Contacts of the helix formed by residues 365 - 383 (chain C) in PDB entry 5KX8
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 THR 365 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C ILE* 3.6 14.9 - - - +
342C TPO 3.7 19.0 + - - +
358C GLU* 4.0 19.1 - - + +
363C GLU* 4.2 12.5 + - + +
364C ILE* 1.3 77.3 - - - +
366C PRO* 1.4 75.9 - - - +
367C LYS* 3.1 26.3 + - + +
368C SER* 3.1 40.6 + - - +
441C LYS* 5.0 3.8 - - + -
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Residues in contact with PRO 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C HIS* 3.5 35.5 - - + +
308C ILE* 3.8 30.0 - - + -
336C SER* 5.4 8.5 - - - +
365C THR* 1.4 87.7 - - - +
367C LYS* 1.3 64.6 + - + +
368C SER 3.1 0.2 - - - -
369C ASP* 3.1 19.9 + - - +
370C ILE* 3.6 5.0 + - - +
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Residues in contact with LYS 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C TPO 2.7 25.4 + - - +
365C THR* 3.1 14.3 - - + +
366C PRO* 1.3 83.6 - - + +
368C SER* 1.3 60.5 + - - +
370C ILE* 3.4 14.1 + - - +
371C TYR 3.4 11.1 + - - -
441C LYS* 3.6 45.3 - - + +
442C ASN* 2.7 29.1 + - - +
444C ARG* 2.9 21.6 + - + +
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Residues in contact with SER 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C ILE* 5.8 0.7 - - - -
356C ALA* 4.0 6.0 + - - +
358C GLU* 3.1 16.3 + - - +
359C ALA* 3.7 27.8 - - - +
363C GLU 4.7 1.1 + - - -
365C THR* 3.1 25.9 + - - +
367C LYS* 1.3 76.8 - - - +
369C ASP* 1.4 65.6 + - - +
371C TYR* 3.2 5.0 + - - +
372C SER* 3.1 25.2 + - - -
444C ARG* 3.9 7.6 - - - +
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Residues in contact with ASP 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ILE* 4.6 6.2 - - + +
303C HIS* 3.0 27.8 + - + +
308C ILE* 3.6 12.0 - - - +
309C HIS* 2.8 32.2 + - - +
310C ARG* 3.0 26.3 + - - -
312C ILE* 4.1 18.3 + - + +
366C PRO 3.1 10.7 + - - +
368C SER* 1.4 78.5 - - - +
370C ILE* 1.4 56.8 + - - +
372C SER* 3.5 6.0 + - - -
373C PHE* 2.9 28.3 + - - +
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Residues in contact with ILE 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ILE* 5.0 0.7 - - + -
303C HIS* 4.1 11.4 - - + -
366C PRO 3.7 11.7 - - - +
367C LYS* 3.5 13.5 - - + +
368C SER 3.2 0.6 - - - -
369C ASP* 1.4 74.8 - - - +
371C TYR* 1.3 66.1 + - - +
373C PHE* 3.1 8.0 + - + +
374C GLY 3.0 17.2 + - - -
436C CYS* 3.4 36.5 - - - +
444C ARG* 4.3 4.9 - - + -
445C PRO* 3.4 26.5 - - + +
446C ASP* 4.1 2.0 - - - -
447C ILE* 3.6 49.8 - - + +
450C VAL* 4.3 3.6 - - + -
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Residues in contact with TYR 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C TYR 3.8 4.3 - - - -
355C MET 3.6 18.2 - - - -
356C ALA* 3.4 21.1 - - + -
357C PRO* 4.1 15.9 - - + +
367C LYS 3.4 2.2 + - - -
368C SER 3.2 10.6 + - - +
370C ILE* 1.3 79.0 - - - +
372C SER* 1.3 56.7 + - - +
374C GLY* 2.9 18.7 + - - -
