Contacts of the helix formed by residues 364 - 381 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D VAL* 3.6 14.7 - - - +
339D ALA* 4.4 6.5 - - - -
356D GLU* 5.0 3.3 + - - -
362D LYS 4.0 2.6 + - - -
363D PHE* 1.3 75.0 - - - +
365D THR* 1.3 66.0 + - - +
366D LYS* 3.0 26.8 + - - +
367D SER* 2.5 30.9 + - - -
368D ASP 3.2 3.8 + - - -
427D ALA* 5.5 0.7 - - - +
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Residues in contact with THR 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D GLU* 3.5 51.4 - - + +
310D PHE 4.5 3.5 + - - -
311D VAL* 3.8 14.5 - - - +
339D ALA* 5.2 1.0 - - - +
364D SER* 1.3 74.0 - - - +
366D LYS* 1.3 69.8 + - + +
368D ASP* 2.9 11.4 + - - +
369D VAL* 2.9 25.3 + - + +
432D THR* 5.6 0.9 - - - -
433D PHE* 3.8 17.0 - - + -
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Residues in contact with LYS 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D GLU* 6.0 0.7 - - - -
356D GLU* 5.2 0.2 - - - +
364D SER* 2.9 13.5 + - - +
365D THR* 1.3 84.2 - - + +
367D SER* 1.3 60.9 + - - +
369D VAL* 3.1 16.3 + - + +
370D TRP 3.1 6.6 + - - -
427D ALA* 3.6 34.8 - - + +
428D ALA* 4.4 12.4 + - - +
430D ARG* 2.7 53.5 + - + +
431D PRO 3.9 5.8 + - - +
432D THR* 3.8 25.8 - - - +
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Residues in contact with SER 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311D VAL* 4.5 1.0 - - - +
353D THR* 5.8 0.2 - - - -
354D ALA* 3.9 19.9 + - - +
356D GLU* 4.4 4.2 + - - -
357D ALA* 4.0 16.6 - - - -
362D LYS 5.2 0.7 - - - -
363D PHE* 3.6 13.7 - - - +
364D SER* 2.5 38.9 + - - -
366D LYS* 1.3 75.6 - - - +
368D ASP* 1.3 67.3 + - - +
370D TRP* 3.2 5.7 + - - +
371D SER* 3.0 23.5 + - - -
430D ARG* 3.9 8.9 - - - +
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Residues in contact with ASP 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D MET* 3.7 25.0 - - + +
310D PHE 4.4 1.2 - - - +
311D VAL* 3.2 19.0 - - - +
312D HIS 2.4 52.0 + - - +
313D ARG* 3.8 4.0 + - - -
315D LEU* 4.2 3.3 - - + +
364D SER 3.2 4.3 + - - +
365D THR* 2.9 12.2 + - - +
367D SER* 1.3 74.8 + - - +
369D VAL* 1.3 55.7 + - - +
371D SER* 3.0 11.9 + - - -
372D PHE* 2.7 34.3 + - - +
433D PHE* 3.9 7.7 - - + -
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Residues in contact with VAL 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365D THR* 2.9 24.1 + - + +
366D LYS* 3.1 18.4 + - + +
368D ASP* 1.3 78.0 - - - +
370D TRP* 1.3 62.1 + - - +
372D PHE* 3.1 5.0 + - - +
373D GLY 2.9 17.5 + - - -
422D CYS* 3.5 26.9 - - + +
430D ARG* 3.9 16.8 - - + -
431D PRO* 3.3 29.8 - - + +
432D THR* 4.9 0.7 - - - -
433D PHE* 3.8 26.7 - - + -
436D LEU* 4.2 5.8 - - + -
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Residues in contact with TRP 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351D LYS 5.1 0.6 + - - -
352D TRP 3.6 10.7 - - - -
353D THR 3.3 21.6 + - - -
354D ALA* 3.7 12.8 - - + -
355D PRO* 3.7 22.2 - - + -
366D LYS 3.1 7.4 + - - +
367D SER 3.2 10.1 + - - +
