Contacts of the helix formed by residues 365 - 383 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308D ILE* 3.6 15.1 - - - +
342D TPO 3.7 20.9 + - + +
358D GLU* 4.0 19.7 - - + +
363D GLU* 4.2 10.0 + - + +
364D ILE* 1.3 76.4 - - - +
366D PRO* 1.4 76.3 - - - +
367D LYS* 3.1 26.2 + - + +
368D SER* 3.1 39.7 + - - +
369D ASP 4.1 0.3 + - - -
441D LYS* 5.0 3.8 - - + -
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Residues in contact with PRO 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D HIS* 3.5 35.5 - - + +
307D HIS 5.4 0.2 - - - +
308D ILE* 3.8 30.3 - - + -
336D SER* 5.3 8.1 - - - +
365D THR* 1.4 89.0 - - - +
367D LYS* 1.3 65.9 + - + +
368D SER 3.1 0.2 - - - -
369D ASP* 3.1 19.3 + - - +
370D ILE* 3.6 5.7 + - - +
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Residues in contact with LYS 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D TPO 2.7 26.3 + - - +
365D THR* 3.1 14.7 - - + +
366D PRO* 1.3 81.9 - - + +
368D SER* 1.3 60.1 + - - +
370D ILE* 3.4 13.6 + - + +
371D TYR 3.4 11.6 + - - -
441D LYS* 3.6 45.9 - - + +
442D ASN* 2.7 29.0 + - - +
444D ARG* 2.9 20.2 + - + +
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Residues in contact with SER 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D ILE* 5.9 0.7 - - - -
310D ARG* 6.6 0.4 - - - -
356D ALA* 4.0 5.4 - - - +
358D GLU* 3.1 16.2 + - - +
359D ALA* 3.7 28.2 - - - +
363D GLU 4.7 1.0 + - - -
365D THR* 3.1 24.9 + - - +
367D LYS* 1.3 76.4 - - - +
369D ASP* 1.4 65.2 + - - +
371D TYR* 3.3 4.7 + - - +
372D SER* 3.1 25.7 + - - -
444D ARG* 3.9 8.0 - - - +
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Residues in contact with ASP 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D ILE* 4.6 6.2 - - + +
302D LEU* 6.0 0.2 - - - +
303D HIS* 3.0 27.2 + - + +
308D ILE* 3.6 12.6 - - - +
309D HIS* 2.8 33.0 + - - +
310D ARG* 3.0 26.9 + - - -
312D ILE* 4.1 17.5 + - + +
365D THR 4.1 0.2 + - - -
366D PRO 3.1 9.7 + - - +
368D SER* 1.4 78.3 - - - +
370D ILE* 1.3 56.8 + - - +
372D SER* 3.5 5.4 + - - -
373D PHE* 2.9 29.0 + - - +
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Residues in contact with ILE 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D ILE* 5.0 0.4 - - + -
303D HIS* 4.1 10.8 - - + -
366D PRO 3.7 12.3 - - - +
367D LYS* 3.5 13.9 - - + +
368D SER 3.2 0.6 - - - -
369D ASP* 1.3 73.7 - - - +
371D TYR* 1.3 65.7 + - - +
373D PHE* 3.1 7.6 + - + +
374D GLY 3.0 17.2 + - - -
436D CYS* 3.4 35.2 - - - +
444D ARG* 4.3 4.5 - - + -
445D PRO* 3.4 25.8 - - + +
446D ASP* 4.1 2.2 - - - +
447D ILE* 3.6 50.5 - - + +
450D VAL* 4.3 3.4 - - + -
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Residues in contact with TYR 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D TYR 3.8 5.4 - - - -
355D MET 3.6 16.6 - - - -
356D ALA* 3.4 19.7 - - + -
357D PRO* 4.1 11.8 - - + +
367D LYS 3.4 2.4 + - - -
368D SER 3.3 9.5 + - - +
370D ILE* 1.3 78.0 - - - +
372D SER* 1.3 56.6 + - - +
