Contacts of the helix formed by residues 394 - 413 (chain D) in PDB entry 5DO7
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 GLY 394 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D ARG* 5.0 5.8 - - - +
392D MET 3.7 2.2 + - - -
393D PRO* 1.3 85.4 - - - +
395D ALA* 1.3 59.6 + - - -
396D VAL* 3.7 2.9 - - - -
397D GLN* 3.3 3.2 + - - -
398D GLN* 3.0 36.9 + - - +
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Residues in contact with ALA 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394D GLY* 1.3 66.5 - - - -
396D VAL* 1.3 67.3 + - - +
398D GLN* 3.2 16.7 - - - +
399D PHE* 3.1 18.9 + - - +
489D THR* 5.9 3.4 - - + -
490D GLY* 4.9 9.0 - - - +
491D PRO* 4.2 19.4 - - + +
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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
----------------------------------------------------------
394D GLY* 5.0 0.9 - - - -
395D ALA* 1.3 75.3 - - - +
397D GLN* 1.3 84.8 + - + +
399D PHE* 2.8 25.4 + - + +
400D THR* 2.8 27.0 + - - +
490D GLY* 6.2 0.4 - - - -
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Residues in contact with GLN 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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172D GLN* 4.0 27.2 + - - +
173D MET* 5.8 0.2 - - - -
177D ARG* 5.6 5.8 - - + -
184D ARG* 5.5 6.9 - - - +
393D PRO* 3.5 24.9 - - + +
394D GLY 3.3 0.6 + - - +
395D ALA 3.3 1.0 - - - -
396D VAL* 1.3 90.1 - - + +
398D GLN* 1.3 65.5 + - - +
400D THR* 3.5 9.2 + - - -
401D THR* 3.1 25.1 + - - -
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Residues in contact with GLN 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D MET* 4.3 22.0 - - + -
393D PRO* 3.7 28.4 - - + +
394D GLY 3.0 21.9 + - - +
395D ALA* 3.2 8.5 - - - +
396D VAL 2.9 0.2 + - - -
397D GLN* 1.3 72.9 - - - +
399D PHE* 1.3 68.9 + - - +
401D THR* 2.8 16.3 + - - -
402D LEU* 2.8 16.7 + - + +
484D ASP 5.0 3.2 + - - -
485D GLY 3.7 24.2 + - - +
486D LEU* 4.6 1.3 - - - -
487D TYR* 3.8 10.6 + - - +
491D PRO* 3.0 29.3 - - + +
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Residues in contact with PHE 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395D ALA 3.1 6.5 + - - +
396D VAL* 2.8 19.2 + - + +
398D GLN* 1.3 74.9 - - - +
400D THR* 1.3 73.6 + - + +
402D LEU* 3.1 3.5 + - - +
403D ILE* 2.8 41.8 + - + +
490D GLY 3.9 15.7 - - - +
491D PRO* 3.9 22.9 - - + +
494D PHE* 3.3 40.8 - + + -
495D ALA* 3.9 12.8 - - - -
498D LEU* 3.7 25.8 - - + -
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Residues in contact with THR 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 VAL* 2.8 30.8 + - - +
397D GLN* 3.7 10.6 - - - -
399D PHE* 1.3 78.0 - - + +
401D THR* 1.3 61.3 + - - +
403D ILE* 2.9 30.1 - - + +
404D ARG* 3.0 38.4 + - - +
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Residues in contact with THR 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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169D PHE* 3.4 40.7 - - + +
172D GLN* 4.1 16.8 + - + +
173D MET* 3.8 23.9 - - + +
397D GLN* 3.1 21.4 + - - -
398D GLN 2.8 12.4 + - - -
400D THR* 1.3 69.8 - - - +
402D LEU* 1.3 68.5 + - - +
404D ARG* 2.8 10.5 + - - +
405D ARG* 2.8 24.2 + - + +
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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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173D MET* 3.9 10.3 - - + -
398D GLN* 2.8 18.7 + - + +
399D PHE* 3.4 7.0 - - - +
401D THR* 1.3 73.0 - - - +
403D ILE* 1.3 60.2 + - - +
405D ARG* 3.5 26.4 + - - +
406D GLN* 2.8 36.1 + - + +
486D LEU* 3.1 45.8 - - + -
491D PRO* 3.4 32.3 - - + +
492D TYR* 4.0 14.1 - - + -
495D ALA* 4.1 10.3 - - + -
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Residues in contact with ILE 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 PHE* 2.8 35.7 + - + +
400D THR* 2.9 32.1 - - + +
402D LEU* 1.3 73.2 - - - +
404D ARG* 1.3 61.3 + - - +
406D GLN* 4.3 3.1 - - + -
407D ILE* 2.8 49.4 + - + +
495D ALA 3.1 18.4 - - - +
498D LEU* 3.7 14.1 - - + -
499D GLY* 3.1 38.6 - - - +
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Residues in contact with ARG 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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169D PHE* 3.9 23.8 - - + -
400D THR* 3.0 41.8 + - - +
401D THR* 2.8 11.4 + - - +
