Contacts of the helix formed by residues 364 - 382 (chain C) in PDB entry 1K9A
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 SER 364 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C VAL* 3.3 19.2 - - - +
339C ALA* 4.1 7.0 - - - -
356C GLU* 5.0 2.6 + - - -
363C PHE* 1.3 79.0 - - - +
365C THR* 1.3 65.5 + - - +
366C LYS* 3.3 19.3 + - - +
367C SER* 2.5 36.3 + - - -
368C ASP 3.0 6.9 + - - -
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Residues in contact with THR 365 (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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306C GLU* 3.3 53.5 - - + +
310C PHE 4.6 6.7 + - - +
311C VAL* 4.0 6.6 - - - +
339C ALA* 5.2 0.2 - - - +
364C SER* 1.3 74.9 - - - +
366C LYS* 1.3 55.5 + - + +
368C ASP* 3.0 12.7 + - - +
369C VAL* 2.7 38.6 + - + +
432C THR* 5.7 0.9 - - - -
433C PHE* 3.6 19.3 - - + -
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Residues in contact with LYS 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C GLU* 6.0 1.6 - - - -
364C SER* 3.0 12.0 + - - +
365C THR* 1.3 83.0 - - + +
367C SER* 1.3 62.2 + - - +
369C VAL* 3.2 6.7 + - + +
370C TRP 3.1 15.9 + - - -
427C ALA* 3.5 43.1 - - + +
428C ALA* 4.3 11.7 + - - +
430C ARG* 2.4 48.5 + - + +
431C PRO 3.3 18.6 + - - +
432C THR* 3.9 13.8 - - - +
435C GLN* 5.3 0.2 + - - -
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Residues in contact with SER 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C VAL* 4.6 0.2 - - - +
354C ALA* 3.7 27.5 + - - +
356C GLU* 4.3 6.5 + - - -
357C ALA* 4.2 15.5 - - - -
362C LYS 4.5 0.4 + - - -
363C PHE* 3.5 14.3 - - - +
364C SER* 2.5 42.9 + - - -
366C LYS* 1.3 73.9 - - - +
368C ASP* 1.3 60.5 + - - +
370C TRP* 3.0 14.9 + - - +
371C SER* 3.0 15.5 + - - -
430C ARG* 4.3 0.4 - - - +
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Residues in contact with ASP 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C MET* 3.9 13.1 - - + +
310C PHE 4.4 1.2 - - - +
311C VAL* 2.9 20.1 - - - +
312C HIS* 2.7 28.1 + - - +
313C ARG* 3.0 26.7 + - - -
314C ASP 4.7 0.2 + - - -
315C LEU* 4.4 7.1 - - - +
363C PHE* 5.8 0.2 - - - -
364C SER 3.0 6.0 + - - +
365C THR* 3.2 11.4 - - - +
367C SER* 1.3 74.2 - - - +
369C VAL* 1.3 60.4 + - - +
371C SER* 3.0 10.9 + - - -
372C PHE* 2.8 27.2 + - - +
433C PHE* 3.8 16.9 - - + -
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Residues in contact with VAL 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C THR* 2.7 25.8 + - + +
366C LYS* 3.5 12.6 - - + +
368C ASP* 1.3 72.4 - - - +
370C TRP* 1.3 65.3 + - - +
372C PHE* 3.0 13.8 + - - +
373C GLY 3.0 9.7 + - - -
422C CYS* 3.6 27.8 - - + -
430C ARG* 4.1 14.8 - - + -
431C PRO* 3.2 29.4 - - + +
433C PHE* 3.7 30.5 - - + +
436C LEU* 4.0 8.1 - - + -
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Residues in contact with TRP 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C LYS 5.0 1.2 + - - -
352C TRP 3.7 9.8 + - - -
353C THR 3.4 10.9 + - - -
354C ALA* 3.5 26.7 - - + -
355C PRO* 3.5 27.8 - - + -
366C LYS 3.1 9.8 + - - +
367C SER 3.0 12.7 + - - +
369C VAL* 1.3 76.2 - - - +
