Contacts of the helix formed by residues 273 - 286 (chain D) in PDB entry 3QLA
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 LEU 273 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192D LEU* 3.6 44.0 - - + +
194D VAL* 4.4 5.8 - - + -
222D TRP* 3.9 25.1 - - + -
248D LEU* 3.8 17.7 - - + -
266D TYR* 3.6 37.7 - - + +
270D PRO* 2.8 12.4 + - + +
272D PRO* 1.3 83.3 - - - +
274D LEU* 1.3 53.7 + - - +
275D ASP 3.2 2.9 - - - -
276D LEU* 2.9 9.9 + - + +
277D VAL* 2.8 43.5 + - + +
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Residues in contact with LEU 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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270D PRO* 3.0 16.6 - - + +
271D GLU* 2.7 55.5 + - + +
272D PRO 3.4 0.6 - - - -
273D LEU* 1.3 76.9 - - - +
275D ASP* 1.3 62.0 + - - +
277D VAL* 3.1 13.0 + - + +
278D THR* 2.8 36.6 + - - +
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Residues in contact with ASP 275 (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 PRO 4.8 4.6 + - - +
273D LEU 3.2 0.6 - - - -
274D LEU* 1.3 80.4 - - - +
276D LEU* 1.3 59.7 + - + +
278D THR* 3.3 8.3 + - - -
279D ALA* 2.8 29.5 + - - +
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Residues in contact with LEU 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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172D THR* 4.0 19.2 - - + +
194D VAL* 3.5 18.3 - - + +
195D LEU* 4.8 1.0 + - - +
222D TRP* 3.8 30.1 - - + -
247D ASN* 3.9 23.1 - - + +
248D LEU* 4.1 16.2 - - + -
272D PRO 5.1 0.7 - - - +
273D LEU* 2.9 14.1 + - + +
275D ASP* 1.3 76.4 - - + +
277D VAL* 1.3 61.8 + - - +
279D ALA* 3.7 10.6 - - + +
280D CYS* 2.9 27.9 + - - +
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Residues in contact with VAL 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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188D ARG* 5.8 0.4 - - - +
192D LEU 3.4 26.0 - - - +
193D GLN* 3.6 25.8 - - + +
194D VAL* 4.1 2.7 - - + -
270D PRO* 5.9 1.3 - - + +
273D LEU* 2.8 23.6 + - + +
274D LEU* 3.5 17.0 - - + +
276D LEU* 1.3 76.5 - - - +
278D THR* 1.3 60.3 + - - +
280D CYS* 3.2 4.2 + - - +
281D ASN* 2.9 42.1 + - - +
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Residues in contact with THR 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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274D LEU* 2.8 20.0 + - - +
275D ASP* 3.5 9.2 + - - -
277D VAL* 1.3 75.3 - - - +
279D ALA* 1.3 60.4 + - - +
281D ASN* 3.0 15.6 + - + +
282D SER* 2.8 34.9 + - - +
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Residues in contact with ALA 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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275D ASP 2.8 20.8 + - - +
276D LEU* 3.7 13.7 - - + +
278D THR* 1.3 73.0 - - - +
280D CYS* 1.3 65.0 + - - +
282D SER* 3.2 9.1 + - - -
283D VAL* 3.0 29.3 + - + +
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Residues in contact with CYS 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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187D TYR 4.6 0.2 - - - -
188D ARG* 3.3 36.6 - - - +
193D GLN 3.8 8.5 - - - +
194D VAL 3.7 1.1 - - - -
195D LEU* 3.5 40.8 - - - +
276D LEU 2.9 15.0 + - - +
277D VAL 3.3 9.4 - - - +
279D ALA* 1.3 75.7 - - - +
281D ASN* 1.3 63.3 + - - +
283D VAL* 3.2 6.5 + - - +
284D TYR* 3.1 35.6 + - - -
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Residues in contact with ASN 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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188D ARG* 2.5 41.8 + - - +
277D VAL* 2.9 31.2 + - - +
278D THR* 3.2 15.1 + - + +
280D CYS* 1.3 76.0 - - - +
282D SER* 1.3 62.4 + - - +
284D TYR* 3.2 4.7 + - - +
285D GLU* 2.9 38.0 + - + +
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Residues in contact with SER 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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278D THR* 2.8 25.5 + - - +
279D ALA* 3.2 11.3 + - - -
281D ASN* 1.3 73.5 - - - +
283D VAL* 1.3 65.8 + - - +
285D GLU* 3.0 18.8 + - - +
286D ASN* 2.8 40.6 + - - -
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Residues in contact with VAL 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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169D VAL* 3.4 31.4 - - + -
180D HIS* 4.6 5.4 - - + -
186D ILE* 3.8 24.2 - - + -
195D LEU* 3.7 28.5 - - + -
279D ALA* 3.0 19.8 + - + +
280D CYS 3.2 8.3 + - - +
282D SER* 1.3 74.7 - - - +
284D TYR* 1.3 66.4 + - - +
286D ASN* 3.5 8.4 + - - +
287D LEU* 3.4 16.5 + - + +
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Residues in contact with TYR 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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183D LYS* 3.4 46.1 - - + -
186D ILE* 2.7 43.0 + - + -
187D TYR* 3.5 0.3 - - - -
188D ARG* 3.4 63.2 + - + +
280D CYS* 3.1 24.0 + - - -
281D ASN 3.3 6.5 - - - +
283D VAL* 1.3 77.0 - - - +
285D GLU* 1.3 69.3 + - - +
287D LEU* 2.9 20.5 + - - +
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Residues in contact with GLU 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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183D LYS* 4.2 6.0 + - - +
281D ASN* 2.9 35.9 + - + +
282D SER* 3.3 19.4 + - - +
284D TYR* 1.3 73.3 - - - +
286D ASN* 1.3 68.4 + - - +
287D LEU 2.8 13.5 + - - +
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Residues in contact with ASN 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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282D SER* 2.8 35.9 + - - +
283D VAL* 3.5 6.1 + - - +
284D TYR 3.2 0.2 - - - -
285D GLU* 1.3 82.1 - - - +
287D LEU* 1.3 58.2 + - - +
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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