Contacts of the helix formed by residues 385 - 406 (chain D) in PDB entry 1ZQ1
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 GLU 385 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308D GLY 5.0 6.5 - - - +
309D GLY* 4.9 7.4 - - - -
384D ALA* 1.3 71.8 - - - +
386D GLU* 1.3 76.5 + - + +
387D GLU* 2.8 21.9 + - - +
388D LYS* 2.6 43.8 + - + +
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Residues in contact with GLU 386 (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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309D GLY* 5.5 0.4 - - - -
310D LYS* 3.2 50.6 + - + +
312D LEU* 3.8 10.8 - - - +
384D ALA 3.2 6.5 + - - -
385D GLU* 1.3 79.5 + - + +
387D GLU* 1.3 69.0 - - + +
389D ALA* 3.3 14.0 + - - +
390D LYS* 3.4 40.8 + - - +
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Residues in contact with GLU 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385D GLU* 2.7 18.3 + - - +
386D GLU* 1.3 76.6 - - + +
388D LYS* 1.3 62.8 + - - +
390D LYS* 2.8 46.4 + - - +
391D ASN* 2.7 41.7 + - - +
394D ARG* 4.3 8.1 + - - -
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Residues in contact with LYS 388 (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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344D TYR* 3.8 32.3 + - + +
345D VAL* 4.2 1.6 - - + -
346D PRO* 5.9 5.3 - - + +
384D ALA* 3.6 16.6 - - + -
385D GLU* 2.6 36.6 + - + +
387D GLU* 1.3 73.5 - - - +
389D ALA* 1.3 56.9 + - - +
391D ASN* 3.3 6.2 + - - +
392D ALA* 2.8 32.6 + - - +
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Residues in contact with ALA 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D LEU* 3.4 23.8 - - + -
382D VAL* 3.2 40.6 - - + +
384D ALA* 3.8 13.6 - - + +
385D GLU 3.5 1.0 + - - -
386D GLU 3.3 5.5 + - - +
387D GLU 3.2 0.2 - - - -
388D LYS* 1.3 79.4 - - - +
390D LYS* 1.3 57.7 + - - +
392D ALA* 3.8 0.4 - - - +
393D LEU* 2.9 37.6 + - - +
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Residues in contact with LYS 390 (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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286D PHE* 3.2 38.3 - - + -
312D LEU* 4.1 10.1 - - + -
386D GLU* 3.4 35.5 + - - +
387D GLU* 2.8 36.3 + - - +
389D ALA* 1.3 75.5 - - - +
391D ASN* 1.3 60.5 + - - +
393D LEU 3.2 1.7 + - - -
394D ARG* 2.8 51.0 + - - +
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Residues in contact with ASN 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D TYR* 3.4 38.1 + - + -
387D GLU* 2.7 45.4 + - - +
388D LYS* 3.9 4.1 - - - +
390D LYS* 1.3 74.1 - - - +
392D ALA* 1.3 64.2 + - - +
394D ARG* 2.8 30.6 + - - +
395D GLU* 2.9 27.0 + - - +
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Residues in contact with ALA 392 (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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341D ALA* 4.3 12.4 - - + +
344D TYR* 3.8 11.6 - - + -
345D VAL* 3.3 28.7 - - + -
382D VAL* 3.9 10.3 - - + -
388D LYS 2.8 19.8 + - - +
389D ALA 3.8 4.9 - - - +
391D ASN* 1.3 77.3 - - - +
393D LEU* 1.3 60.4 + - - +
395D GLU* 3.2 5.8 + - - +
396D VAL* 2.9 28.0 + - - +
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Residues in contact with LEU 393 (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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286D PHE* 3.5 17.9 - - + -