403D ILE* 1.3 81.9 - - - +
405D ARG* 1.3 57.8 + - - +
407D ILE* 3.4 8.6 - - + +
408D SER* 2.8 39.2 + - - +
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Residues in contact with ARG 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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158D LEU* 3.6 22.8 - - + +
161D LEU* 3.8 14.9 - - + +
166D THR* 5.6 6.2 - - - +
169D PHE* 3.7 48.2 - - + -
170D ILE* 4.3 9.9 - - - +
173D MET* 4.1 14.4 - - - +
401D THR* 2.8 18.9 + - + +
402D LEU* 3.5 28.1 + - - +
404D ARG* 1.3 75.0 - - - +
406D GLN* 1.3 67.8 + - - +
407D ILE 3.2 0.7 + - - -
408D SER* 3.2 7.6 + - - -
409D ASN* 3.2 16.6 + - - +
480D TYR* 2.7 50.5 + - - -
486D LEU* 5.1 0.2 - - - +
492D TYR* 5.7 3.8 + - - -
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Residues in contact with GLN 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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158D LEU* 5.2 5.6 - - - -
402D LEU* 2.8 24.4 + - + +
403D ILE* 3.9 5.6 - - - +
405D ARG* 1.3 80.9 - - - +
407D ILE* 1.3 59.9 + - - +
409D ASN* 4.3 2.9 - - - +
410D ASP* 3.4 36.6 + - - +
474D GLU* 4.5 11.8 - - - +
492D TYR* 5.4 2.4 + - - -
495D ALA 4.8 6.5 - - - +
496D LYS* 4.2 22.0 + - - +
499D GLY* 4.0 34.2 + - - -
500D GLU* 4.5 4.8 + - - +
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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 ILE* 2.8 41.5 + - + +
404D ARG* 3.4 13.0 - - + +
406D GLN* 1.3 75.5 - - + +
408D SER* 1.3 74.2 + - - +
410D ASP* 4.6 2.5 - - + -
411D PHE* 3.1 35.4 + - + +
498D LEU 4.8 0.9 - - - +
499D GLY* 3.7 25.6 - - - +
502D PRO* 4.1 20.2 - - + -
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Residues in contact with SER 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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161D LEU* 4.1 17.0 - - - -
169D PHE* 4.4 9.5 - - - -
404D ARG* 2.8 27.5 + - - +
405D ARG* 3.6 6.1 - - - -
407D ILE* 1.3 75.7 - - - +
409D ASN* 1.3 67.6 + - - +
411D PHE* 2.8 16.1 + - - +
412D ARG* 2.8 25.9 + - - +
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Residues in contact with ASN 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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158D LEU* 3.1 44.5 - - - +
159D PRO* 4.4 5.9 - - - +
160D ASN* 3.5 27.9 - - + +
161D LEU* 4.0 17.3 - - + -
405D ARG 3.2 6.7 + - - +
406D GLN* 4.3 5.1 + - - +
408D SER* 1.3 79.4 - - - +
410D ASP* 1.3 84.0 + - - +
412D ARG* 3.0 9.9 + - - +
413D ASP* 2.8 27.9 + - - +
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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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406D GLN* 3.4 33.2 + - - +
407D ILE* 4.3 4.0 - - + +
408D SER 3.2 0.6 - - - -
409D ASN* 1.3 88.1 + - - +
411D PHE* 1.3 67.1 + - + +
413D ASP* 3.4 22.5 - - - +
416D THR* 4.6 7.3 + - - -
417D LEU* 4.2 12.0 - - - +
470D LYS* 4.0 16.1 + - - +
499D GLY 4.9 5.1 - - - +
500D GLU* 5.1 4.2 - - - +
503D GLU* 3.6 23.8 - - - +
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Residues in contact with PHE 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* 3.1 29.7 + - + +
408D SER* 2.8 11.1 + - - +
410D ASP* 1.3 77.5 - - + +
412D ARG* 1.3 57.9 + - + +
413D ASP 3.2 11.2 + - - +
414D LEU* 4.7 4.7 + - - +
417D LEU* 4.0 27.4 - - + +
499D GLY 5.7 1.1 - - - -
502D PRO* 4.2 29.2 - - + -
503D GLU* 4.2 20.0 - - + -
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Residues in contact with ARG 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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160D ASN* 3.1 36.2 + - + +
161D LEU* 3.9 4.2 - - - +
162D THR* 4.5 4.9 - - - +
165D GLU* 3.1 35.1 + - - -
204D ARG* 3.5 38.2 + - - +
408D SER* 2.8 41.5 + - - +
409D ASN* 3.0 5.6 + - - +
411D PHE* 1.3 70.5 - - + +
413D ASP* 1.3 59.7 + - - +
414D LEU* 3.3 7.8 + - - +
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Residues in contact with ASP 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D ASN* 3.2 17.9 + - - +
409D ASN* 2.8 8.9 + - - +
410D ASP* 3.4 24.0 - - - +
411D PHE 3.2 1.1 - - - -
412D ARG* 1.3 74.8 - - - +
414D LEU* 1.3 61.4 + - - +
415D PRO* 3.2 24.1 - - - +
416D THR* 2.3 41.4 + - - +
417D LEU* 3.3 20.4 - - - +
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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