Contacts of the helix formed by residues 364 - 384 (chain V) 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 V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359V ASP 3.2 14.9 - - - +
360V ALA* 3.1 16.6 + - - -
361V ALA 4.3 1.5 - - - -
363V VAL* 1.3 82.1 - - - +
365V GLN* 1.3 64.8 + - - -
366V GLU 3.5 2.2 - - - -
367V HIS* 4.1 5.6 - - - -
368V TYR* 3.2 12.6 + - - +
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Residues in contact with GLN 365 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360V ALA* 3.0 33.5 + - + +
364V GLY* 1.3 69.3 - - - -
366V GLU* 1.3 69.7 + - - +
368V TYR* 3.2 10.1 - - - +
369V ASP* 2.8 51.0 + - - +
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Residues in contact with GLU 366 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364V GLY* 4.5 0.4 - - - -
365V GLN* 1.3 80.0 - - - +
367V HIS* 1.3 61.5 + - - +
369V ASP* 3.0 11.0 + - - +
370V VAL* 2.9 41.5 + - + +
438V VAL* 5.3 7.9 - - + -
442V LYS* 4.8 16.8 + - + +
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Residues in contact with HIS 367 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142V ASP 4.7 3.7 + - - -
143V LEU* 3.1 53.4 - - + +
146V PRO* 5.1 5.8 - - + -
358V LEU* 5.5 3.3 - - + +
363V VAL* 4.1 29.1 - - + +
364V GLY* 3.8 10.3 + - - +
365V GLN 3.4 0.4 - - - -
366V GLU* 1.3 77.8 - - - +
368V TYR* 1.3 62.2 + - - +
370V VAL* 3.8 6.5 - - - +
371V ALA* 3.4 22.4 + - + +
434V LEU* 5.0 15.6 + - + +
437V THR* 6.1 0.2 - - - -
438V VAL* 3.5 37.7 - - + +
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Residues in contact with TYR 368 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364S ARG* 2.7 38.7 + - - -
358V LEU* 3.1 46.1 - - + +
359V ASP* 3.2 24.2 - - - +
360V ALA* 4.8 3.4 - - + -
363V VAL* 5.6 0.2 - - - -
364V GLY 3.2 16.4 + - - +
365V GLN* 3.2 17.0 - - - +
366V GLU 3.1 0.2 - - - -
367V HIS* 1.3 80.9 + - - +
369V ASP* 1.3 70.2 + - - +
371V ALA* 3.8 2.3 + - - +
372V SER* 2.8 49.3 + - - -
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Residues in contact with ASP 369 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365V GLN* 2.8 41.6 + - - +
366V GLU* 3.0 13.5 + - - +
368V TYR* 1.3 91.7 - - - +
370V VAL* 1.3 61.1 + - - +
372V SER* 3.8 8.1 - - - -
373V LYS* 3.2 26.9 + - - +
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Residues in contact with VAL 370 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143V LEU* 4.4 17.0 - - + -
366V GLU* 2.9 28.2 + - + +
367V HIS* 3.8 7.0 - - - +
368V TYR 3.3 0.4 - - - -
369V ASP* 1.3 77.0 - - - +
371V ALA* 1.3 62.1 + - - +
373V LYS* 3.7 5.2 + - - +
374V VAL* 3.1 23.7 + - - +
437V THR 4.6 3.6 - - - +
438V VAL* 4.0 29.2 - - + +
441V PHE* 4.1 23.6 - - + -
442V LYS* 4.4 17.0 - - + +
445V LEU* 4.2 4.3 - - + +
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Residues in contact with ALA 371 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143V LEU* 3.6 34.8 - - + +
144V LEU* 3.7 21.4 - - + +
358V LEU* 4.7 9.9 - - + -
367V HIS* 3.4 11.5 + - + +