369D VAL* 1.3 79.0 - - - +
371D SER* 1.3 59.2 + - - +
373D GLY* 2.9 17.7 + - - -
374D ILE* 3.1 25.5 + - + +
387D TYR* 4.3 12.9 + - - -
399D VAL* 3.6 31.4 - - + -
403D TYR 5.5 1.6 - - - -
404D LYS* 4.9 2.7 - - + -
422D CYS 3.6 23.5 + - - -
423D TRP* 3.4 46.4 + + + -
424D HIS 3.7 5.4 - - - -
425D LEU* 4.3 7.9 - - + -
430D ARG* 3.7 19.1 - - - +
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Residues in contact with SER 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D HIS 5.5 0.2 + - - -
313D ARG 5.8 1.7 - - - -
314D ASP 5.7 0.3 + - - -
315D LEU* 3.6 35.5 + - - +
352D TRP* 2.9 26.9 + - - -
353D THR* 4.7 2.1 - - - -
367D SER 3.0 13.7 + - - -
368D ASP* 3.0 13.6 + - - -
370D TRP* 1.3 73.6 - - - +
372D PHE* 1.3 66.1 + - - +
374D ILE* 2.8 17.5 + - - +
375D LEU* 2.9 12.6 + - - +
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Residues in contact with PHE 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D SER* 3.7 10.1 - - - -
298D VAL* 3.7 22.2 - - + -
299D CYS* 3.6 40.8 - - + -
302D MET* 4.7 0.2 - - + -
315D LEU* 3.5 13.1 - - + +
368D ASP 2.7 15.1 + - - +
369D VAL* 3.4 7.9 - - - +
371D SER* 1.3 72.5 - - - +
373D GLY* 1.3 57.8 + - - +
375D LEU* 3.2 7.7 + - + +
376D LEU* 2.8 55.3 + - + +
379D ILE* 6.3 1.1 - - + -
422D CYS* 4.1 6.3 - - - -
433D PHE* 3.7 19.5 - + + -
436D LEU* 3.9 27.8 - - + -
440D LEU* 4.1 13.2 - - + -
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Residues in contact with GLY 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369D VAL 2.9 6.9 + - - -
370D TRP 2.9 10.6 + - - -
372D PHE* 1.3 77.0 - - - +
374D ILE* 1.3 62.8 + - - +
376D LEU* 3.0 17.8 + - - +
377D TRP 3.1 8.7 + - - -
419D MET* 3.9 3.5 - - - +
422D CYS* 3.7 19.3 - - - -
423D TRP* 3.6 23.7 - - - -
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Residues in contact with ILE 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351D LYS 3.7 17.3 - - - +
352D TRP* 3.5 29.6 - - + +
370D TRP* 3.1 31.6 + - + +
371D SER* 2.8 10.8 + - - +
373D GLY* 1.3 70.6 - - - +
375D LEU* 1.3 57.5 + - - +
377D TRP* 3.0 8.4 + - - +
378D GLU* 2.9 25.0 + - - +
386D PRO* 3.9 20.4 - - + -
387D TYR* 4.0 15.3 - - + +
405D MET* 3.9 14.1 - - + -
423D TRP* 3.4 26.5 - - + +
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Residues in contact with LEU 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D LEU* 4.0 7.0 - - + -
298D VAL* 3.6 32.8 - - + -
315D LEU* 3.6 24.2 - - + -
316D ALA* 4.4 4.7 - - - -
317D ALA* 3.5 33.7 - - + +
320D VAL* 4.1 9.9 - - + -
352D TRP* 4.7 0.2 - - - +
371D SER 2.9 11.5 + - - +
372D PHE* 3.5 12.8 - - + +
374D ILE* 1.3 73.3 - - - +
376D LEU* 1.3 65.2 - - - +
378D GLU* 3.3 11.7 + - - +
379D ILE* 2.9 39.8 + - + +
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Residues in contact with LEU 376 (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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295D SER* 3.2 34.8 - - - +
372D PHE* 2.8 32.7 + - + +
373D GLY* 3.0 11.2 + - - +