371C SER* 1.3 63.8 + - - +
373C GLY* 3.0 12.5 + - - -
374C ILE* 3.3 21.2 + - + +
387C TYR* 4.4 11.9 + - - -
399C VAL* 3.9 22.2 - - + -
403C TYR 5.5 1.8 - - - -
404C LYS* 4.8 1.8 - - - -
422C CYS 3.7 18.6 + - - +
423C TRP* 3.2 46.2 + + + -
424C HIS 3.7 2.5 - - - -
425C LEU* 4.4 7.0 - - + -
430C ARG* 3.0 36.6 - - - -
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Residues in contact with SER 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C ARG 5.7 3.1 - - - -
315C LEU* 3.7 33.5 + - - +
352C TRP* 2.8 27.7 + - - +
353C THR* 4.5 2.6 - - - -
367C SER 3.0 11.8 + - - -
368C ASP* 3.0 13.9 + - - -
370C TRP* 1.3 73.4 - - - +
372C PHE* 1.3 66.3 + - - +
374C ILE* 2.7 8.3 + - - +
375C LEU* 2.7 24.3 + - - +
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Residues in contact with PHE 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C SER* 3.8 9.4 - - - -
298C VAL* 3.7 22.0 - - + -
299C CYS* 3.7 40.2 - - + -
302C MET* 4.6 2.0 - - + -
315C LEU* 4.4 5.3 - - + +
368C ASP 2.8 13.0 + - - +
369C VAL* 3.0 11.2 + - - +
371C SER* 1.3 75.0 - - - +
373C GLY* 1.3 52.2 + - - +
375C LEU* 3.2 12.2 + - + +
376C LEU* 2.7 65.4 + - + +
422C CYS* 3.9 14.8 - - - -
433C PHE* 3.7 21.1 - + + -
436C LEU* 4.0 20.9 - - + -
440C LEU* 4.1 11.7 - - + -
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Residues in contact with GLY 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C VAL 3.0 10.7 + - - -
370C TRP 3.0 5.7 + - - -
372C PHE* 1.3 78.2 - - - +
374C ILE* 1.3 55.7 + - - +
376C LEU* 3.1 9.0 + - - +
377C TRP 2.9 24.3 + - - -
419C MET* 3.9 5.3 - - - +
422C CYS* 3.7 17.7 - - - -
423C TRP* 3.4 23.8 - - - -
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Residues in contact with ILE 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C LYS 3.8 16.8 - - - +
352C TRP* 3.4 33.4 - - + +
370C TRP* 3.3 23.9 + - + +
371C SER* 2.7 12.6 + - - +
373C GLY* 1.3 72.1 - - - +
375C LEU* 1.3 61.6 + - - +
377C TRP* 3.0 6.0 + - - +
378C GLU* 2.9 21.7 + - - +
386C PRO* 3.9 20.9 - - + -
387C TYR* 4.1 15.7 - - - +
405C MET* 3.4 24.0 - - + -
423C TRP* 3.3 23.3 - - + +
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Residues in contact with LEU 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C LEU* 4.6 1.8 - - + -
298C VAL* 4.4 18.6 - - + -
315C LEU* 3.2 24.2 - - + -
316C ALA* 3.2 10.3 - - - +
317C ALA* 3.0 38.4 - - + +
320C VAL* 4.1 10.5 - - + -
352C TRP* 4.7 0.6 - - - -
371C SER 2.7 14.8 + - - +
372C PHE* 3.3 13.2 - - + +
374C ILE* 1.3 72.5 - - - +
376C LEU* 1.3 59.7 + - + +
378C GLU* 3.1 15.3 + - - +
379C ILE* 2.9 53.5 + - + -
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Residues in contact with LEU 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C SER* 3.3 31.6 - - - +
372C PHE* 2.7 46.0 + - + +
373C GLY* 3.2 10.8 - - - +
375C LEU* 1.3 77.2 - - + +
377C TRP* 1.3 63.2 + - - +
379C ILE* 3.1 6.4 + - + +
380C TYR* 3.1 41.2 + - + +
415C VAL* 4.3 7.9 - - + +
418C VAL* 3.8 26.0 - - + -
419C MET* 3.8 21.1 - - + +
422C CYS* 5.3 0.2 - - - -
440C LEU* 5.0 4.9 - - + -
