Contacts of the helix formed by residues 365 - 383 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308A ILE* 3.6 16.1 - - - +
342A TPO 3.7 26.0 + - + +
358A GLU* 4.0 19.7 - - + +
363A GLU* 4.2 4.2 + - + +
364A ILE* 1.3 79.2 - - - +
366A PRO* 1.4 76.3 - - - +
367A LYS* 3.1 26.1 + - + +
368A SER* 3.1 39.6 + - - +
441A LYS* 4.9 3.8 - - + -
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Residues in contact with PRO 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A HIS* 3.5 35.0 - - + +
307A HIS 5.3 0.2 - - - +
308A ILE* 3.8 30.5 - - + -
336A SER* 4.7 8.7 - - - +
365A THR* 1.4 88.3 - - - +
367A LYS* 1.3 65.2 + - + +
369A ASP* 3.1 19.4 + - - +
370A ILE* 3.6 5.4 + - - +
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Residues in contact with LYS 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A TPO 2.7 25.0 + - - +
365A THR* 3.1 15.6 - - + +
366A PRO* 1.3 83.4 - - + +
368A SER* 1.3 59.3 + - - +
370A ILE* 3.4 14.4 + - + +
371A TYR 3.4 10.9 + - - -
441A LYS* 3.6 45.9 - - + +
442A ASN* 2.7 29.6 + - - +
444A ARG* 2.9 20.0 + - + +
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Residues in contact with SER 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ILE* 5.8 0.7 - - - -
310A ARG* 6.6 0.2 - - - -
356A ALA* 4.0 5.2 + - - +
358A GLU* 3.1 19.2 + - - +
359A ALA* 3.7 25.7 - - - +
363A GLU 4.6 1.1 + - - -
365A THR* 3.1 25.3 + - - +
367A LYS* 1.3 76.6 - - - +
369A ASP* 1.4 66.6 + - - +
371A TYR* 3.2 4.7 + - - +
372A SER* 3.1 25.1 + - - -
444A ARG* 3.9 7.8 - - - +
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Residues in contact with ASP 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A ILE* 4.6 6.2 - - + +
303A HIS* 3.0 27.2 + - + +
308A ILE* 3.6 12.4 - - - +
309A HIS* 2.8 34.1 + - - +
310A ARG* 3.0 26.3 + - - -
311A ASP 4.6 0.2 + - - -
312A ILE* 4.1 17.8 - - + +
365A THR 4.1 0.2 + - - -
366A PRO 3.1 10.3 + - - +
368A SER* 1.4 77.7 - - - +
370A ILE* 1.3 58.1 + - - +
372A SER* 3.5 5.6 + - - -
373A PHE* 2.9 28.8 + - - +
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Residues in contact with ILE 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ILE* 5.0 0.7 - - + -
303A HIS* 4.1 11.0 - - + -
366A PRO 3.7 12.1 - - - +
367A LYS* 3.5 13.2 - - + +
368A SER 3.2 0.2 - - - -
369A ASP* 1.3 74.1 - - - +
371A TYR* 1.3 65.1 + - - +
373A PHE* 3.1 7.7 + - + +
374A GLY 3.0 17.3 + - - -
436A CYS* 3.4 36.3 - - - +
444A ARG* 4.3 5.4 - - + -
445A PRO* 3.4 26.2 - - + +
446A ASP* 4.1 1.6 - - - -
447A ILE* 3.6 50.3 - - + +
450A VAL* 4.3 3.1 - - + -
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Residues in contact with TYR 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A TYR 3.8 5.4 - - - -
355A MET 3.6 17.0 - - - -
356A ALA* 3.4 21.1 - - + -
357A PRO* 4.0 13.0 - - + +
367A LYS 3.4 2.6 + - - -
368A SER 3.2 10.0 + - - +
370A ILE* 1.3 77.8 - - - +
372A SER* 1.3 57.3 + - - +
374A GLY* 2.9 18.4 + - - -
375A VAL* 3.3 8.5 + - + +