368V TYR 4.3 2.9 - - - +
370V VAL* 1.3 76.9 - - - +
372V SER* 1.3 61.2 + - - +
373V LYS 3.4 0.2 - - - -
374V VAL* 3.3 6.8 - - - +
375V GLN* 3.1 32.0 + - - +
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Residues in contact with SER 372 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360S TYR 5.1 0.2 - - - +
364S ARG* 4.0 15.4 + - - -
358V LEU* 4.8 3.5 - - - +
368V TYR* 2.8 43.6 + - - -
369V ASP* 4.1 9.4 - - - -
370V VAL 3.3 0.2 - - - -
371V ALA* 1.3 74.6 - - - +
373V LYS* 1.3 59.3 + - - +
374V VAL 3.1 1.3 - - - -
375V GLN* 3.1 15.4 + - - +
376V GLU* 2.9 41.0 + - - +
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Residues in contact with LYS 373 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369V ASP 3.2 19.9 + - - +
370V VAL* 4.0 1.3 - - - +
371V ALA 3.4 0.2 - - - -
372V SER* 1.3 75.8 - - - +
374V VAL* 1.3 57.8 + - - +
376V GLU* 3.2 23.8 + - + +
377V THR* 2.8 36.4 + - - +
445V LEU* 3.7 36.8 - - + -
446V GLU* 6.6 0.7 - - - -
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Residues in contact with VAL 374 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143V LEU* 4.8 7.0 - - + -
144V LEU* 5.2 9.9 - - + -
350V PRO* 5.5 3.6 - - + -
370V VAL 3.1 17.5 - - - +
371V ALA* 3.3 12.3 - - - +
372V SER 3.1 0.4 - - - -
373V LYS* 1.3 78.0 - - - +
375V GLN* 1.3 62.4 + - - +
377V THR* 3.5 3.7 + - - -
378V LEU* 3.2 39.3 + - + +
410V ILE* 3.5 34.5 - - + -
441V PHE* 4.1 18.8 - - + -
445V LEU* 4.3 10.8 - - + -
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Residues in contact with GLN 375 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360S TYR* 3.6 30.3 - - + +
364S ARG* 3.8 18.9 + - - -
144V LEU* 3.4 19.8 - - + +
350V PRO* 6.5 0.7 - - + -
351V LEU* 5.3 6.1 - - + +
354V LYS* 3.0 37.5 - - - +
358V LEU* 3.8 22.8 - - - +
371V ALA 3.1 15.5 + - - +
372V SER* 3.1 13.1 + - - +
374V VAL* 1.3 77.2 - - + +
376V GLU* 1.3 60.3 + - - +
378V LEU* 4.4 4.2 - - - +
379V GLN* 3.4 26.5 + - - +
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Residues in contact with GLU 376 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360S TYR 4.7 1.3 - - - +
361S LYS* 3.3 31.5 - - + +
362S GLY* 4.7 7.5 - - - -
431S LYS* 4.8 7.0 + - - -
372V SER* 2.9 27.1 + - - +
373V LYS* 3.2 36.4 + - + +
374V VAL 3.2 0.4 - - - -
375V GLN* 1.3 77.4 - - - +
377V THR* 1.3 60.4 + - - +
378V LEU 3.4 0.2 - - - -
379V GLN* 4.7 1.1 - - - +
380V THR* 3.0 26.5 + - - -
403V THR* 5.8 0.2 - - - +
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Residues in contact with THR 377 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373V LYS* 2.8 25.3 + - - +
374V VAL* 4.1 3.8 - - - -
376V GLU* 1.3 77.6 - - - +
378V LEU* 1.3 63.6 + - - +
380V THR* 4.0 4.8 + - - -
381V TYR 3.8 7.4 + - - -
403V THR* 4.1 20.1 - - + +
406V ARG* 3.7 17.4 - - + +
407V ALA* 3.0 49.6 - - + +
410V ILE* 5.0 2.7 - - + -
445V LEU* 3.6 16.4 - - + +
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Residues in contact with LEU 378 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350V PRO* 4.1 28.9 - - + -
