Contacts of the helix formed by residues 364 - 383 (chain X) 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 X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359X ASP 3.8 0.5 + - - +
360X ALA* 3.4 16.8 + - - -
361X ALA 4.9 0.4 - - - -
362X VAL 3.5 2.8 - - - -
363X VAL* 1.3 81.7 - - - +
365X GLN* 1.3 66.4 + - - -
366X GLU* 3.1 4.0 - - - -
367X HIS 3.5 0.8 + - - -
368X TYR* 3.2 23.7 + - - +
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Residues in contact with GLN 365 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433U ASN* 5.9 0.5 + - - -
360X ALA* 3.2 36.3 + - - +
364X GLY* 1.3 71.0 - - - -
366X GLU* 1.3 56.3 + - - +
368X TYR* 4.0 8.7 - - - -
369X ASP* 2.9 58.4 + - - +
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Residues in contact with GLU 366 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364X GLY* 3.1 1.3 - - - -
365X GLN* 1.3 77.6 - - - +
367X HIS* 1.3 66.3 + - - +
369X ASP* 3.2 5.2 + - - +
370X VAL* 3.0 32.0 + - + +
438X VAL* 5.0 10.3 - - + +
442X LYS* 2.8 44.4 + - + +
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Residues in contact with HIS 367 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142X ASP 3.3 20.2 + - - -
143X LEU* 3.0 28.5 + - + -
146X PRO* 4.7 1.2 - - - +
358X LEU* 4.0 9.7 - - + +
363X VAL* 3.0 49.8 + - + +
364X GLY* 3.5 2.5 + - - +
366X GLU* 1.3 79.3 - - - +
368X TYR* 1.3 58.0 + - - +
370X VAL* 3.3 2.5 + - - +
371X ALA* 2.9 24.7 + - + +
434X LEU* 3.7 18.4 - - + +
438X VAL* 3.3 43.1 - - + +
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Residues in contact with TYR 368 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364U ARG* 3.9 28.6 + - - -
433U ASN* 5.3 10.4 + - - -
434U GLN* 5.8 0.3 + - - -
354X LYS* 6.4 0.4 - - - -
358X LEU* 3.9 37.9 - - + -
359X ASP* 4.2 15.5 - - - -
360X ALA* 4.1 19.1 - - + +
363X VAL* 5.0 0.2 - - + -
364X GLY 3.2 16.0 + - - +
365X GLN* 4.2 18.2 - - - +
367X HIS* 1.3 78.8 - - - +
369X ASP* 1.3 66.0 + - - +
371X ALA* 4.0 0.3 - - - +
372X SER* 2.9 53.0 + - - -
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Residues in contact with ASP 369 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365X GLN* 2.9 49.1 + - - +
366X GLU* 3.2 5.3 + - - +
368X TYR* 1.3 82.6 - - - +
370X VAL* 1.3 61.4 + - + +
372X SER* 4.2 3.9 - - - -
373X LYS* 3.0 41.2 + - - +
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Residues in contact with VAL 370 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143X LEU* 4.0 19.5 - - + -
366X GLU* 3.0 22.1 + - + +
367X HIS* 3.6 5.6 - - - +
369X ASP* 1.3 75.6 - - + +
371X ALA* 1.3 67.7 + - - +
372X SER 3.1 1.3 - - - -
373X LYS* 3.0 10.2 + - - +
374X VAL* 2.9 24.6 + - + +
438X VAL* 4.5 11.0 - - + +
441X PHE* 4.3 14.4 - - + -
442X LYS* 3.9 34.1 - - + +
445X LEU* 3.8 20.1 - - + +
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Residues in contact with ALA 371 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143X LEU* 3.3 29.8 - - + +
144X LEU* 3.6 14.5 - - + +
358X LEU* 4.4 17.7 - - + -
367X HIS* 2.9 19.0 + - + +
368X TYR 4.1 2.9 - - - +
370X VAL* 1.3 80.2 - - - +
372X SER* 1.3 56.7 + - - +
374X VAL* 3.5 3.6 + - - +
375X GLN* 3.1 34.0 + - - +
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Residues in contact with SER 372 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360U TYR 4.8 0.2 - - - +
364U ARG* 4.1 20.1 + - - +
358X LEU* 5.8 1.0 - - - +
368X TYR* 2.9 47.9 + - - -
369X ASP* 4.2 5.8 - - - -
371X ALA* 1.3 76.6 - - - +
373X LYS* 1.3 59.6 + - - +
375X GLN* 3.3 10.6 + - - +
376X GLU* 2.9 38.7 + - - +
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Residues in contact with LYS 373 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369X ASP* 3.0 31.4 + - - +
370X VAL* 3.0 11.4 + - - +
372X SER* 1.3 76.7 - - - +
374X VAL* 1.3 60.2 + - - +
376X GLU* 3.4 20.8 + - - +
377X THR* 2.9 32.4 + - - -
442X LYS* 6.2 1.8 - - - +
445X LEU* 4.2 24.6 - - + +
446X GLU* 6.1 3.0 - - - +
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Residues in contact with VAL 374 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143X LEU* 4.5 9.2 - - + -
144X LEU* 4.3 15.7 - - + -
370X VAL* 2.9 26.1 + - + +
371X ALA* 3.6 8.3 - - - +
373X LYS* 1.3 77.4 - - - +
375X GLN* 1.3 58.3 + - - +
377X THR* 3.4 3.3 + - - -
378X LEU* 3.1 45.3 + - + +
