Contacts of the helix formed by residues 268 - 275 (chain D) in PDB entry 6NR8
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 268 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494 ASN* 5.9 1.5 + - - -
326 LYS* 3.2 16.1 + - - +
366 GLN* 4.4 0.7 - - - +
266D VAL* 3.5 10.4 - - - +
267D SER* 1.3 81.7 - - - +
269D TYR* 1.3 76.1 + - - +
270D ALA* 2.9 29.2 + - - +
271D GLN* 3.3 32.4 + - + +
272D MET* 3.5 4.7 - - - +
274D ARG* 5.5 0.7 + - - -
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Residues in contact with TYR 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885 THR* 3.1 38.1 - - - +
895 GLY* 4.1 14.7 + - - -
366 GLN* 3.7 14.0 - - - +
596 LEU* 3.7 32.9 + - - +
606 LEU* 4.7 6.1 - - + -
616 GLY* 4.3 10.6 + - - -
796 ARG* 4.0 20.6 - - - -
268D ASP* 1.3 88.1 - - - +
270D ALA* 1.3 79.2 + - + +
272D MET* 3.2 16.7 - - + +
273D ASP* 3.2 22.5 + - - +
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Residues in contact with ALA 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494 ASN* 5.4 2.0 - - - +
606 LEU* 4.1 23.6 - - + -
268D ASP* 2.9 11.6 + - - +
269D TYR* 1.3 90.8 - - + +
271D GLN* 1.3 60.4 + - - +
273D ASP* 3.0 5.3 + - - +
274D ARG* 2.9 50.0 + - - +
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Residues in contact with GLN 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484 GLN* 6.0 1.8 - - - +
264D ILE* 4.2 19.3 - - + +
265D VAL* 4.3 5.4 + - - +
266D VAL* 3.4 8.9 - - + +
267D SER* 3.1 31.5 - - - +
268D ASP* 3.3 27.9 + - + +
270D ALA* 1.3 78.1 - - - +
272D MET* 1.3 61.6 + - - +
274D ARG* 4.1 20.5 - - - +
275D VAL* 3.3 27.0 + - - +
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Residues in contact with MET 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885 THR* 4.0 14.6 - - + +
326 LYS* 3.3 20.2 - - - -
336 LEU* 3.7 15.0 - - + -
366 GLN* 3.3 22.2 - - - +
796 ARG* 4.7 17.3 - - + -
826 TYR* 4.9 8.1 - - + -
836 ILE* 4.9 8.7 - - + -
866 GLU* 5.1 2.7 - - - +
264D ILE* 4.0 15.3 - - + -
266D VAL* 3.9 12.1 - - + -
268D ASP 3.5 7.2 - - - +
269D TYR* 3.2 28.7 - - + +
271D GLN* 1.3 80.9 - - - +
273D ASP* 1.3 60.1 + - + +
275D VAL 4.5 0.2 - - - -
276D LEU* 3.3 34.5 - - + +
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Residues in contact with ASP 273 (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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564 ASP* 5.0 1.9 - - - +
586 LYS* 5.9 0.9 + - - -
606 LEU* 5.4 4.4 - - + +
756 THR* 5.4 1.7 - - - +
786 LYS* 6.0 0.3 - - - +
796 ARG* 2.8 49.2 + - - +
826 TYR* 5.0 4.4 - - - -
269D TYR 3.2 17.9 + - - +
270D ALA* 3.0 7.0 + - - +
272D MET* 1.3 80.9 - - + +
274D ARG* 1.3 65.0 + - + +
275D VAL 3.4 0.2 - - - -
276D LEU* 5.2 0.4 - - - -
277D ARG* 2.7 68.3 + - - +
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Residues in contact with ARG 274 (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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484 GLN* 4.3 9.4 + - - +
494 ASN* 2.7 59.1 + - - +
524 ASP* 3.3 46.8 - - + +
534 ALA* 3.5 7.3 - - - +
564 ASP* 5.4 3.4 - - + -
606 LEU* 5.4 10.1 - - + -
268D ASP* 5.5 0.6 + - - -
270D ALA* 2.9 30.4 + - + +
271D GLN* 4.1 22.9 - - - +
272D MET 3.6 0.2 - - - -
273D ASP* 1.3 81.3 - - + +
275D VAL* 1.3 57.6 + - + +
277D ARG* 3.5 22.4 + - - +
278D GLU* 3.2 32.2 + - - +
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Residues in contact with VAL 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D ILE* 4.0 24.9 - - + -
271D GLN 3.3 20.3 + - - +
274D ARG* 1.3 80.8 - - + +
276D LEU* 1.3 70.8 + - + +
277D ARG 3.5 0.4 - - - -
278D GLU* 3.6 15.0 + - - +
279D GLU* 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
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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