397A LEU* 3.7 31.7 - - + +
436A CYS 3.4 8.7 + - - -
437A LEU* 3.4 57.1 - - + +
438A HIS 3.7 3.8 - - - -
439A GLU* 3.1 22.4 + - - -
444A ARG* 3.6 33.0 - - - +
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Residues in contact with SER 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A ASP* 6.0 0.2 - - - -
312A ILE* 3.4 31.5 + - - -
354A TYR* 2.7 30.6 + - - +
355A MET* 4.2 5.5 - - - +
368A SER 3.1 11.7 + - - -
369A ASP* 3.6 9.0 - - - -
371A TYR* 1.3 76.7 - - - +
373A PHE* 1.3 63.8 + - - +
375A VAL* 3.1 15.5 + - - +
376A VAL* 3.1 15.6 + - - +
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Residues in contact with PHE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A ALA* 3.6 22.2 - - - -
295A ALA* 3.6 23.8 - - + -
296A ALA* 3.9 9.0 - - + -
299A ILE* 3.5 26.0 - - + -
312A ILE* 3.9 9.6 - - + +
317A ILE* 5.3 1.1 - - + -
369A ASP 2.9 17.6 + - - +
370A ILE* 3.1 8.9 + - - +
372A SER* 1.3 76.5 - - - +
374A GLY* 1.4 56.2 + - - +
376A VAL* 3.2 17.9 + - + +
377A LEU* 2.9 57.1 + - + +
380A ILE* 5.9 0.4 - - + -
436A CYS* 4.6 4.3 - - - -
447A ILE* 4.8 3.8 - - + -
450A VAL* 3.6 32.1 - - + -
454A LEU* 4.0 3.8 - - + -
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Residues in contact with GLY 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A ILE 3.0 6.7 + - - -
371A TYR 2.9 11.0 + - - -
373A PHE* 1.4 72.6 - - - +
375A VAL* 1.3 62.3 + - - +
377A LEU* 3.2 5.7 + - - +
378A LEU* 3.1 25.1 + - - +
433A ALA* 3.8 9.8 - - - +
436A CYS* 3.6 21.7 - - - +
437A LEU* 4.1 11.7 - - - -
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Residues in contact with VAL 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A ALA 4.0 15.9 - - - +
354A TYR* 3.7 32.8 - - + +
371A TYR* 3.3 7.9 + - + +
372A SER 3.1 8.1 + - - +
374A GLY* 1.3 74.0 - - - +
376A VAL* 1.3 58.1 + - - +
378A LEU* 3.1 10.6 + - - +
379A GLU* 2.9 26.3 + - + +
386A ALA* 3.7 23.3 - - + -
396A LEU* 4.0 10.3 - - + +
397A LEU* 4.1 16.2 - - + +
437A LEU* 3.7 20.0 - - + -
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Residues in contact with VAL 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 4.1 15.7 - - + -
312A ILE* 4.3 7.2 - - + -
313A LYS* 3.7 16.4 - - - +
314A SER* 3.6 24.7 - - - +
317A ILE* 3.8 23.8 - - + -
354A TYR* 4.1 2.0 - - + -
372A SER 3.1 12.7 + - - +
373A PHE* 3.2 19.9 + - + +
375A VAL* 1.3 75.1 - - - +
377A LEU* 1.4 57.0 + - - +
379A GLU* 3.0 14.7 + - - +
380A ILE* 2.9 34.6 + - + +
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Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A ALA* 3.8 29.6 - - + -
373A PHE* 2.9 46.8 + - + +
374A GLY* 3.2 8.3 + - - +
376A VAL* 1.4 73.8 - - - +
378A LEU* 1.3 57.3 + - - +
380A ILE* 3.3 9.3 + - + +
381A ILE* 3.0 34.6 + - - +
429A MET* 4.1 19.0 - - + +
432A VAL* 3.6 33.2 - - + -
433A ALA* 3.9 21.1 - - + +
436A CYS* 4.8 0.7 - - - -
454A LEU* 4.5 4.5 - - + -
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Residues in contact with LEU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A GLY 3.1 15.3 + - - +