374D GLY* 2.9 18.7 + - - -
375D VAL* 3.3 8.7 + - + +
397D LEU* 3.3 40.7 - - + +
436D CYS 3.4 8.9 + - - -
437D LEU* 3.4 43.2 - - + +
438D HIS 3.6 9.9 - - - -
439D GLU* 3.1 22.0 + - - -
444D ARG* 3.6 29.8 - - - +
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Residues in contact with SER 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D ILE* 3.5 32.3 + - - -
354D TYR* 2.6 30.9 + - - +
355D MET* 4.2 5.5 - - - +
368D SER 3.1 10.3 + - - -
369D ASP* 3.6 10.0 - - - -
370D ILE 3.3 0.2 - - - -
371D TYR* 1.3 77.0 - - - +
373D PHE* 1.3 62.4 + - - +
375D VAL* 3.1 8.5 + - - +
376D VAL* 3.1 23.0 + - - +
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Residues in contact with PHE 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D ALA* 3.5 23.1 - - - -
295D ALA* 3.6 24.2 - - + -
296D ALA* 3.9 8.3 - - + -
299D ILE* 3.5 26.0 - - + -
312D ILE* 3.8 8.0 - - + +
317D ILE* 5.4 1.1 - - + -
369D ASP 2.9 17.8 + - - +
370D ILE* 3.1 8.5 + - - +
372D SER* 1.3 76.2 - - - +
374D GLY* 1.4 56.6 + - - +
376D VAL* 3.2 18.3 + - + +
377D LEU* 2.9 56.7 + - + +
380D ILE* 5.9 0.2 - - + -
436D CYS* 4.6 4.3 - - - -
447D ILE* 4.9 3.8 - - + -
450D VAL* 3.6 32.3 - - + -
454D LEU* 4.0 3.8 - - + -
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Residues in contact with GLY 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D ILE 3.0 6.1 + - - -
371D TYR 2.9 11.0 + - - -
373D PHE* 1.4 72.9 - - - +
375D VAL* 1.3 62.4 + - - +
377D LEU* 3.2 5.3 + - - +
378D LEU* 3.1 25.5 + - - +
433D ALA* 3.8 9.4 - - - +
436D CYS* 3.6 23.0 - - - +
437D LEU* 4.1 12.6 - - - -
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Residues in contact with VAL 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D ALA 3.9 9.9 - - - +
354D TYR* 3.7 32.1 - - + +
371D TYR* 3.3 7.3 + - + +
372D SER 3.1 7.7 + - - +
374D GLY* 1.3 74.2 - - - +
376D VAL* 1.3 57.3 + - - +
378D LEU* 3.1 10.4 + - - +
379D GLU* 3.0 26.6 + - + +
386D ALA* 3.7 24.0 - - + -
396D LEU* 4.9 9.0 - - + -
397D LEU* 3.4 34.5 - - + +
437D LEU* 3.7 9.2 - - + -
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Residues in contact with VAL 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D LEU* 4.1 15.0 - - + -
312D ILE* 4.3 7.4 - - + -
313D LYS* 3.7 32.5 - - - +
314D SER 3.7 8.1 - - - +
317D ILE* 3.7 22.2 - - + -
354D TYR* 4.1 2.0 - - + -
372D SER 3.1 14.4 + - - +
373D PHE* 3.2 22.0 + - + +
375D VAL* 1.3 75.0 - - - +
377D LEU* 1.4 57.2 + - - +
379D GLU* 3.0 16.0 + - - +
380D ILE* 2.9 34.1 + - + +
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Residues in contact with LEU 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D ALA* 3.8 29.6 - - + -
373D PHE* 2.9 46.6 + - + +
374D GLY* 3.2 8.5 + - - +
376D VAL* 1.4 73.9 - - - +
378D LEU* 1.3 57.3 + - - +
380D ILE* 3.3 10.0 + - + +
381D ILE* 3.0 33.3 + - - +
429D MET* 4.1 18.8 - - + +
432D VAL* 3.6 32.8 - - + -
433D ALA* 3.9 20.6 - - + +
436D CYS* 4.8 0.7 - - - -
454D LEU* 4.5 5.4 - - + -
