Contacts of the helix formed by residues 393 - 411 (chain D) in PDB entry 6B0Z
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 393 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D GLU* 2.8 37.0 + - + +
325D THR 3.1 16.6 - - - +
326D SER* 4.1 4.7 - - - -
373D THR* 5.0 0.7 - - - -
388D ARG* 4.0 2.0 - - - +
391D TYR* 4.9 0.9 - - + -
392D LEU* 1.3 74.7 - - - +
394D THR* 1.3 65.4 + - - +
395D PHE* 2.9 16.5 + - + +
396D GLU* 2.6 60.6 + - - +
397D PHE* 3.0 21.5 + - - +
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Residues in contact with THR 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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18D MET* 4.2 10.1 - - + -
21D ILE* 6.2 0.7 - - + -
22D ILE* 4.0 28.7 - - + -
25D LEU* 5.3 4.2 - - + +
325D THR* 2.6 33.2 + - - -
326D SER* 3.9 0.4 - - - +
327D THR* 3.0 35.7 + - - +
329D PRO* 5.7 3.0 - - + +
373D THR* 5.1 0.4 - - - -
393D ASN* 1.3 73.1 - - - +
395D PHE* 1.3 75.8 + - + +
397D PHE* 4.1 3.9 - - - +
398D MET* 3.3 22.2 + - - +
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Residues in contact with PHE 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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18D MET* 5.5 1.3 - - + -
21D ILE* 4.5 13.2 - - + -
25D LEU* 3.9 29.6 - - + -
319D TYR* 3.7 35.0 - + - -
325D THR* 4.8 6.1 - - - -
393D ASN* 2.9 13.4 + - + +
394D THR* 1.3 87.4 - - + +
396D GLU* 1.3 60.9 + - - +
398D MET* 3.2 6.1 + - - +
399D ASP* 2.9 39.5 + - - +
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Residues in contact with GLU 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388D ARG* 3.1 19.5 + - - -
392D LEU* 3.3 27.5 - - + +
393D ASN* 2.6 56.9 + - - +
395D PHE* 1.3 72.2 - - + +
397D PHE* 1.3 57.4 + - - +
399D ASP* 3.2 11.0 + - - +
400D LYS* 2.9 28.9 + - - +
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Residues in contact with PHE 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D ASN* 4.7 1.1 - - - -
329D PRO* 3.5 37.5 - - + -
330D ILE* 4.0 11.7 - - + -
366D THR* 4.0 13.0 - - + -
367D ILE* 4.0 19.3 - - + -
371D PHE 3.1 29.4 - - - -
372D MET* 3.8 15.3 - - - -
373D THR* 4.0 15.9 - - + -
376D LEU* 5.3 0.9 - - + -
392D LEU* 3.8 14.5 - - + +
393D ASN 3.0 16.6 + - - +
394D THR 4.1 2.7 - - - +
396D GLU* 1.3 76.0 - - - +
398D MET* 1.3 62.4 + - - +
400D LYS* 3.3 1.4 + - + +
401D LEU* 2.9 52.1 + - + +
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Residues in contact with MET 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ILE* 5.5 1.8 - - - -
25D LEU* 3.6 31.0 - - + +
26D ILE* 3.5 48.0 - - + +
29D LYS* 4.0 17.7 - - + +
30D LEU* 3.5 22.1 - - + +
329D PRO* 4.3 23.8 - - - -
333D ILE* 4.7 0.4 - - + -
394D THR* 3.3 13.5 + - + +
395D PHE* 3.2 11.4 + - - +
397D PHE* 1.3 78.6 - - - +
399D ASP* 1.3 62.8 + - - +
401D LEU* 3.4 8.6 + - - +
402D GLY* 3.0 19.8 + - - -
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Residues in contact with ASP 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LYS* 3.4 30.4 + - - +
395D PHE* 2.9 24.8 + - - +
396D GLU* 3.5 10.7 - - - +
398D MET* 1.3 75.7 - - - +
400D LYS* 1.3 56.9 + - - +
402D GLY* 3.2 2.4 + - - -
403D GLU* 2.8 48.7 + - - +
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Residues in contact with LYS 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366D THR* 4.0 18.6 - - + -
371D PHE* 3.7 47.5 - - + -
392D LEU* 4.3 10.1 - - + -
396D GLU 2.9 14.6 + - - +
397D PHE* 3.7 4.9 - - + +
399D ASP* 1.3 76.4 - - - +
401D LEU* 1.3 58.4 + - - +
403D GLU* 3.3 16.2 + - - +
404D ASN* 2.8 60.6 + - - +
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Residues in contact with LEU 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D LEU* 4.1 11.4 - - + +
329D PRO* 4.3 3.4 - - + -
330D ILE* 4.5 1.6 - - + -
333D ILE* 3.6 29.4 - - + -
359D LEU* 6.3 1.1 - - + -
362D VAL* 3.8 7.7 - - + +
363D SER* 3.7 25.6 - - - +
366D THR* 3.6 31.4 - - + +
397D PHE* 2.9 51.0 + - + +
398D MET* 3.7 9.9 - - - +
400D LYS* 1.3 76.1 - - - +
402D GLY* 1.3 57.0 + - - +
404D ASN 3.3 1.7 + - - -
405D LEU* 2.9 30.0 + - - +
