Contacts of the helix formed by residues 364 - 384 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360O ALA* 2.8 17.8 + - - -
361O ALA 5.4 0.2 - - - -
362O VAL 3.2 3.2 + - - -
363O VAL* 1.3 78.0 - - - +
365O GLN* 1.3 67.3 + - - -
366O GLU* 3.1 4.5 - - - -
367O HIS 3.0 13.3 + - - -
368O TYR* 3.0 12.5 + - - +
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Residues in contact with GLN 365 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360O ALA* 3.6 28.8 + - + +
364O GLY* 1.3 69.7 - - - +
366O GLU* 1.3 62.6 + - - +
368O TYR* 3.6 5.5 - - - +
369O ASP* 3.0 59.4 + - - +
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Residues in contact with GLU 366 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364O GLY 3.1 1.5 - - - -
365O GLN* 1.3 75.5 - - - +
367O HIS* 1.3 68.2 + - - +
369O ASP* 3.2 6.4 + - - +
370O VAL* 2.9 36.9 + - + +
435O LYS* 5.6 4.0 + - - -
438O VAL* 4.9 9.8 - - + +
442O LYS* 3.0 34.7 + - - +
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Residues in contact with HIS 367 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142O ASP 3.2 22.2 + - - -
143O LEU* 3.1 34.8 + - + +
146O PRO* 4.5 2.3 - - + +
358O LEU* 4.5 3.3 - - + +
363O VAL* 3.1 51.7 + - + +
364O GLY 3.0 2.9 + - - +
366O GLU* 1.3 77.6 - - - +
368O TYR* 1.3 66.1 + - - +
370O VAL* 3.2 3.1 + - - +
371O ALA* 2.9 23.5 + - + +
434O LEU* 3.9 16.1 - - + +
438O VAL* 3.7 37.6 - - + +
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Residues in contact with TYR 368 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364L ARG* 4.2 27.3 + - - -
433L ASN* 5.8 0.7 + - - -
358O LEU* 3.1 37.2 - - + -
359O ASP* 4.5 3.8 - - - -
360O ALA* 3.8 29.4 - - + -
363O VAL* 4.1 5.8 - - + +
364O GLY 3.0 11.0 + - - +
365O GLN* 3.6 13.0 - - - +
367O HIS* 1.3 79.2 - - - +
369O ASP* 1.3 71.8 + - - +
371O ALA* 3.2 4.5 + - - +
372O SER* 2.9 48.6 + - - -
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Residues in contact with ASP 369 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365O GLN* 3.0 49.4 + - - +
366O GLU* 3.8 4.6 - - - +
368O TYR* 1.3 87.4 - - - +
370O VAL* 1.3 63.3 + - + +
372O SER* 3.8 5.6 + - - -
373O LYS* 3.1 37.8 + - + +
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Residues in contact with VAL 370 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143O LEU* 4.4 8.5 - - + -
366O GLU* 2.9 27.1 + - + +
367O HIS 3.5 3.6 - - - +
369O ASP* 1.3 77.0 - - + +
371O ALA* 1.3 64.4 + - - +
373O LYS* 4.8 3.6 - - - +
374O VAL* 3.1 28.6 + - + +
438O VAL* 3.7 30.7 - - + +
441O PHE* 4.3 11.0 - - + -
442O LYS* 3.9 45.8 - - + +
445O LEU* 3.8 9.8 - - + +
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Residues in contact with ALA 371 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143O LEU* 3.8 31.4 - - + +
144O LEU* 4.4 7.5 - - + +
358O LEU* 4.2 20.0 - - + -
367O HIS* 2.9 18.3 + - + +
368O TYR 3.6 3.8 - - - +
370O VAL* 1.3 77.0 - - - +
372O SER* 1.3 57.3 + - - +
374O VAL* 3.2 8.1 + - - +
375O GLN* 2.9 35.5 + - - +
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Residues in contact with SER 372 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364L ARG* 4.7 15.8 + - - +
358O LEU* 6.0 1.6 - - - +
368O TYR* 2.9 44.6 + - - -
369O ASP* 3.8 8.1 - - - -
370O VAL 3.3 0.2 - - - -
371O ALA* 1.3 76.3 - - - +
373O LYS* 1.3 58.3 + - - +
375O GLN* 3.1 13.0 + - - +
376O GLU* 2.8 38.6 + - - +
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Residues in contact with LYS 373 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369O ASP* 3.1 26.0 + - + +
370O VAL* 4.8 4.0 - - - +
372O SER* 1.3 78.7 - - - +
374O VAL* 1.3 55.3 + - - +
376O GLU* 3.4 20.5 + - - +
377O THR* 2.7 33.4 + - - -
442O LYS* 5.5 8.6 - - - +
445O LEU* 3.7 34.0 - - + +
446O GLU* 5.3 9.7 + - - +
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Residues in contact with VAL 374 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143O LEU* 4.4 6.3 - - + -
144O LEU* 4.2 19.1 - - + -
370O VAL 3.1 18.2 + - - +
371O ALA* 3.4 8.7 - - - +
373O LYS* 1.3 77.4 - - - +
375O GLN* 1.3 61.1 + - - +
377O THR* 3.1 17.8 + - - -
378O LEU* 3.2 22.9 + - + +
410O ILE* 3.9 22.9 - - + -
414O LEU* 5.8 1.6 - - + -
441O PHE* 4.2 27.1 - - + -
445O LEU* 3.7 21.1 - - + -
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Residues in contact with GLN 375 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359L PHE* 5.8 0.5 - - - -