351V LEU* 5.8 10.5 - - + +
374V VAL* 3.2 40.1 + - + +
375V GLN* 4.4 5.2 - - - +
377V THR* 1.3 79.3 - - - +
379V GLN* 1.3 62.3 + - - +
380V THR 3.4 0.2 - - - -
381V TYR* 3.4 6.8 + - + +
382V LYS* 3.3 22.5 + - - +
407V ALA* 3.1 31.2 - - + +
410V ILE* 4.7 6.5 - - + -
411V GLN* 3.5 32.8 - - + +
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Residues in contact with GLN 379 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357S GLU* 2.9 46.7 + - + +
360S TYR* 4.2 8.2 - - + +
361S LYS* 4.2 28.7 - - + +
351V LEU* 3.3 33.5 - - + +
375V GLN 3.4 18.2 + - - +
376V GLU 4.7 2.0 - - - +
377V THR 3.5 0.2 - - - -
378V LEU* 1.3 75.1 - - - +
380V THR* 1.3 64.7 + - - +
381V TYR 3.1 1.8 - - - -
382V LYS* 4.4 16.3 - - - +
383V SER* 3.2 32.7 + - - +
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Residues in contact with THR 380 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361S LYS* 5.4 9.8 - - - +
407S GLN* 5.3 0.2 - - - +
376V GLU 3.0 19.3 + - - -
377V THR* 4.2 6.0 - - - -
378V LEU 3.4 0.4 - - - -
379V GLN* 1.3 78.1 - - - +
381V TYR* 1.3 61.0 + - - +
383V SER* 4.9 1.6 - - - -
384V LEU* 3.3 44.9 + - + +
400V ASP* 4.2 17.0 - - - +
403V THR* 4.8 15.2 - - + +
404V VAL* 6.1 0.6 - - + +
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Residues in contact with TYR 381 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377V THR 3.8 0.6 + - - -
378V LEU* 3.4 12.9 + - + +
379V GLN 3.1 0.2 - - - -
380V THR* 1.3 79.9 - - - +
382V LYS* 1.3 62.2 + - + +
384V LEU 3.5 2.9 - - - +
385V GLN* 3.1 59.6 + - + +
388V ILE* 5.7 9.8 - - + +
404V VAL* 3.2 44.9 - - + -
407V ALA* 3.6 26.2 - - + +
408V ARG* 3.2 47.4 + - + -
411V GLN* 5.3 10.3 - - - -
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Residues in contact with LYS 382 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339V ILE* 5.9 5.1 - - - +
349V ASP* 5.5 5.3 + - - -
351V LEU* 4.5 24.4 - - + +
378V LEU 3.3 12.1 + - - +
379V GLN* 4.3 13.5 - - - +
380V THR 3.5 0.2 - - - -
381V TYR* 1.3 82.1 - - + +
383V SER* 1.3 62.8 + - - +
385V GLN* 3.9 23.3 + - - +
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Residues in contact with SER 383 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357S GLU* 5.4 2.2 - - - -
361S LYS* 4.9 13.0 + - - -
379V GLN* 3.2 27.3 + - - +
380V THR* 4.5 1.6 - - - -
382V LYS* 1.3 78.4 - - - +
384V LEU* 1.3 73.2 + - - +
385V GLN 3.5 1.7 + - - -
386V ASP* 5.0 2.9 + - - +
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Residues in contact with LEU 384 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403S ALA 5.0 0.4 - - - +
404S ALA* 3.8 23.1 - - + -
407S GLN* 3.1 50.9 - - + +
380V THR* 3.3 38.5 + - + +
381V TYR* 3.5 5.8 - - - +
383V SER* 1.3 89.3 - - - +
385V GLN* 1.3 57.3 + - - +
386V ASP 3.6 1.6 - - - +
387V ILE* 3.7 27.3 - - + +
388V ILE* 3.5 18.9 - - - +
396V LEU* 6.0 0.5 - - - +
400V ASP* 4.0 1.6 - - - +
404V VAL* 5.6 3.1 - - - +
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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