4 5.9 - - - +
358N LEU* 4.1 26.2 - - - +
371N ALA* 3.1 18.2 + - - +
372N SER* 4.0 7.8 - - - +
374N VAL* 1.3 79.8 - - - +
376N GLU* 1.3 63.4 - - - +
377N THR 3.1 0.3 + - - -
378N LEU* 3.1 8.4 + - + +
379N GLN* 3.0 26.0 + - - +
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Residues in contact with GLU 376 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372N SER* 3.0 21.5 + - - +
373N LYS* 3.3 10.1 + - - +
375N GLN* 1.3 75.7 - - - +
377N THR* 1.3 58.7 + - - +
379N GLN* 3.8 7.1 + - + +
380N THR* 3.1 34.6 + - + +
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Residues in contact with THR 377 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373N LYS* 2.6 24.1 + - - +
374N VAL* 3.6 6.6 - - - -
375N GLN 3.1 0.2 - - - -
376N GLU* 1.3 75.7 - - - +
378N LEU* 1.3 63.6 - - - +
379N GLN 3.2 2.0 - - - -
380N THR* 2.7 20.9 + - - +
381N TYR* 3.1 11.6 + - - +
403N THR* 3.7 40.0 - - + +
406N ARG* 5.1 4.9 - - + -
407N ALA* 4.1 13.2 - - + +
410N ILE* 6.2 3.4 - - + -
445N LEU* 4.5 12.0 - - + +
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Residues in contact with LEU 378 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144N LEU* 5.2 0.4 - - + -
350N PRO* 3.8 32.3 - - + -
351N LEU* 4.0 17.3 - - + +
374N VAL* 3.1 33.6 + - + +
375N GLN* 3.1 8.6 + - - +
377N THR* 1.3 78.2 - - - +
379N GLN* 1.3 57.2 + - - +
381N TYR* 3.4 11.5 + - + +
382N LYS* 3.0 27.5 + - - +
407N ALA* 4.1 15.0 - - + +
410N ILE* 4.8 4.7 - - + -
411N GLN* 4.1 35.2 - - + +
414N LEU* 4.5 8.1 - - + -
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Residues in contact with GLN 379 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360K TYR* 5.5 6.9 + - - +
351N LEU* 3.3 30.3 - - - +
375N GLN 3.0 15.4 + - - +
376N GLU* 4.1 8.1 - - + +
377N THR 3.2 0.4 - - - -
378N LEU* 1.3 77.9 - - - +
380N THR* 1.3 61.5 + - + +
381N TYR 3.3 0.2 - - - -
382N LYS* 3.9 18.7 - - - +
383N SER* 3.4 19.8 + - - -
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Residues in contact with THR 380 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376N GLU* 3.1 20.1 + - + +
377N THR* 2.7 28.4 + - - +
379N GLN* 1.3 75.6 - - + +
381N TYR* 1.3 61.0 + - - +
383N SER* 2.8 20.9 + - - -
384N LEU* 3.2 26.5 - - - +
403N THR* 5.0 7.3 + - - -
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Residues in contact with TYR 381 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377N THR 3.1 16.9 + - - +
378N LEU* 3.7 13.2 - - + +
380N THR* 1.3 76.0 + - - +
382N LYS* 1.3 64.3 + - + +
383N SER 3.2 0.4 - - - -
384N LEU* 3.4 17.6 + - + +
385N GLN* 2.8 43.8 + - - +
388N ILE* 5.1 8.3 - - + -
404N VAL* 4.3 31.2 - - + -
407N ALA* 3.7 25.8 - - + -
408N ARG* 3.2 37.1 + - + +
411N GLN* 4.0 25.3 + - - -
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Residues in contact with LYS 382 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349N ASP* 5.8 2.4 + - - -
351N LEU* 3.8 26.2 - - + +
378N LEU 3.0 17.9 + - - +
379N GLN* 4.1 19.5 - - - +
380N THR 3.4 0.2 - - - -
381N TYR* 1.3 80.0 - - + +
383N SER* 1.3 58.0 + - - +
385N GLN* 3.0 26.7 - - + +
386N ASP* 5.4 0.7 - - - +
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Residues in contact with SER 383 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379N GLN* 3.4 10.7 + - - +
380N THR* 2.8 28.4 + - - -
382N LYS* 1.3 77.3 - - - +
384N LEU* 1.3 57.9 + - - +
385N GLN 3.0 9.4 + - - -
386N ASP* 3.3 25.5 + - - +
387N ILE* 4.3 3.0 - - - +
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Residues in contact with LEU 384 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380N THR* 3.2 27.9 + - - +
381N TYR* 3.4 10.9 + - + +
383N SER* 1.3 78.4 + - - +
385N GLN* 1.3 64.0 + - - +
386N ASP 3.0 4.0 + - - -
387N ILE* 3.4 25.1 - - + +
388N ILE* 3.0 35.8 + - + +
396N LEU* 4.0 20.0 - - + -
400N ASP* 4.9 16.8 - - - +
403N THR* 5.9 1.1 - - - +
404N VAL* 3.5 31.4 - - + -
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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