375A VAL* 3.1 9.6 + - - +
377A LEU* 1.3 72.8 - - - +
379A GLU* 1.4 60.2 + - - +
381A ILE* 3.4 6.2 + - + +
382A THR* 2.9 36.3 + - + +
396A LEU* 3.7 35.7 - - + +
397A LEU* 4.2 8.5 - - - +
399A ILE* 4.0 16.6 - - + -
400A LYS* 5.1 2.9 - - + +
410A ILE* 5.2 1.6 - - + -
430A TYR* 3.7 34.5 - - + -
433A ALA* 3.8 13.0 - - + -
437A LEU* 3.5 25.4 - - + -
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Residues in contact with GLU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LEU* 3.8 8.7 - - - +
274A LEU* 3.8 16.3 - - + +
314A SER* 3.1 26.8 + - - -
354A TYR* 2.7 40.6 + - - -
375A VAL 2.9 15.0 + - - +
376A VAL* 3.0 13.4 + - + +
378A LEU* 1.4 74.5 - - - +
380A ILE* 1.4 55.4 + - - +
383A GLY* 2.6 35.3 + - - -
384A LEU 3.5 22.4 - - - +
385A PRO* 3.9 2.9 - - - +
386A ALA* 3.4 14.9 + - - +
396A LEU* 3.6 9.4 - - + +
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Residues in contact with ILE 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A LEU* 3.8 32.5 - - + -
274A LEU* 4.1 9.4 - - + -
285A TRP* 4.5 2.8 - - + -
288A ARG* 2.8 66.1 + - + +
291A ILE* 4.4 5.2 - - + -
292A ALA* 4.2 29.6 - - + +
317A ILE* 6.0 0.2 - - + -
373A PHE* 5.9 0.2 - - + -
376A VAL* 2.9 24.4 + - + +
377A LEU* 3.5 13.7 - - + +
378A LEU 3.3 0.2 - - - -
379A GLU* 1.4 75.7 - - - +
381A ILE* 1.4 58.9 + - - +
429A MET* 3.8 17.9 - - + -
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Residues in contact with ILE 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A TRP* 4.3 14.6 - - + -
377A LEU* 3.0 26.9 + - + +
378A LEU* 3.9 13.0 - - + +
379A GLU 3.4 0.2 - - - -
380A ILE* 1.4 75.4 - - - +
382A THR* 1.3 62.3 + - + +
410A ILE* 3.9 23.8 - - + -
414A ILE* 3.6 8.4 - - + -
415A ASP* 2.8 25.6 + - - +
418A MET* 4.0 5.2 - - - +
426A VAL* 3.9 18.6 - - + +
429A MET* 3.8 23.3 - - + +
430A TYR* 3.7 38.8 - - + +
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Residues in contact with THR 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU* 2.9 22.1 + - - +
379A GLU 3.7 0.3 + - - -
381A ILE* 1.3 84.9 - - + +
383A GLY* 1.3 60.5 + - - +
384A LEU* 3.0 41.9 + - + +
396A LEU* 3.9 6.0 - - + +
399A ILE* 4.1 17.7 - - + -
410A ILE* 5.0 1.1 - - + -
413A TYR* 3.3 38.5 - - + +
415A ASP* 3.6 18.2 - - - +
417A LYS* 5.3 0.5 + - - -
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Residues in contact with GLY 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LEU* 4.0 28.9 - - - +
275A SER* 5.2 2.6 - - - -
288A ARG* 4.5 2.5 - - - -
379A GLU 2.6 22.0 + - - -
380A ILE 4.1 1.0 + - - -
381A ILE 3.7 1.2 - - - -
382A THR* 1.3 71.4 - - - +
384A LEU* 1.3 60.5 + - - +
385A PRO* 4.1 3.1 - - - +
415A ASP* 3.4 19.2 + - - -
417A LYS* 4.8 6.0 + - - -
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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
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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