375D LEU* 1.3 77.0 - - - +
377D TRP* 1.3 58.5 + - - +
379D ILE* 3.2 5.6 + - + +
380D TYR* 2.9 50.7 + - + -
415D VAL* 4.5 8.3 - - + +
418D VAL* 3.7 34.3 - - + -
419D MET* 3.7 21.8 - - + +
440D LEU* 4.7 6.1 - - + -
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Residues in contact with TRP 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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373D GLY 3.1 6.0 + - - +
374D ILE 3.0 9.8 + - - +
376D LEU* 1.3 77.6 - - - +
378D GLU* 1.3 68.3 + - + +
380D TYR 3.1 1.7 + - - -
381D SER* 2.6 52.9 + - - -
384D ARG* 3.1 42.8 - - + -
385D VAL 3.2 22.4 - - - -
386D PRO* 3.4 12.8 - - + -
388D PRO* 3.9 17.5 - - + -
405D MET* 3.1 44.5 - - + +
406D ASP 3.3 20.5 + - - +
408D PRO* 3.4 23.3 - - + +
419D MET* 3.7 20.1 - - - -
423D TRP* 4.4 3.6 - + + -
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Residues in contact with GLU 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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275D VAL* 4.6 10.2 - - - +
278D LEU* 4.3 1.8 - - + -
279D ARG* 5.7 0.3 + - - -
317D ALA* 3.1 40.1 + - + +
318D ARG 4.8 0.3 + - - -
352D TRP* 2.7 43.7 + - - -
374D ILE 2.9 16.1 + - - +
375D LEU* 3.3 11.6 + - - +
377D TRP* 1.3 83.3 - - + +
379D ILE* 1.3 64.4 + - - +
381D SER* 3.0 2.3 + - - -
382D PHE 3.0 5.2 + - - -
383D GLY* 2.9 31.0 + - - +
384D ARG 4.4 8.5 - - - +
386D PRO* 4.2 17.2 - - + +
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Residues in contact with ILE 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D LEU* 4.1 19.3 - - + -
278D LEU* 3.8 14.2 - - + +
291D LEU* 3.7 46.2 - - + +
294D PHE* 4.1 8.3 - - + +
295D SER* 3.8 29.8 - - - +
298D VAL* 5.0 2.7 - - + -
372D PHE* 6.3 0.7 - - + -
375D LEU* 2.9 39.8 + - + +
376D LEU* 3.4 9.9 - - + +
377D TRP 3.2 0.2 - - - -
378D GLU* 1.3 77.8 - - - +
380D TYR* 1.3 73.2 + - + +
382D PHE* 3.3 10.4 + - - -
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Residues in contact with TYR 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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288D GLY* 4.3 5.3 + - - -
291D LEU* 3.8 26.4 - - + +
292D LEU* 3.4 38.3 + - + +
295D SER* 3.7 18.2 - - - -
376D LEU* 2.9 24.2 + - + +
377D TRP 3.6 1.8 - - - +
379D ILE* 1.3 82.7 - - + +
381D SER* 1.3 56.8 + - - +
382D PHE* 3.2 19.4 + - - -
408D PRO* 3.3 18.6 - - + +
409D ASP 4.3 6.2 - - - +
410D GLY 5.5 0.4 - - - -
411D CYS* 4.1 21.4 + - + +
412D PRO* 3.7 33.9 - - + -
415D VAL* 3.6 25.0 - - + +
419D MET* 4.2 1.1 - - + -
449D HIS* 5.1 2.1 - - + +
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Residues in contact with SER 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377D TRP* 2.6 41.1 + - - -
378D GLU 3.0 2.7 + - - -
380D TYR* 1.3 76.0 - - - +
382D PHE* 1.3 71.3 + - - +
383D GLY 3.1 1.9 + - - -
384D ARG* 3.1 45.0 + - - +
408D PRO* 2.9 24.1 - - - +
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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