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Residues in contact with GLY 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LYS* 4.5 12.1 - - - -
30D LEU* 3.8 17.2 - - - +
34D TYR* 4.2 1.7 + - - -
398D MET 3.0 14.2 + - - -
399D ASP* 3.6 2.9 - - - -
401D LEU* 1.3 73.8 - - - +
403D GLU* 1.3 64.9 - - - +
405D LEU* 3.2 3.4 + - - +
406D LYS* 3.1 27.4 + - - +
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Residues in contact with GLU 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399D ASP* 2.8 39.1 + - - +
400D LYS* 3.7 20.8 + - - +
402D GLY* 1.3 73.7 - - - +
404D ASN* 1.3 65.7 + - - +
406D LYS* 3.6 4.6 + - - +
407D ILE* 3.0 33.4 + - + +
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Residues in contact with ASN 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362D VAL* 3.9 16.6 - - + +
365D GLU* 5.6 0.8 - - - +
366D THR* 3.5 25.3 + - - +
369D ALA* 6.0 1.6 - - - +
371D PHE* 5.3 2.2 - - - -
400D LYS* 2.8 47.1 + - - +
401D LEU 3.9 2.7 - - - +
403D GLU* 1.3 78.6 - - - +
405D LEU* 1.3 63.7 + - - +
407D ILE* 4.0 5.6 - - - +
408D LYS* 3.2 23.7 + - - +
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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
----------------------------------------------------------
29D LYS 4.4 0.7 - - - +
30D LEU* 3.5 47.6 - - + +
34D TYR* 3.5 16.6 - - + +
355D PHE* 4.7 2.2 - - + -
358D ALA 4.9 0.4 - - - +
359D LEU* 4.0 28.0 - - + +
362D VAL* 3.9 20.8 - - + +
401D LEU 2.9 18.4 + - - +
402D GLY 3.2 6.0 + - - +
404D ASN* 1.3 73.8 - - - +
406D LYS* 1.3 66.8 + - - +
408D LYS* 3.3 1.9 + - - +
409D LEU* 2.9 54.6 + - + +
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Residues in contact with LYS 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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33D PRO* 3.9 16.6 + - - +
34D TYR* 2.9 47.2 + - + +
402D GLY 3.1 10.8 + - - +
403D GLU* 3.7 11.2 - - - +
404D ASN 3.5 0.2 - - - -
405D LEU* 1.3 77.6 - - - +
407D ILE* 1.3 59.9 + - + +
409D LEU* 3.0 2.6 + - - +
410D ALA* 2.5 37.1 + - - +
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Residues in contact with ILE 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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403D GLU* 3.0 28.2 + - + +
404D ASN* 4.3 4.9 - - - +
405D LEU 3.3 0.8 - - - -
406D LYS* 1.3 87.2 - - + +
408D LYS* 1.3 63.4 + - - +
410D ALA* 3.4 20.7 + - + +
411D GLN* 4.2 13.3 + - - +
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Residues in contact with LYS 408 (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 PHE* 5.9 2.3 - - - -
358D ALA* 4.2 19.6 + - + +
361D GLU* 3.0 34.5 + - - +
362D VAL* 3.6 16.2 - - + -
365D GLU* 3.4 32.3 - - - +
404D ASN 3.2 18.6 + - - +
405D LEU 3.6 2.9 - - - +
407D ILE* 1.3 79.1 - - - +
409D LEU* 1.3 61.4 + - + +
411D GLN* 3.2 26.0 + - - +
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Residues in contact with LEU 409 (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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5D ILE* 6.4 0.4 - - + -
34D TYR* 3.6 36.8 - - + -
354D PHE* 5.1 11.2 - - + -
355D PHE* 3.7 24.2 - - + -
358D ALA* 4.0 26.9 - - + -
405D LEU* 2.9 38.1 + - + +
406D LYS 3.3 2.5 - - - +
408D LYS* 1.3 78.4 - - + +
410D ALA* 1.3 67.0 + - - +
411D GLN 3.1 11.6 + - - -
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Residues in contact with ALA 410 (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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406D LYS 2.5 17.9 + - - +
407D ILE* 3.4 19.2 + - + +
409D LEU* 1.3 72.4 - - - +
411D GLN* 1.3 61.7 + - + +
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Residues in contact with GLN 411 (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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407D ILE* 4.3 10.6 + - - +
408D LYS* 3.2 21.6 - - - +
409D LEU* 3.1 14.1 - - - -
410D ALA* 1.3 82.6 - - + +
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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
------------------------------------------------------------
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