312D LEU* 3.5 34.5 - - + +
314D ILE* 3.3 35.7 - - + +
380D VAL* 3.7 22.9 - - + +
382D VAL* 3.4 28.0 - - + -
389D ALA 2.9 23.5 + - - +
390D LYS 3.7 2.7 - - - +
392D ALA* 1.3 76.7 - - - +
394D ARG* 1.3 61.5 + - - +
396D VAL* 3.0 9.1 + - + +
397D ILE* 2.8 31.7 + - - +
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Residues in contact with ARG 394 (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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284D GLU* 3.2 31.0 + - - +
286D PHE* 3.6 17.6 - - + -
387D GLU* 4.3 7.7 + - - -
390D LYS* 2.8 45.8 + - - +
391D ASN* 2.8 44.3 + - - +
393D LEU* 1.3 76.7 - - - +
395D GLU* 1.3 55.1 + - + +
397D ILE* 2.8 39.1 + - + +
398D LYS* 2.9 8.6 + - - +
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Residues in contact with GLU 395 (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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340D ARG* 3.8 40.6 + - - +
341D ALA* 4.6 0.7 - - - -
343D LYS* 3.8 23.0 + - + -
344D TYR* 4.0 20.0 - - + -
391D ASN 2.9 13.6 + - - +
392D ALA 3.4 9.6 - - - +
394D ARG* 1.3 75.8 - - + +
396D VAL* 1.3 61.8 + - - +
398D LYS* 3.5 35.0 + - - +
399D ARG* 3.3 21.1 + - - +
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Residues in contact with VAL 396 (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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314D ILE* 5.9 3.1 - - + -
316D LEU* 5.3 4.3 - - + -
337D PHE* 3.9 40.5 - - + +
341D ALA* 4.0 19.3 - - + -
348D ILE* 4.8 3.1 - - + -
380D VAL* 4.2 28.5 - - + -
382D VAL* 5.1 0.4 - - + -
392D ALA 2.9 19.5 + - - +
393D LEU* 3.0 19.7 + - + +
395D GLU* 1.3 73.6 - - - +
397D ILE* 1.3 64.6 + - + +
399D ARG* 3.5 5.1 + - - +
400D ALA* 2.9 23.1 + - - +
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Residues in contact with ILE 397 (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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282D ILE* 4.1 14.6 - - + +
283D LYS 5.6 0.2 - - - +
284D GLU* 3.3 35.2 - - + -
286D PHE* 5.0 1.8 - - + -
314D ILE* 4.8 21.8 - - + -
316D LEU* 5.7 1.6 - - - -
393D LEU 2.8 23.1 + - - +
394D ARG* 2.8 30.7 + - + +
396D VAL* 1.3 74.4 - - - +
398D LYS* 1.3 66.8 + - - +
400D ALA* 2.9 18.7 + - - +
401D ARG* 2.9 47.7 + - - +
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Residues in contact with LYS 398 (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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340D ARG* 4.0 14.7 - - - +
394D ARG 2.9 10.9 + - - +
395D GLU* 3.5 33.7 + - - +
397D ILE* 1.3 78.5 - - - +
399D ARG* 1.3 63.2 + - - +
401D ARG* 3.3 8.7 + - - +
402D GLU* 3.0 45.6 + - + +
422D TYR* 5.7 1.8 + - - -
425D PRO* 5.2 12.3 - - - +
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Residues in contact with ARG 399 (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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265D LEU* 3.3 37.2 - - - +
333D LEU* 4.2 7.6 - - - +
336D GLU* 4.0 26.8 + - - +
337D PHE* 4.2 22.0 - - + -
340D ARG* 2.9 41.8 - - + +
395D GLU 3.3 9.3 + - - +
396D VAL* 3.8 7.9 - - - +
397D ILE 3.2 0.4 - - - -
398D LYS* 1.3 78.8 - - - +
400D ALA* 1.3 65.5 + - - +
402D GLU* 2.8 10.1 + - - +
403D ALA* 2.7 49.7 + - - +
406D GLY 3.8 2.0 + - - -
408D PRO* 3.4 31.8 - - - +
410D GLU* 4.8 4.0 + - - -