375C VAL* 3.3 8.7 + - + +
397C LEU* 3.3 39.3 - - + +
436C CYS 3.4 9.6 + - - -
437C LEU* 3.4 46.6 + - + +
438C HIS 4.1 4.0 - - - -
439C GLU* 4.8 7.2 - - + +
444C ARG* 3.6 31.9 - - - +
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Residues in contact with SER 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C ASP* 6.0 0.3 - - - -
312C ILE* 3.5 31.5 + - - -
354C TYR* 2.7 30.9 + - - +
355C MET* 4.2 4.9 - - - +
356C ALA 4.7 0.2 + - - -
368C SER 3.1 11.1 + - - -
369C ASP* 3.6 10.2 - - - -
371C TYR* 1.3 77.7 - - - +
373C PHE* 1.3 63.0 + - - +
375C VAL* 3.1 15.5 + - - +
376C VAL* 3.1 15.2 + - - +
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Residues in contact with PHE 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C ALA* 3.5 22.7 - - - -
295C ALA* 3.6 24.0 - - + -
296C ALA* 3.9 9.4 - - + -
299C ILE* 3.5 26.2 - - + -
312C ILE* 3.8 8.2 - - + +
317C ILE* 5.4 0.9 - - + -
369C ASP 2.9 17.6 + - - +
370C ILE* 3.1 8.2 + - - +
372C SER* 1.3 75.7 - - - +
374C GLY* 1.4 55.5 + - - +
376C VAL* 3.2 17.0 + - + +
377C LEU* 2.9 56.9 + - + +
436C CYS* 4.6 4.7 - - - -
447C ILE* 4.8 3.8 - - + -
450C VAL* 3.6 32.5 - - + -
454C LEU* 4.0 3.6 - - + -
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Residues in contact with GLY 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C ILE 3.0 6.5 + - - -
371C TYR 2.9 10.8 + - - -
373C PHE* 1.4 71.5 - - - +
375C VAL* 1.3 64.0 + - - +
377C LEU* 3.2 5.4 + - - +
378C LEU* 3.1 25.6 + - - +
433C ALA* 3.8 9.4 - - - +
436C CYS* 3.6 22.2 - - - +
437C LEU* 4.1 12.3 - - - -
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Residues in contact with VAL 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C ALA 3.9 10.5 - - - +
354C TYR* 3.7 32.3 - - + +
371C TYR* 3.3 7.7 + - + +
372C SER 3.1 7.9 + - - +
374C GLY* 1.3 73.2 - - - +
376C VAL* 1.3 62.1 + - - +
378C LEU* 3.1 10.3 + - + +
379C GLU* 3.0 22.4 + - + +
386C ALA* 3.7 23.6 - - + -
396C LEU* 4.9 8.7 - - + -
397C LEU* 3.4 34.3 - - + +
437C LEU* 3.7 9.2 - - + -
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Residues in contact with VAL 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C LEU* 4.1 16.6 - - + -
295C ALA* 5.7 0.7 - - + -
312C ILE* 4.3 4.7 - - + -
313C LYS* 3.7 16.6 - - - +
314C SER 3.6 24.5 - - - +
317C ILE* 3.7 24.0 - - + -
354C TYR* 4.1 2.2 - - + -
372C SER 3.1 12.7 + - - +
373C PHE* 3.2 20.8 + - + +
375C VAL* 1.3 75.4 - - - +
377C LEU* 1.4 57.1 + - - +
379C GLU* 3.0 16.0 + - - +
380C ILE* 2.9 34.4 + - + +
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Residues in contact with LEU 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C ALA* 3.8 28.9 - - + -
373C PHE* 2.9 47.3 + - + +
374C GLY* 3.2 8.9 + - - +
376C VAL* 1.4 72.3 - - - +
378C LEU* 1.3 57.8 + - - +
380C ILE* 3.3 9.3 + - + +
381C ILE* 3.0 34.4 + - - +
429C MET* 4.2 18.1 - - + +
432C VAL* 3.6 32.8 - - + -
433C ALA* 3.8 21.5 - - + +
436C CYS* 4.8 0.9 - - - -
