Contacts of the helix formed by residues 391 - 407 (chain D) in PDB entry 1XSK
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 ASN 391 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363D LYS 5.4 0.4 + - - -
364D GLY 3.3 24.5 + - - -
365D TYR* 4.4 4.1 - - - -
388D ASP* 3.0 17.2 + - + +
389D PHE 3.0 0.8 - - - -
390D THR* 1.3 78.1 - - - +
392D PRO* 1.3 68.8 - - - +
393D ASP* 2.9 23.2 + - - +
394D ALA* 3.1 14.8 + - + +
395D CYS* 3.0 25.1 + - - -
428D PHE* 3.3 41.3 - - + +
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Residues in contact with PRO 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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390D THR 3.5 7.4 - - - +
391D ASN* 1.3 84.4 - - - +
393D ASP* 1.3 64.7 + - - +
395D CYS* 3.7 8.5 + - + +
396D LYS* 3.3 19.6 + - - +
428D PHE* 3.4 24.7 - - + -
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Residues in contact with ASP 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365D TYR* 3.6 28.2 + - + +
391D ASN* 2.9 10.1 + - - +
392D PRO* 1.3 78.7 - - - +
394D ALA* 1.3 66.9 + - - +
395D CYS 3.2 0.4 - - - -
396D LYS* 3.2 13.7 + - - +
397D TRP* 3.0 23.4 + - - +
428D PHE* 6.1 1.2 - - - -
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Residues in contact with ALA 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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365D TYR* 3.5 42.5 - - + +
387D TYR* 5.2 5.9 - - + -
388D ASP 3.5 25.6 - - - +
389D PHE* 5.0 3.4 - - + -
391D ASN* 3.1 13.5 + - + +
393D ASP* 1.3 77.3 - - - +
395D CYS* 1.3 63.2 + - - +
397D TRP* 3.3 3.8 + - - +
398D TYR* 3.1 24.4 + - - +
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Residues in contact with CYS 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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389D PHE* 2.7 43.1 - - - -
391D ASN 3.0 17.8 + - - +
392D PRO* 3.8 7.9 - - + +
394D ALA* 1.3 77.6 - - - +
396D LYS* 1.3 56.8 + - - +
398D TYR 3.5 0.2 + - - -
399D ALA* 2.9 31.5 + - - +
443D ILE* 5.4 2.5 - - - -
447D LEU* 3.7 27.8 - - + +
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Residues in contact with LYS 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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392D PRO 3.3 11.8 + - - +
393D ASP* 3.2 18.0 + - - +
395D CYS* 1.3 77.1 - - - +
397D TRP* 1.3 58.9 + - - +
399D ALA* 3.6 6.3 - - + +
400D ASP* 2.9 60.7 + - - +
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Residues in contact with TRP 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D ASP 4.4 8.1 - - - -
318D PHE* 4.3 5.8 - + - -
356D VAL* 3.3 36.3 - - + -
359D GLU* 3.6 18.7 + - - -
360D LEU* 3.6 10.5 - - + +
363D LYS* 4.2 10.5 - - - -
365D TYR* 3.8 26.2 - + + -
387D TYR* 3.3 41.5 - + - -
393D ASP 3.0 12.6 + - - +
394D ALA 3.6 8.1 - - - +
396D LYS* 1.3 78.2 - - - +
398D TYR* 1.3 65.3 + - - +
400D ASP* 3.5 7.4 + - - +
401D LYS* 3.3 68.7 + - + +
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Residues in contact with TYR 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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318D PHE* 3.4 30.0 - + - -
346D ILE* 3.9 10.2 - - - +
347D ASN 2.7 33.3 + - - -
387D TYR* 3.8 34.3 - + + -
389D PHE* 3.8 27.6 - + + -
394D ALA 3.1 13.4 + - - +
395D CYS 3.8 3.4 - - - +
397D TRP* 1.3 84.7 - - + +
399D ALA* 1.3 66.2 + - - +
401D LYS* 3.2 14.2 + - - +
402D LEU* 3.2 36.6 + - + +
444D TYR* 3.9 9.1 - + - -
447D LEU* 3.7 20.9 - - + -
448D VAL* 4.5 7.6 - - + -
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Residues in contact with ALA 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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395D CYS 2.9 19.3 + - - +
396D LYS* 3.6 7.6 - - + +
398D TYR* 1.3 79.0 - - - +
400D ASP* 1.3 64.5 + - - +
402D LEU* 3.0 6.2 + - - +
403D LYS* 3.0 35.1 + - - +
447D LEU* 4.5 11.0 - - + -
