Contacts of the helix formed by residues 364 - 383 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360M ALA* 3.3 15.8 + - - -
362M VAL 3.4 1.8 - - - -
363M VAL* 1.3 79.4 - - - +
365M GLN* 1.3 61.3 + - - -
366M GLU* 3.0 4.7 - - - -
367M HIS 3.0 4.2 + - - -
368M TYR* 2.8 28.6 + - - +
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Residues in contact with GLN 365 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360M ALA* 3.3 33.7 + - + +
364M GLY* 1.3 70.9 - - - -
366M GLU* 1.3 57.1 + - - +
368M TYR* 3.9 6.0 - - - -
369M ASP* 3.0 66.4 + - - +
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Residues in contact with GLU 366 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364M GLY* 3.0 1.5 - - - -
365M GLN* 1.3 77.1 - - - +
367M HIS* 1.3 67.0 + - - +
369M ASP* 4.0 2.6 - - - +
370M VAL* 3.0 36.0 + - + +
438M VAL* 5.7 4.5 - - + -
442M LYS* 3.2 34.8 - - + +
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Residues in contact with HIS 367 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133M ILE* 6.2 0.2 - - - +
142M ASP 3.0 20.8 + - - -
143M LEU* 3.0 37.6 - - + +
146M PRO* 4.7 2.2 - - + +
358M LEU* 4.4 7.7 - - + +
363M VAL* 3.1 48.3 - - + +
364M GLY* 3.0 2.7 + - - +
366M GLU* 1.3 78.3 - - - +
368M TYR* 1.3 65.5 + - - +
370M VAL* 3.8 1.4 - - - +
371M ALA* 3.0 20.4 + - - +
434M LEU* 3.8 17.5 - - + +
438M VAL* 3.3 34.0 - - + +
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Residues in contact with TYR 368 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364J ARG* 2.6 31.7 + - - -
358M LEU* 3.5 32.9 - - + +
359M ASP* 3.9 5.4 - - - -
360M ALA* 3.4 34.5 - - + +
363M VAL* 4.1 4.0 - - + +
364M GLY 2.8 19.2 + - - +
365M GLN* 3.9 10.1 - - - +
367M HIS* 1.3 75.8 + - - +
369M ASP* 1.3 66.8 + - - +
371M ALA* 3.0 6.4 + - - +
372M SER* 2.7 62.6 + - - -
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Residues in contact with ASP 369 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365M GLN* 3.0 51.7 + - - +
366M GLU* 4.0 3.9 - - - +
368M TYR* 1.3 86.8 - - - +
370M VAL* 1.3 58.9 + - + +
372M SER* 3.2 7.7 + - - -
373M LYS* 2.8 43.9 + - - +
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Residues in contact with VAL 370 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M LEU* 4.3 10.1 - - + -
366M GLU* 3.0 29.4 + - + +
367M HIS* 3.8 4.3 - - - +
369M ASP* 1.3 76.6 - - + +
371M ALA* 1.3 64.2 + - - +
373M LYS* 3.1 8.3 + - + +
374M VAL* 3.0 25.8 + - + +
438M VAL* 3.7 23.1 - - + +
441M PHE* 4.1 10.5 - - + -
442M LYS* 3.9 35.7 - - + +
445M LEU* 3.7 19.2 - - + +
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Residues in contact with ALA 371 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143M LEU* 3.5 41.1 - - + +
144M LEU* 3.9 5.7 - - + +
358M LEU* 4.3 14.6 - - + -
367M HIS* 3.0 18.8 + - - +
368M TYR 3.6 2.5 - - - +
370M VAL* 1.3 76.8 - - - +
372M SER* 1.3 62.2 + - - +
374M VAL* 3.3 8.6 + - - +
375M GLN* 3.3 28.3 + - - +
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Residues in contact with SER 372 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364J ARG* 4.8 12.4 + - - +
358M LEU* 6.2 0.2 - - - +
368M TYR* 2.7 54.6 + - - -
369M ASP* 3.3 9.0 - - - -
371M ALA* 1.3 73.8 - - - +
373M LYS* 1.3 62.6 + - - +
375M GLN* 3.6 7.7 + - - +
376M GLU* 3.1 38.2 + - - +
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Residues in contact with LYS 373 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369M ASP* 2.8 25.9 + - - +
370M VAL* 3.1 9.4 + - + +
372M SER* 1.3 72.7 - - - +
374M VAL* 1.3 61.9 + - - +
376M GLU* 3.2 12.2 + - - +
377M THR* 2.7 34.7 + - - +
445M LEU* 3.8 26.7 - - + -
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Residues in contact with VAL 374 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M LEU* 3.9 23.8 - - + -
144M LEU* 3.7 19.7 - - + -
370M VAL* 3.0 22.7 + - + +
371M ALA 3.3 8.0 + - - +
373M LYS* 1.3 78.1 - - - +
375M GLN* 1.3 63.8 + - - +
377M THR* 3.1 6.6 + - - -
378M LEU* 3.0 30.0 + - + +
410M ILE* 3.8 24.4 - - + +
414M LEU* 5.1 1.6 - - + -
441M PHE* 4.1 15.0 - - + -
445M LEU* 4.2 17.7 - - + +