410X ILE* 4.1 16.1 - - + +
414X LEU* 5.3 2.2 - - + -
441X PHE* 4.4 18.2 - - + -
445X LEU* 3.6 26.0 - - + -
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Residues in contact with GLN 375 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359U PHE* 5.2 1.7 - - - -
360U TYR* 3.3 41.0 - - + +
364U ARG* 4.1 17.9 + - - +
144X LEU* 3.9 27.3 + - + +
350X PRO 3.7 18.3 + - - +
351X LEU* 3.4 18.2 - - + +
353X SER 4.1 10.5 + - - -
354X LYS* 5.0 5.4 + - - +
358X LEU* 5.5 6.8 - - - +
371X ALA* 3.1 18.9 + - - +
372X SER* 3.3 7.8 + - - +
374X VAL* 1.3 75.5 - - + +
376X GLU* 1.3 64.6 - - - +
378X LEU* 4.7 0.9 - - + -
379X GLN* 3.2 21.5 + - - +
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Residues in contact with GLU 376 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360U TYR 3.4 7.4 - - - +
361U LYS* 3.9 9.0 - - - +
362U GLY* 3.3 34.2 - - - +
364U ARG* 5.9 1.5 + - - +
428U GLN* 5.4 0.7 + - - -
431U LYS* 3.8 12.3 + - - -
372X SER* 2.9 24.4 + - - +
373X LYS* 3.4 32.3 + - - +
374X VAL 3.3 0.2 - - - -
375X GLN* 1.3 77.6 - - - +
377X THR* 1.3 58.2 + - - +
379X GLN* 4.2 1.4 - - - +
380X THR* 3.0 26.9 + - - -
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Residues in contact with THR 377 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373X LYS 2.9 18.0 + - - -
374X VAL 3.9 4.5 - - - -
375X GLN 3.3 0.2 - - - -
376X GLU* 1.3 77.6 - - - +
378X LEU* 1.3 64.2 + - + +
380X THR* 3.2 7.6 + - - -
381X TYR* 3.2 19.2 + - - +
403X THR* 3.6 37.4 - - + +
406X ARG* 4.9 5.1 - - + -
407X ALA* 3.8 16.0 - - + +
410X ILE* 4.3 13.9 - - + -
445X LEU* 4.2 9.8 - - + +
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Residues in contact with LEU 378 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144X LEU* 5.5 0.4 - - + -
350X PRO* 3.6 30.1 - - + -
351X LEU* 3.7 20.5 - - + +
374X VAL* 3.1 33.9 + - + +
375X GLN* 5.0 0.4 - - - -
377X THR* 1.3 80.1 - - - +
379X GLN* 1.3 58.0 + - - +
381X TYR* 3.2 13.7 + - + +
382X LYS* 2.9 26.2 + - - +
407X ALA* 3.9 11.9 - - + +
410X ILE* 4.3 7.2 - - + -
411X GLN* 3.7 40.8 - - + +
414X LEU* 4.0 11.0 - - + -
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Residues in contact with GLN 379 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357U GLU* 3.7 36.8 + - + +
360U TYR* 3.6 26.0 - - + +
361U LYS* 4.0 23.6 - - + +
351X LEU* 3.6 19.2 - - + +
375X GLN 3.2 18.8 + - - +
376X GLU 4.2 2.7 - - - +
378X LEU* 1.3 74.9 - - - +
380X THR* 1.3 56.2 + - - +
382X LYS* 3.0 33.2 + - - +
383X SER* 2.7 38.7 + - - +
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Residues in contact with THR 380 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361U LYS* 5.2 9.5 - - - +
376X GLU 3.0 15.8 + - - -
377X THR 3.2 10.2 + - - -
379X GLN* 1.3 78.5 - - - +
381X TYR* 1.3 60.3 + - - +
383X SER* 3.4 6.4 + - - +
384X LEU* 3.4 38.3 + - + +
400X ASP* 5.6 4.7 - - - +
403X THR* 4.3 23.1 - - + +
404X VAL* 6.2 0.7 - - + -
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Residues in contact with TYR 381 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377X THR 3.2 4.6 + - - +
378X LEU* 3.5 13.0 - - + +
379X GLN 3.2 0.6 - - - -
380X THR* 1.3 76.5 - - - +
382X LYS* 1.3 62.7 + - - +
384X LEU* 3.5 6.9 + - + -
385X GLN* 3.4 50.3 + - - -
388X ILE* 5.6 10.5 - - + +
393X MET* 5.7 2.7 - - + +
403X THR* 5.8 0.4 - - + +
404X VAL* 3.5 41.1 - - + -
407X ALA* 3.7 26.5 - - + -
408X ARG* 3.5 33.9 + - + -
411X GLN* 3.5 27.9 + - - -
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Residues in contact with LYS 382 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357U GLU* 6.2 1.2 - - - +
360U TYR* 6.2 0.4 - - - -
349X ASP* 5.9 0.8 + - - -
351X LEU* 3.7 27.9 + - + +
378X LEU 2.9 12.1 + - - +
379X GLN* 3.3 33.4 + - - +
381X TYR* 1.3 78.6 - - - +
383X SER* 1.3 55.7 + - - +
384X LEU 3.2 3.6 + - - -
385X GLN* 3.4 27.0 - - + +
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Residues in contact with SER 383 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357U GLU* 3.9 18.5 + - - -
361U LYS* 6.1 4.0 - - - -
379X GLN* 2.7 21.5 + - - +
380X THR* 3.4 9.6 + - - -
381X TYR 3.2 0.4 - - - -
382X LYS* 1.3 76.0 - - - +
384X LEU* 1.3 65.4 + - - +
385X GLN 3.7 0.4 - - - -
387X ILE* 5.0 3.8 - - - +
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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