451D VAL* 4.0 22.3 - - + +
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Residues in contact with ASP 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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396D LYS* 2.9 54.3 + - - +
397D TRP* 3.8 7.8 + - - +
399D ALA* 1.3 77.0 - - - +
401D LYS* 1.3 61.9 + - + +
403D LYS* 3.3 24.4 + - - +
404D GLY* 2.9 25.1 + - - -
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Residues in contact with LYS 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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317D ASP 4.5 0.2 - - - -
318D PHE* 3.6 44.1 - - + +
319D GLU* 4.3 15.0 - - - +
356D VAL* 6.0 0.9 - - - -
397D TRP* 3.3 51.6 + - + +
398D TYR 3.2 9.6 + - - +
400D ASP* 1.3 81.4 - - - +
402D LEU* 1.3 62.6 + - - +
404D GLY* 3.3 4.1 + - - +
405D LEU* 3.3 23.8 + - - +
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Residues in contact with LEU 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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318D PHE* 3.7 23.8 - - + -
346D ILE* 4.0 14.8 - - + -
398D TYR* 3.2 35.6 + - + +
399D ALA 3.0 6.9 + - - +
401D LYS* 1.3 72.9 - - - +
403D LYS* 1.3 68.6 + - - +
404D GLY 3.0 1.6 - - - -
405D LEU* 2.9 6.6 + - + +
406D VAL* 2.9 27.0 + - - +
413D PHE* 3.6 28.9 - - + -
447D LEU* 4.0 14.6 - - + -
448D VAL* 4.2 15.9 - - + -
451D VAL* 3.9 20.6 - - + -
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Residues in contact with LYS 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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399D ALA* 3.0 29.7 + - - +
400D ASP* 3.3 25.7 + - - +
402D LEU* 1.3 75.6 - - - +
404D GLY* 1.3 57.1 - - - +
406D VAL* 3.3 9.5 + - - +
407D ALA* 2.8 32.9 + - - +
451D VAL* 3.9 21.3 - - + +
454D ASP* 5.3 12.0 + - - +
455D THR* 4.2 19.0 - - + +
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Residues in contact with GLY 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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400D ASP 2.9 14.3 + - - -
401D LYS* 3.6 6.3 - - - -
402D LEU 3.0 0.6 - - - -
403D LYS* 1.3 78.1 - - - +
405D LEU* 1.3 60.8 + - - +
407D ALA* 3.4 8.1 + - - +
408D MET* 3.2 26.1 + - - +
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Residues in contact with LEU 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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309D TRP* 4.0 19.1 - - + -
318D PHE* 3.9 32.8 - - + +
320D TRP* 3.5 36.1 - - + +
344D VAL* 4.2 6.5 - - + -
346D ILE* 4.9 0.7 - - + -
401D LYS 3.3 10.2 + - - +
402D LEU* 2.9 7.7 + - + +
404D GLY* 1.3 75.4 - - - +
406D VAL* 1.3 59.9 + - - +
408D MET* 2.8 32.6 + - + +
409D GLY 3.2 3.8 + - - -
410D VAL* 3.2 20.8 + - + +
413D PHE* 3.6 27.6 - - + -
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Residues in contact with VAL 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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402D LEU 2.9 21.2 + - - +
403D LYS* 3.6 9.9 - - - +
405D LEU* 1.3 70.2 - - - +
407D ALA* 1.3 59.4 + - - +
408D MET 2.9 4.7 - - - -
409D GLY* 2.8 21.3 + - - -
410D VAL* 3.5 16.7 + - - +
411D ASP 5.7 1.6 - - - +
413D PHE* 3.9 22.0 - - + -
451D VAL* 4.4 4.9 - - + -
452D LEU* 5.4 4.0 - - + -
455D THR* 3.6 25.8 - - + +
456D VAL* 3.6 31.2 - - + -
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Residues in contact with ALA 407 (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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329D GLU* 3.2 14.5 - - - +
403D LYS 2.8 17.9 + - - +
404D GLY* 3.6 8.3 - - - +
406D VAL* 1.3 76.6 - - - +
408D MET* 1.3 57.0 + - - +
409D GLY 3.3 0.6 + - - -
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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
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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