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Residues in contact with GLN 375 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360J TYR* 3.6 32.0 - - + +
364J ARG* 4.4 12.6 + - - -
144M LEU* 3.9 37.3 + - + +
350M PRO 3.5 23.8 + - - +
351M LEU* 3.5 16.0 - - + +
353M SER 4.3 8.3 + - - -
354M LYS* 5.0 3.7 + - - +
358M LEU* 4.9 9.3 - - - +
371M ALA* 3.3 15.3 + - - +
372M SER* 4.1 5.9 - - - +
374M VAL* 1.3 79.6 - - - +
376M GLU* 1.3 53.2 + - - +
378M LEU* 3.0 6.0 + - - +
379M GLN* 2.7 36.7 + - - +
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Residues in contact with GLU 376 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360J TYR 3.1 22.9 - - - +
361J LYS* 3.7 20.6 - - - +
362J GLY* 3.5 14.6 - - - +
364J ARG* 5.7 3.5 + - - +
431J LYS* 5.2 4.5 + - - -
372M SER* 3.1 30.6 + - - +
373M LYS* 3.5 13.0 - - - +
375M GLN* 1.3 76.1 - - - +
377M THR* 1.3 63.3 + - - +
379M GLN* 3.3 4.1 + - - +
380M THR* 3.2 26.0 + - - -
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Residues in contact with THR 377 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373M LYS* 2.7 21.6 + - - +
374M VAL* 3.1 9.6 + - - -
376M GLU* 1.3 77.3 - - - +
378M LEU* 1.3 61.0 + - - +
380M THR* 3.9 0.4 + - - -
381M TYR 3.6 12.3 + - - -
403M THR* 3.7 39.9 - - + +
406M ARG* 4.8 9.2 - - + -
407M ALA* 3.6 19.1 - - + +
410M ILE* 5.3 5.4 - - + -
445M LEU* 4.1 15.3 - - + +
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Residues in contact with LEU 378 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144M LEU* 5.2 0.2 - - + -
350M PRO* 3.8 30.1 - - + -
351M LEU* 4.2 13.6 - - + +
374M VAL* 3.0 26.4 + - + +
375M GLN* 3.0 10.6 + - - +
377M THR* 1.3 79.1 - - - +
379M GLN* 1.3 58.8 + - - +
381M TYR* 3.1 13.0 + - + +
382M LYS* 3.0 28.2 + - - +
407M ALA* 3.7 16.6 - - + +
410M ILE* 4.2 8.3 - - + -
411M GLN* 3.7 32.8 - - + +
414M LEU* 4.0 15.7 - - + -
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Residues in contact with GLN 379 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357J GLU* 2.7 57.9 + - - +
360J TYR* 3.8 25.0 - - + +
361J LYS* 4.3 17.5 - - + +
351M LEU* 3.5 22.0 - - + +
375M GLN 2.7 19.3 + - - +
376M GLU* 3.7 6.5 - - - +
378M LEU* 1.3 71.0 - - - +
380M THR* 1.3 56.5 + - - +
382M LYS* 3.2 15.9 + - - +
383M SER* 2.7 42.4 + - - +
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Residues in contact with THR 380 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361J LYS* 5.2 9.7 - - - +
376M GLU 3.2 14.3 + - - -
377M THR* 4.1 5.6 - - - -
379M GLN* 1.3 78.8 - - - +
381M TYR* 1.3 61.9 + - - +
383M SER* 3.4 11.4 + - - -
384M LEU* 3.4 32.5 - - + +
400M ASP* 4.6 12.6 - - - +
403M THR* 4.4 19.1 - - + -
404M VAL* 5.7 2.0 - - + -
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Residues in contact with TYR 381 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401L GLU* 4.8 3.1 + - - -
405L PHE* 4.7 4.5 - + - -
377M THR 3.6 3.0 + - - +
378M LEU* 3.1 16.4 + - + +
379M GLN 3.1 0.6 - - - -
380M THR* 1.3 81.3 - - - +
382M LYS* 1.3 63.0 + - + +
384M LEU* 3.3 13.4 + - - +
385M GLN* 3.5 37.3 + - - +
388M ILE* 5.3 4.5 - - + -
403M THR* 5.6 0.4 - - + +
404M VAL* 3.7 32.5 - - + -
407M ALA* 3.3 34.8 - - + -
408M ARG* 2.8 51.8 + - + +
411M GLN* 3.9 23.0 + - - -
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Residues in contact with LYS 382 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357J GLU* 4.5 9.7 + - - -
349M ASP* 5.1 4.9 + - - -
351M LEU* 3.5 37.7 + - + +
378M LEU 3.0 15.8 + - - +
379M GLN* 3.8 21.7 + - - +
381M TYR* 1.3 77.6 - - + +
383M SER* 1.3 61.2 + - - +
384M LEU 3.2 0.2 - - - -
385M GLN* 3.4 36.8 - - + +
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Residues in contact with SER 383 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357J GLU* 4.0 6.0 + - - -
361J LYS* 5.3 6.7 - - - -
379M GLN* 2.7 35.7 + - - +
380M THR* 3.6 10.7 - - - -
381M TYR 3.1 0.4 - - - -
382M LYS* 1.3 77.4 - - - +
384M LEU* 1.3 63.1 + - - +
385M GLN 3.4 1.5 + - - -
386M ASP 5.3 0.3 + - - -
387M ILE* 3.4 17.3 - - - +
15P ASN* 4.7 5.4 + - - -
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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