Contacts of the helix formed by residues 401 - 417 (chain D) in PDB entry 5TT2
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 ASP 401 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C PHE 4.5 5.2 - - - +
35C GLN* 5.4 0.2 - - - -
36C HIS 3.0 17.9 + - - +
37C PHE* 3.9 8.7 + - - +
38C ALA* 2.8 21.8 + - - +
39C THR* 2.8 34.5 + - - +
287D LYS* 4.8 3.4 - - - +
400D GLU* 1.3 73.4 - - - +
402D GLU* 1.3 66.5 + - - +
403D GLU* 4.1 11.3 - - + +
404D ASP* 3.0 25.4 + - - +
405D LEU* 3.2 11.4 + - - +
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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
----------------------------------------------------------
287D LYS* 5.2 1.9 - - - +
290D LYS* 4.7 18.5 + - - +
291D ASN* 3.5 21.9 + - - +
294D ALA* 3.4 32.4 - - + +
295D VAL* 6.4 0.2 - - - -
400D GLU 3.4 4.6 + - - -
401D ASP* 1.3 70.9 - - - +
403D GLU* 1.3 77.5 + - + +
405D LEU* 3.4 7.9 + - - +
406D LEU* 3.0 39.0 + - + +
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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
----------------------------------------------------------
401D ASP* 4.1 9.8 - - + +
402D GLU* 1.3 91.6 + - + +
404D ASP* 1.3 59.3 + - - +
406D LEU* 3.1 10.2 + - + +
407D GLU* 2.7 48.1 + - + +
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Residues in contact with ASP 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C HIS* 2.8 45.5 + - - +
39C THR* 2.6 34.3 + - + +
353D LEU* 3.6 15.8 - - + +
401D ASP* 3.0 13.8 + - - +
403D GLU* 1.3 79.1 - - - +
405D LEU* 1.3 62.3 + - - +
407D GLU* 3.5 13.3 + - - +
408D ASP* 3.1 23.9 + - - +
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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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291D ASN* 4.0 22.9 - - + +
295D VAL* 4.5 10.8 - - + -
353D LEU* 3.6 21.5 - - + -
354D PHE* 4.0 15.2 - - + -
365D SER* 3.2 27.6 - - - +
397D VAL* 3.7 28.7 - - + -
400D GLU* 3.6 16.2 - - + +
401D ASP 3.2 11.9 + - - +
402D GLU* 3.6 8.1 - - - +
403D GLU 3.2 0.4 - - - -
404D ASP* 1.3 74.9 - - - +
406D LEU* 1.3 66.5 + - - +
408D ASP* 3.1 4.4 + - - +
409D LEU* 3.0 28.8 + - - +
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Residues in contact with LEU 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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294D ALA* 4.2 4.0 - - + +
295D VAL* 4.1 37.5 - - + +
298D PHE* 3.8 36.3 - - + -
402D GLU* 3.0 45.5 + - + +
403D GLU* 3.5 11.7 - - + +
405D LEU* 1.3 75.9 - - - +
407D GLU* 1.3 59.3 + - + +
409D LEU* 3.4 7.5 + - + +
410D ASP* 2.9 30.9 + - - +
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Residues in contact with GLU 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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36C HIS* 5.0 6.3 - - - -
403D GLU* 2.7 31.2 + - + +
404D ASP* 3.8 16.9 - - - +
406D LEU* 1.3 74.0 - - + +
408D ASP* 1.3 58.2 + - - +
410D ASP* 3.5 6.3 + - - +
411D GLN* 2.9 31.0 + - - +
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Residues in contact with ASP 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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351D LEU* 3.8 6.9 - - - +
352D LYS* 2.8 27.2 + - - +
353D LEU* 2.8 34.2 + - + -
354D PHE* 3.0 23.0 + - + -
404D ASP 3.1 17.1 + - - +
405D LEU 3.1 5.1 + - - +
407D GLU* 1.3 77.2 - - - +
409D LEU* 1.3 57.0 + - - +
411D GLN* 3.1 22.0 - - - +
412D ALA* 3.0 27.7 + - - +
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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
----------------------------------------------------------
295D VAL* 3.6 35.2 - - + -
298D PHE* 4.1 15.3 - - + -
299D LEU* 4.4 12.3 - - + -
347D PHE* 3.8 24.9 - - + -
351D LEU* 4.0 6.3 - - + -
354D PHE* 3.6 32.3 - - + -
395D LEU* 4.2 12.6 - - + -
405D LEU 3.0 20.6 + - - +
406D LEU* 3.8 4.7 - - - +
408D ASP* 1.3 72.7 - - - +
