Contacts of the helix formed by residues 275 - 286 (chain D) in PDB entry 6QPA
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 275 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185D TRP* 3.5 26.4 - - + -
271D HIS* 3.1 26.5 + - + +
273D MET 5.0 0.7 - - - -
274D VAL* 1.3 79.0 - - - +
276D TYR* 1.3 60.5 + - - +
277D GLU* 2.9 13.8 + - - +
278D LEU* 2.8 29.4 + - + -
279D ARG* 2.8 32.8 + - - +
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Residues in contact with TYR 276 (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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274D VAL 4.1 1.4 + - - -
275D ASP* 1.3 74.1 + - - +
277D GLU* 1.3 67.9 + - + +
279D ARG* 3.4 12.6 + - - +
280D GLN* 3.1 63.3 + - + +
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Residues in contact with GLU 277 (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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185D TRP* 2.8 32.0 + - + +
275D ASP* 2.9 9.6 + - - +
276D TYR* 1.3 87.2 - - + +
278D LEU* 1.3 62.3 + - - +
280D GLN* 3.2 14.4 + - - +
281D ILE* 3.3 22.4 + - + +
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Residues in contact with LEU 278 (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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182D THR* 3.9 23.6 - - + +
185D TRP* 3.6 51.3 - - + -
186D MET* 3.6 23.8 - - + -
271D HIS* 3.7 31.4 - - + +
272D VAL* 3.7 14.1 - - + +
275D ASP* 2.8 17.6 + - - +
277D GLU* 1.3 74.8 - - - +
279D ARG* 1.3 57.0 + - - +
281D ILE* 3.2 8.8 + - + -
282D HIS* 2.9 28.3 + - - +
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Residues in contact with ARG 279 (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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272D VAL 3.3 22.8 + - - +
273D MET* 2.9 31.1 + - - +
275D ASP 2.8 17.6 + - - +
276D TYR* 3.4 13.3 - - - +
278D LEU* 1.3 78.2 - - - +
280D GLN* 1.3 66.7 + - - +
282D HIS* 4.1 0.6 - - - +
283D ASN* 2.9 54.3 + - - +
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Residues in contact with GLN 280 (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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276D TYR* 3.1 61.3 + - + +
277D GLU* 3.7 7.0 - - - +
278D LEU 3.2 0.4 - - - -
279D ARG* 1.3 87.0 + - - +
281D ILE* 1.3 68.0 + - + +
283D ASN* 4.5 7.6 + - - +
284D ASN* 3.0 45.1 + - - +
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Residues in contact with ILE 281 (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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178D GLY* 4.3 2.0 - - - +
181D GLU* 3.7 49.8 - - + +
182D THR* 3.6 23.5 + - - +
185D TRP* 3.9 30.5 - - + +
277D GLU* 3.3 21.1 + - + +
278D LEU* 3.2 9.9 + - + +
280D GLN* 1.3 77.3 - - + +
282D HIS* 1.3 57.5 + - - +
284D ASN* 4.6 0.6 - - - +
285D GLY* 2.9 29.3 + - - -
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Residues in contact with HIS 282 (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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165D HIS* 5.2 1.0 + - - -
182D THR* 3.7 24.9 - - + +
272D VAL* 3.5 42.7 + - + +
278D LEU 2.9 15.6 + - - +
279D ARG 4.1 2.2 - - - +
281D ILE* 1.3 76.4 - - - +
283D ASN* 1.3 60.2 + - - +
286D VAL* 2.9 58.9 + - + +
287D LEU* 3.0 42.2 + - + +
294D PRO* 4.7 11.3 - - + +
296D TYR* 5.2 10.1 + + - -
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Residues in contact with ASN 283 (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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272D VAL 4.7 2.6 - - - +
279D ARG* 2.9 45.5 + - - +
280D GLN* 4.1 10.7 + - - +
282D HIS* 1.3 80.9 + - - +
284D ASN* 1.3 65.0 + - - +
287D LEU* 3.2 28.6 + - + +
288D ALA* 3.0 30.0 + - - +
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Residues in contact with ASN 284 (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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280D GLN* 3.0 38.0 + - - +
281D ILE 4.6 0.2 - - - +
283D ASN* 1.3 81.5 - - - +
285D GLY* 1.3 58.0 + - - +
286D VAL 3.6 0.2 - - - -
288D ALA* 3.7 12.6 - - - +
289D HIS* 3.3 18.9 + - - -
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Residues in contact with GLY 285 (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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174D ALA 3.5 5.2 - - - +
175D PHE* 3.8 4.7 - - - -
178D GLY* 3.3 27.4 - - - -
281D ILE 2.9 16.7 + - - -
284D ASN* 1.3 79.8 - - - +
286D VAL* 1.3 62.4 + - - +
289D HIS* 3.3 18.5 - - - -
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Residues in contact with VAL 286 (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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165D HIS* 3.9 17.7 - - + +
175D PHE* 3.9 22.1 - - + -
178D GLY 3.8 3.4 - - - -
179D ALA* 3.6 33.7 - - + +
182D THR* 3.8 4.3 - - - +
282D HIS* 2.9 45.1 + - + +
285D GLY* 1.3 83.9 - - - +
287D LEU* 1.3 67.2 + - + +
288D ALA 3.2 1.6 - - - -
289D HIS* 3.1 14.8 + - - +
290D LEU* 3.2 20.0 - - + +
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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