360L TYR* 3.4 46.4 + - + +
364L ARG* 4.3 12.9 + - - +
144O LEU* 4.1 25.0 + - + +
350O PRO* 3.6 18.7 + - + +
351O LEU* 3.7 10.1 - - + +
353O SER 4.8 3.8 + - - -
354O LYS* 5.6 2.4 - - - +
358O LEU* 4.6 20.9 - - - +
371O ALA* 2.9 18.3 + - - +
372O SER* 3.6 11.9 + - - +
374O VAL* 1.3 74.0 - - - +
376O GLU* 1.3 66.0 + - - +
378O LEU* 3.3 4.0 + - - +
379O GLN* 3.1 25.6 + - - +
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Residues in contact with GLU 376 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360L TYR 3.3 20.6 + - - +
361L LYS* 3.3 24.0 - - - +
362L GLY* 3.4 13.2 - - - +
431L LYS* 4.7 5.0 + - - -
372O SER* 2.8 22.8 + - - +
373O LYS* 3.5 25.0 - - - +
375O GLN* 1.3 75.9 - - - +
377O THR* 1.3 61.0 + - - +
379O GLN* 3.6 2.4 + - - +
380O THR* 2.9 27.7 + - - -
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Residues in contact with THR 377 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373O LYS 2.7 20.5 + - - -
374O VAL 3.1 7.5 + - - -
376O GLU* 1.3 76.5 - - - +
378O LEU* 1.3 64.3 + - + +
380O THR* 3.1 15.7 + - - -
381O TYR* 3.2 11.4 + - - +
403O THR* 3.9 26.3 - - + +
406O ARG* 4.9 2.7 - - + -
407O ALA* 3.8 22.8 - - + +
410O ILE* 4.0 18.4 - - + -
445O LEU* 3.6 15.4 - - + +
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Residues in contact with LEU 378 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144O LEU* 5.9 0.2 - - + -
350O PRO* 3.6 36.8 - - + -
351O LEU* 4.1 15.1 - - + +
374O VAL* 3.2 28.7 + - + +
375O GLN* 4.0 7.0 - - - +
377O THR* 1.3 80.7 - - - +
379O GLN* 1.3 57.5 + - - +
381O TYR* 3.2 12.0 + - + +
382O LYS* 2.9 29.1 + - - +
407O ALA* 4.2 16.2 - - + +
410O ILE* 4.6 6.7 - - + -
411O GLN* 4.0 37.0 - - + +
414O LEU* 4.5 6.5 - - + -
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Residues in contact with GLN 379 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356L ALA 4.8 0.2 - - - +
357L GLU* 3.6 48.9 + - + +
360L TYR* 4.0 29.9 - - + +
361L LYS* 4.5 7.9 - - + +
351O LEU* 3.8 21.2 - - + +
375O GLN 3.1 16.8 + - - +
376O GLU 3.9 4.7 - - - +
378O LEU* 1.3 77.2 - - - +
380O THR* 1.3 56.0 + - - +
382O LYS* 3.4 17.4 + - - +
383O SER* 3.0 28.2 + - - +
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Residues in contact with THR 380 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361L LYS* 5.8 3.8 - - - +
376O GLU 2.9 14.4 + - - -
377O THR* 3.1 9.5 + - - -
379O GLN* 1.3 76.5 - - - +
381O TYR* 1.3 63.9 + - - +
383O SER* 3.3 15.4 + - - -
384O LEU* 3.3 28.0 + - + +
400O ASP* 5.0 12.6 - - + +
403O THR* 4.4 22.8 - - + +
404O VAL* 4.9 1.8 - - + -
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Residues in contact with TYR 381 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377O THR 3.2 3.4 + - - +
378O LEU* 3.2 11.9 + - + +
380O THR* 1.3 78.9 - - - +
382O LYS* 1.3 64.3 + - - +
384O LEU 3.4 2.3 + - - +
385O GLN* 3.2 47.5 + - - +
388O ILE* 4.2 17.3 - - + -
393O MET* 6.3 0.4 - - - -
403O THR* 5.8 0.2 - - - +
404O VAL* 3.7 32.7 - - + +
407O ALA* 3.7 28.9 - - + -
408O ARG* 3.6 39.4 + - + -
411O GLN* 3.5 31.7 + - - -
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Residues in contact with LYS 382 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349O ASP* 4.8 10.5 + - - -
351O LEU* 3.7 30.4 - - + +
378O LEU 2.9 17.3 + - - +
379O GLN* 3.6 19.8 + - - +
380O THR 3.2 0.2 - - - -
381O TYR* 1.3 76.7 - - + +
383O SER* 1.3 60.6 + - - +
384O LEU 3.1 4.9 - - - -
385O GLN* 3.1 26.9 + - + +
386O ASP* 4.8 1.0 + - - +
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Residues in contact with SER 383 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357L GLU* 4.0 18.5 + - - -
379O GLN* 3.0 19.8 + - - +
380O THR* 3.3 11.2 + - - -
382O LYS* 1.3 76.7 - - - +
384O LEU* 1.3 68.1 + - - +
385O GLN 3.5 0.4 + - - -
386O ASP* 5.1 2.5 + - - +
387O ILE* 4.6 5.5 - - - +
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Residues in contact with LEU 384 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407L GLN* 5.4 8.7 - - - +
380O THR* 3.3 22.9 + - + +
381O TYR 3.4 6.3 + - - +
382O LYS 3.1 0.4 - - - -
383O SER* 1.3 86.1 - - - +
385O GLN* 1.3 65.5 + - - +
386O ASP 3.3 2.9 - - - -
387O ILE* 3.9 21.5 - - + -
388O ILE* 3.0 38.0 + - + +
396O LEU* 3.8 26.9 - - + -
400O ASP* 4.4 23.1 - - + +
404O VAL* 4.2 9.9 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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