410D ASP* 1.3 60.8 + - - +
412D ALA* 3.4 0.5 + - - -
413D LEU* 2.9 41.3 + - + +
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Residues in contact with ASP 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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298D PHE* 3.5 21.0 - - + -
302D ASN* 3.9 14.6 + - - -
304D TRP* 6.1 0.3 - - - -
406D LEU 2.9 18.5 + - - +
407D GLU* 3.7 7.4 - - - +
409D LEU* 1.3 77.1 - - - +
411D GLN* 1.3 62.5 + - - +
413D LEU* 3.8 4.1 - - - +
414D LYS* 3.0 57.4 + - - +
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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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350D ASN* 2.9 44.3 + - - +
352D LYS* 3.3 30.3 - - - +
407D GLU 2.9 17.1 + - - +
408D ASP* 3.1 25.4 - - - +
409D LEU 3.3 0.2 - - - -
410D ASP* 1.3 78.2 + - - +
412D ALA* 1.3 55.2 + - - +
414D LYS* 3.3 9.9 + - - +
415D ALA* 3.0 27.8 + - + +
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Residues in contact with ALA 412 (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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347D PHE* 3.5 40.8 - - + +
350D ASN* 3.8 21.1 - - + -
351D LEU* 3.6 11.9 - - + -
408D ASP 3.0 17.0 + - - +
411D GLN* 1.3 74.6 + - - +
413D LEU* 1.3 66.7 - - - +
415D ALA* 3.2 11.5 + - - +
416D ALA* 3.3 13.7 + - - +
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Residues in contact with LEU 413 (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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298D PHE* 4.5 2.0 - - + -
299D LEU* 4.1 21.1 - - + -
302D ASN* 3.4 37.9 - - - +
304D TRP* 4.1 19.3 - - + +
305D VAL* 4.1 6.3 - - + -
335D PHE* 4.7 3.4 - - + -
337D ILE* 3.7 24.9 - - + -
347D PHE* 3.7 24.2 - - + -
409D LEU 2.9 27.3 + - - +
410D ASP* 3.8 4.0 - - - +
412D ALA* 1.3 77.4 - - - +
414D LYS* 1.3 62.4 + - - +
416D ALA* 3.1 12.0 + - - +
417D HIS* 3.4 20.8 - - - -
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Residues in contact with LYS 414 (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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304D TRP* 4.5 19.3 - - + +
410D ASP* 3.0 50.8 + - - +
411D GLN* 3.6 7.4 - - - +
413D LEU* 1.3 76.7 - - - +
415D ALA* 1.3 60.9 + - - +
417D HIS 3.3 20.9 + - - +
418D PRO* 4.0 3.6 - - - +
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Residues in contact with ALA 415 (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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346D ILE* 3.8 10.8 - - - +
350D ASN* 3.2 33.2 + - + +
411D GLN* 3.0 16.4 + - - +
412D ALA 3.4 10.3 - - - +
413D LEU 3.1 0.4 - - - -
414D LYS* 1.3 76.0 - - - +
416D ALA* 1.3 59.6 + - - +
417D HIS 3.3 0.4 + - - -
418D PRO* 4.2 10.5 - - - +
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Residues in contact with ALA 416 (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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337D ILE* 4.8 1.8 - - + -
343D HIS* 3.6 44.2 - - + +
346D ILE* 3.7 19.3 - - + +
347D PHE* 4.1 5.8 - - + +
412D ALA 3.3 8.9 + - - +
413D LEU 3.1 10.4 + - - +
415D ALA* 1.3 77.1 - - - +
417D HIS* 1.3 74.2 + - + +
418D PRO* 3.6 8.2 - - - +
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Residues in contact with HIS 417 (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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304D TRP* 3.3 75.3 + + + +
337D ILE* 4.4 4.5 - - + +
338D LYS* 3.5 31.8 + - + -
339D GLY* 4.7 1.3 - - - -
343D HIS* 3.7 24.5 - + - +
413D LEU* 3.4 16.8 + - - +
414D LYS* 3.3 12.6 + - - +
415D ALA 3.3 0.2 - - - -
416D ALA* 1.3 87.1 + - + +
418D PRO* 1.3 66.2 - - - +
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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
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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