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Residues in contact with LEU 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D GLY 3.1 15.4 + - - +
375D VAL* 3.1 9.6 + - - +
377D LEU* 1.3 73.6 - - - +
379D GLU* 1.4 63.6 + - - +
381D ILE* 4.4 6.7 - - + +
382D THR* 2.9 34.9 + - + +
396D LEU* 3.9 37.2 - - + +
397D LEU* 4.5 5.6 - - - +
399D ILE* 4.1 15.7 - - + -
400D LYS* 5.2 3.1 - - + +
410D ILE* 5.2 1.6 - - + -
430D TYR* 3.7 34.3 - - + -
433D ALA* 3.8 13.5 - - + -
437D LEU* 3.5 24.7 - - + -
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Residues in contact with GLU 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D LEU* 3.8 9.0 - - - +
274D LEU* 3.8 17.5 - - + +
314D SER* 2.7 36.5 + - - -
354D TYR* 2.9 31.5 + - - -
375D VAL 3.0 14.0 + - - +
376D VAL* 3.0 14.0 + - - +
378D LEU* 1.4 76.4 - - - +
380D ILE* 1.4 55.7 + - - +
383D GLY* 2.6 35.5 + - - -
384D LEU 3.5 20.9 - - - +
385D PRO* 4.0 2.9 - - - +
386D ALA* 3.6 13.6 + - - +
396D LEU* 3.7 8.3 - - + -
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Residues in contact with ILE 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D LEU* 4.0 31.9 - - + -
274D LEU* 4.1 10.5 - - + -
285D TRP* 4.5 1.7 - - + -
288D ARG* 2.8 64.5 + - + +
291D ILE* 4.4 4.7 - - + -
292D ALA* 4.2 30.7 - - + +
373D PHE* 5.9 0.7 - - + -
376D VAL* 2.9 24.2 + - + +
377D LEU* 3.5 13.5 - - + +
378D LEU 3.3 0.2 - - - -
379D GLU* 1.4 75.0 - - - +
381D ILE* 1.4 57.6 + - - +
418D MET* 4.8 0.2 - - - +
429D MET* 3.8 18.2 - - + -
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Residues in contact with ILE 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D TRP* 4.3 14.8 - - + -
377D LEU 3.0 26.4 + - - +
378D LEU* 3.9 13.5 - - + +
380D ILE* 1.4 75.9 - - - +
382D THR* 1.3 61.5 + - + +
410D ILE* 3.9 23.8 - - + -
414D ILE* 3.6 8.5 - - - -
415D ASP* 2.8 24.8 + - - +
418D MET* 3.8 5.7 - - - +
426D VAL* 3.9 20.2 - - + +
429D MET* 3.8 22.2 - - + +
430D TYR* 3.7 38.1 - - + +
433D ALA* 4.9 0.4 - - + -
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Residues in contact with THR 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378D LEU* 2.9 22.9 + - - +
379D GLU 3.7 0.2 + - - -
381D ILE* 1.3 85.3 - - + +
383D GLY* 1.3 61.0 + - - +
384D LEU* 2.9 41.2 + - + +
396D LEU* 3.9 6.9 - - + +
399D ILE* 4.2 16.8 - - + -
410D ILE* 5.0 1.1 - - + -
413D TYR* 3.3 39.4 - - + +
415D ASP* 3.6 18.4 - - - +
417D LYS* 5.3 0.2 + - - -
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Residues in contact with GLY 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D LEU* 3.9 28.4 - - - +
275D SER* 5.2 2.6 - - - -
288D ARG* 4.4 2.9 - - - -
379D GLU 2.6 21.9 + - - -
380D ILE 4.1 0.6 + - - -
381D ILE 3.7 1.2 - - - -
382D THR* 1.3 72.0 - - - +
384D LEU* 1.4 60.4 + - - +
385D PRO* 4.1 2.6 - - - +
415D ASP* 3.5 19.6 + - - -
417D LYS* 4.8 5.4 + - - -
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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