Contacts of the helix formed by residues 382 - 391 (chain D) in PDB entry 3A4Y
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 382 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165D ASN* 5.3 0.2 - - - -
189D TYR* 3.9 2.5 - - - -
193D PRO* 4.1 5.4 - - - -
194D HIS* 3.6 25.7 - - - -
380D HIS 3.3 4.8 + - - -
381D ALA* 1.3 78.9 - - - +
383D GLN* 1.3 67.6 + - - -
384D ASP* 3.2 12.3 + - - -
385D GLU* 3.3 13.0 + - - -
386D LEU* 2.9 17.5 + - - +
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Residues in contact with GLN 383 (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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189D TYR 3.1 24.0 + - - +
190D GLY* 2.9 16.8 - - - +
191D ASP 2.7 31.5 + - - +
192D ARG* 3.6 13.0 - - - +
193D PRO* 3.7 19.0 - - - +
382D GLY* 1.3 71.4 - - - -
384D ASP* 1.3 61.4 + - - +
386D LEU* 3.4 8.2 - - - +
387D LEU* 3.0 39.8 + - + +
408D ALA* 5.3 1.0 - - - +
409D LEU* 4.3 7.6 - - + +
412D LEU* 4.1 22.8 - - - +
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Residues in contact with ASP 384 (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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193D PRO* 3.2 28.8 - - + +
194D HIS 4.8 0.2 + - - -
382D GLY* 3.5 10.0 - - - -
383D GLN* 1.3 72.8 - - - +
385D GLU* 1.3 84.1 + - - +
387D LEU* 3.0 26.8 + - + +
388D ASP* 3.0 19.5 + - - +
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Residues in contact with GLU 385 (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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164D GLY 3.6 1.4 - - - +
165D ASN* 2.9 35.0 + - - -
166D ARG* 3.4 32.3 + - + +
167D GLU* 3.7 19.9 - - - +
381D ALA* 3.5 8.8 - - + -
382D GLY* 3.3 17.7 + - - +
384D ASP* 1.3 94.2 + - - +
386D LEU* 1.3 50.9 + - - +
388D ASP* 2.8 31.1 + - - +
389D TRP* 2.8 19.8 + - - +
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Residues in contact with LEU 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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163D LEU* 3.9 25.4 - - + -
185D ALA* 5.7 0.2 - - + -
186D GLU* 3.3 37.0 - - + +
187D GLY* 3.6 17.5 - - - -
188D THR 5.1 0.2 - - - +
189D TYR 4.7 0.9 - - - +
190D GLY* 4.4 10.3 - - - +
381D ALA* 4.1 22.2 - - + +
382D GLY 2.9 14.2 + - - +
383D GLN 3.4 6.1 - - - +
385D GLU* 1.3 75.7 - - - +
387D LEU* 1.3 62.0 + - - +
389D TRP* 3.3 3.5 + - - -
390D LEU* 2.9 40.0 + - + +
409D LEU* 4.2 21.5 - - + -
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Residues in contact with LEU 387 (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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383D GLN* 3.0 33.0 + - + +
384D ASP* 3.0 20.7 + - + +
386D LEU* 1.3 75.8 - - - +
388D ASP* 1.3 63.5 + - - +
390D LEU* 3.4 2.0 + - - -
391D GLN* 3.2 8.1 + - - -
409D LEU* 3.8 20.0 - - + -
412D LEU* 3.7 37.5 - - + -
413D LEU* 3.9 17.5 - - + +
416D ARG* 2.7 40.4 + - - +
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Residues in contact with ASP 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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166D ARG* 5.6 4.1 + - - +
176D LEU* 4.4 12.2 - - + +
384D ASP* 3.4 15.0 - - - +
385D GLU* 2.8 17.6 + - - +
387D LEU* 1.3 79.0 - - - +
389D TRP* 1.3 61.8 + - - +
391D GLN* 3.5 20.9 - - - +
416D ARG* 5.0 3.8 + - - -
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Residues in contact with TRP 389 (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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128A ARG* 5.2 0.5 + - - -
147D PHE* 4.0 16.6 - + - -
158D VAL* 3.7 17.5 - - + -
160D SER* 3.5 34.3 - - - -
163D LEU* 3.1 44.8 - - + +
174D PRO* 4.7 7.4 - - + -
175D SER 2.8 27.6 + - - -
176D LEU* 4.4 8.5 - - + +
177D PRO* 3.2 55.1 - - + +
183D VAL* 3.8 19.5 - - + -
185D ALA* 4.2 2.5 - - + -
385D GLU 2.8 11.5 + - - +
386D LEU* 3.7 8.1 - - - +
387D LEU 3.3 0.2 - - - -
388D ASP* 1.3 78.2 - - - +
390D LEU* 1.3 79.1 + - + +
391D GLN* 3.5 3.5 + - - +
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Residues in contact with LEU 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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183D VAL* 4.0 21.5 - - + -
185D ALA* 4.1 11.2 - - + -
386D LEU* 2.9 37.8 + - + +
387D LEU 3.9 3.4 - - - +
389D TRP* 1.3 95.6 - - + +
391D GLN* 1.3 69.9 + - - +
393D GLU* 3.1 20.6 + - + +
396D VAL* 3.6 40.8 - - + -
409D LEU* 5.7 2.7 - - + -
413D LEU* 4.2 22.9 - - + -
416D ARG* 4.2 0.4 - - - +
418D GLN* 3.1 10.7 + - - +
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Residues in contact with GLN 391 (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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128A ARG* 4.0 14.2 + - - +
387D LEU 3.2 8.6 + - - +
388D ASP* 3.5 20.2 - - - +
389D TRP 3.3 2.7 - - - +
390D LEU* 1.3 86.2 - - - +
392D GLY* 1.3 65.8 + - - +
393D GLU* 2.7 15.2 + - - +
416D ARG* 3.7 34.3 - - - +
418D GLN* 4.2 1.3 - - - +
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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