454C LEU* 4.5 5.6 - - + -
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Residues in contact with LEU 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C GLY 3.1 16.2 + - - +
375C VAL* 3.1 9.8 + - - +
377C LEU* 1.3 72.7 - - - +
379C GLU* 1.3 60.2 + - - +
381C ILE* 4.4 7.2 - - + +
382C THR* 2.9 36.5 + - + +
396C LEU* 3.8 38.8 - - + +
397C LEU* 4.5 5.6 - - - +
399C ILE* 4.1 16.6 - - + -
400C LYS* 5.2 2.9 - - + +
410C ILE* 5.6 0.7 - - + -
430C TYR* 3.7 35.4 - - + -
433C ALA* 3.8 13.0 - - + -
437C LEU* 3.5 24.5 - - + -
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Residues in contact with GLU 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C LEU* 3.7 9.4 - - - +
274C LEU* 3.7 17.6 - - + +
314C SER* 3.0 24.7 + - - -
354C TYR* 2.9 43.3 + - - -
375C VAL 3.0 12.5 + - - +
376C VAL* 3.2 14.7 - - - +
378C LEU* 1.3 77.2 - - - +
380C ILE* 1.4 55.9 + - - +
382C THR* 4.0 0.2 - - - -
383C GLY* 2.7 34.5 + - - -
384C LEU 3.4 21.1 - - - +
385C PRO* 3.9 3.5 - - - +
386C ALA* 3.6 13.5 + - + +
396C LEU* 3.8 7.9 - - + -
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Residues in contact with ILE 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C LEU* 4.0 31.9 - - + -
274C LEU* 4.1 10.3 - - + -
285C TRP* 4.5 1.9 - - + -
288C ARG* 2.8 63.7 + - + +
291C ILE* 4.4 5.4 - - + -
292C ALA* 4.2 31.0 - - + +
376C VAL* 2.9 24.7 + - + +
377C LEU* 3.5 13.7 - - + +
379C GLU* 1.4 75.0 - - - +
381C ILE* 1.3 59.2 + - - +
429C MET* 3.8 17.9 - - - -
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Residues in contact with ILE 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C TRP* 4.3 13.9 - - + -
377C LEU 3.0 24.8 + - - +
378C LEU* 3.9 13.9 - - + +
379C GLU 3.4 0.2 - - - -
380C ILE* 1.3 77.9 - - - +
382C THR* 1.3 63.6 + - + +
410C ILE* 3.8 23.1 - - + -
414C ILE* 3.6 7.2 - - - -
415C ASP* 2.8 25.3 + - - +
418C MET* 4.0 5.4 - - - +
426C VAL* 3.9 17.5 - - + +
429C MET* 3.8 22.2 - - + +
430C TYR* 3.7 38.6 - - + +
433C ALA* 4.9 0.7 - - + -
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Residues in contact with THR 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C LEU* 2.9 24.4 + - + +
381C ILE* 1.3 84.0 - - + +
383C GLY* 1.3 61.0 + - - +
384C LEU* 3.0 41.5 + - + +
396C LEU* 3.9 3.7 - - + +
399C ILE* 3.8 28.7 - - + -
410C ILE* 5.6 0.7 - - + -
413C TYR* 3.3 31.1 - - + +
415C ASP* 3.6 18.2 - - - +
417C LYS* 5.3 0.3 + - - -
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Residues in contact with GLY 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C LEU* 4.0 27.2 - - - +
275C SER* 5.2 2.4 - - - -
288C ARG* 4.4 2.9 - - - -
379C GLU 2.7 22.6 + - - -
380C ILE 4.1 0.6 + - - -
381C ILE 3.7 1.8 - - - -
382C THR* 1.3 70.5 - - - +
384C LEU* 1.4 59.8 + - - +
385C PRO* 4.1 3.1 - - - +
415C ASP* 3.5 19.8 + - - -
417C LYS* 4.8 6.3 + - - -
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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