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Residues in contact with ALA 400 (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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282D ILE* 4.2 7.6 - - + -
316D LEU* 4.2 25.4 - - + -
319D PHE* 3.5 11.0 - - + -
337D PHE* 3.9 24.1 - - + -
396D VAL 2.9 14.4 + - - +
397D ILE* 2.9 13.4 + - - +
399D ARG* 1.3 71.8 - - - +
401D ARG* 1.3 65.8 + - - +
403D ALA* 3.1 17.2 + - - +
404D ILE* 3.3 9.9 + - - +
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Residues in contact with ARG 401 (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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279D PRO* 3.0 36.0 + - + +
280D LYS* 5.3 3.3 + - - +
282D ILE* 2.7 50.9 + - + -
283D LYS* 4.4 1.0 - - - +
284D GLU* 4.1 15.4 - - - +
397D ILE* 2.9 33.2 + - + +
398D LYS* 3.5 9.2 - - - +
400D ALA* 1.3 74.9 - - - +
402D GLU* 1.3 55.9 + - + +
404D ILE* 2.8 35.3 + - - +
405D GLU* 3.3 12.8 + - - +
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Residues in contact with GLU 402 (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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340D ARG* 2.7 33.2 + - - -
398D LYS* 3.0 31.3 + - + +
399D ARG* 2.8 13.4 + - - +
401D ARG* 1.3 75.5 - - + +
403D ALA* 1.3 50.9 + - - +
405D GLU* 3.0 17.2 + - - +
406D GLY 2.7 37.9 + - - +
408D PRO* 3.2 30.9 - - + +
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Residues in contact with ALA 403 (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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265D LEU* 5.0 2.6 - - + +
268D ILE* 5.6 2.1 - - + +
269D ARG* 3.6 19.6 + - - +
272D LEU* 3.7 7.8 - - + +
319D PHE* 4.4 10.5 - - + -
333D LEU* 4.6 17.7 - - + -
337D PHE* 5.2 0.2 - - + -
399D ARG* 2.7 35.7 + - - +
400D ALA* 3.2 16.2 - - - +
401D ARG 3.0 0.4 + - - -
402D GLU* 1.3 73.4 - - - +
404D ILE* 1.3 62.9 + - - +
405D GLU 3.3 0.3 + - - -
406D GLY 3.6 5.9 + - - +
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Residues in contact with ILE 404 (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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269D ARG* 2.9 21.7 - - - +
272D LEU* 3.4 21.1 - - + -
273D ARG* 4.4 12.6 + - + +
277D VAL* 3.5 43.3 - - + +
278D LYS* 3.8 15.7 - - - +
279D PRO* 4.1 4.7 - - + -
282D ILE* 3.4 30.7 - - + -
319D PHE* 3.4 14.1 - - + -
400D ALA 3.4 8.3 - - - +
401D ARG* 2.8 17.8 + - - +
403D ALA* 1.3 72.9 - - - +
405D GLU* 1.3 58.2 + - + +
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Residues in contact with GLU 405 (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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269D ARG* 2.9 20.4 + - - -
273D ARG* 4.6 6.7 + - - +
279D PRO* 3.9 28.8 - - + +
401D ARG* 3.7 11.1 - - - +
402D GLU* 3.0 24.3 + - - +
404D ILE* 1.3 80.5 - - - +
406D GLY* 1.3 57.4 + - - +
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Residues in contact with GLY 406 (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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265D LEU* 5.2 5.9 - - - +
266D LEU* 4.3 8.1 - - - -
269D ARG* 3.8 15.0 - - - -
399D ARG* 3.8 6.4 + - - -
402D GLU 2.7 21.2 + - - +
403D ALA* 3.6 7.4 + - - +
405D GLU* 1.3 77.0 - - - +
407D VAL* 1.3 64.4 + - - -
408D PRO* 3.3 9.2 - - - +
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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