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Residues in contact with TRP 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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373C GLY 2.9 12.2 + - - +
374C ILE 3.0 8.3 + - - +
376C LEU* 1.3 76.0 - - - +
378C GLU* 1.3 63.4 + - + +
380C TYR* 3.3 1.2 + - - -
381C SER* 2.6 59.4 + - - -
384C ARG* 3.7 33.4 - - - -
385C VAL 3.3 31.0 - - - -
386C PRO* 3.6 10.3 - - + -
388C PRO* 3.9 13.9 - - + -
405C MET* 3.5 38.6 - - + +
406C ASP 3.0 23.8 + - - -
408C PRO* 3.2 26.5 - - + +
419C MET* 3.8 19.2 - - - -
423C TRP* 4.0 9.0 - + + -
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Residues in contact with GLU 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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275C VAL* 4.1 10.2 - - - +
278C LEU* 4.2 1.1 - - - -
279C ARG* 5.8 0.3 + - - -
317C ALA* 3.2 37.6 + - + +
318C ARG 4.7 0.2 + - - -
352C TRP* 2.5 45.0 + - - -
374C ILE 2.9 14.7 + - - +
375C LEU* 3.3 11.9 - - - +
377C TRP* 1.3 83.2 - - + +
379C ILE* 1.3 57.0 + - - +
381C SER* 3.0 3.3 + - - -
382C PHE 2.8 25.5 + - - -
383C GLY* 3.0 15.1 + - - +
384C ARG 4.2 13.7 - - - +
386C PRO* 4.0 16.6 - - + +
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Residues in contact with ILE 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C LEU* 4.0 22.9 - - + -
278C LEU* 3.7 20.5 - - + +
291C LEU* 4.0 34.1 - - + +
294C PHE* 4.2 8.1 - - + +
295C SER* 3.8 28.7 - - - +
298C VAL* 5.1 0.7 - - + -
317C ALA* 5.5 0.7 - - + -
375C LEU* 2.9 39.9 + - + +
376C LEU* 3.1 10.0 + - + +
378C GLU* 1.3 76.8 - - + +
380C TYR* 1.3 73.3 + - + +
382C PHE* 3.1 18.5 + - - -
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Residues in contact with TYR 380 (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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288C GLY* 4.3 4.4 + - - -
291C LEU* 3.9 26.2 - - + +
292C LEU* 3.3 37.3 + - + +
295C SER* 3.7 20.2 - - - -
376C LEU* 3.1 21.5 + - + +
377C TRP 3.7 2.5 - - - +
379C ILE* 1.3 86.0 - - + +
381C SER* 1.3 57.1 + - - +
382C PHE* 3.3 20.1 - - - -
408C PRO* 3.7 14.1 - - + +
409C ASP 4.3 6.1 - - - +
410C GLY 5.4 0.9 - - - -
411C CYS* 4.1 21.7 - - + +
412C PRO* 3.7 33.4 - - + -
415C VAL* 3.6 27.6 - - + +
419C MET* 4.3 4.7 - - + -
449C HIS* 4.9 3.1 - - + +
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Residues in contact with SER 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C TRP* 2.6 43.2 + - - -
378C GLU 3.0 4.7 + - - -
380C TYR* 1.3 75.7 - - - +
382C PHE* 1.3 74.7 + - - +
384C ARG* 3.6 33.2 + - - +
408C PRO* 3.1 22.1 - - - +
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Residues in contact with PHE 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C LEU* 3.4 32.6 - - + +
279C ARG* 3.6 8.5 + - - +
282C GLY* 3.7 11.2 - - - -
283C ARG* 3.3 66.6 - - + -
286C LEU* 4.2 24.7 - - + -
291C LEU* 3.9 22.0 - - + -
378C GLU 2.8 6.3 + - - -
379C ILE 3.1 9.1 + - - -
380C TYR 3.5 15.7 - - - -
381C SER* 1.3 84.1 - - - +
383C GLY* 1.3 57.6 + - - +
384C ARG 3.6 0.5 + - - -
409C ASP 5.1 1.8 - - - -
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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