Contacts of the helix formed by residues 276 - 293 (chain D) in PDB entry 2Y05
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 GLN 276 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D TYR* 2.8 42.1 + - - +
274D ARG 3.7 5.4 + - - +
275D TRP* 1.3 78.1 + - - +
277D GLY* 1.3 69.2 + - - +
278D ASP 3.4 1.7 + - - -
279D ALA* 3.7 7.1 + - - +
280D ARG* 3.5 28.8 + - - +
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Residues in contact with GLY 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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276D GLN* 1.3 77.8 + - - +
278D ASP* 1.3 59.6 + - - -
280D ARG* 3.3 4.4 + - - +
281D GLN* 3.0 29.9 + - - +
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Residues in contact with ASP 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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276D GLN 3.4 1.0 + - - -
277D GLY* 1.3 70.1 - - - -
279D ALA* 1.3 56.8 + - - +
281D GLN* 3.5 9.2 - - - +
282D LYS* 2.6 38.1 + - - +
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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
----------------------------------------------------------
130D TYR* 5.5 0.2 - - - -
131D PHE* 3.4 23.3 - - + -
135D GLU* 6.0 0.7 - - - +
275D TRP* 4.5 15.3 - - + -
276D GLN 3.7 8.6 + - - +
277D GLY 3.4 0.6 - - - -
278D ASP* 1.3 76.6 - - - +
280D ARG* 1.3 63.3 + - - +
282D LYS* 3.8 6.8 - - - +
283D ALA* 3.0 18.4 + - - +
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Residues in contact with ARG 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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66D GLN* 6.2 0.2 - - - +
86D LEU* 5.4 1.4 - - - +
103D GLU* 2.9 39.4 + - - -
123D GLY* 6.2 0.6 - - - -
127D LEU* 3.9 27.7 - - + +
131D PHE* 4.3 10.5 - - + -
273D TYR* 6.4 0.4 - - - -
275D TRP 3.5 25.6 - - - +
276D GLN* 3.5 28.2 + - - +
277D GLY 3.3 9.7 + - - +
278D ASP 3.2 0.4 - - - -
279D ALA* 1.3 78.1 - - - +
281D GLN* 1.3 66.8 + - - +
283D ALA* 3.2 3.5 + - - +
284D LEU* 2.9 54.9 + - + +
1331D EDO 4.7 4.2 + - - -
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Residues in contact with GLN 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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106D LEU* 3.5 26.6 - - - +
107D THR 6.0 0.2 - - - +
108D GLU* 5.6 0.2 + - - -
277D GLY 3.0 17.5 + - - +
278D ASP* 3.6 13.0 - - - +
280D ARG* 1.3 84.1 + - - +
282D LYS* 1.3 62.4 + - - +
284D LEU* 3.4 13.8 + - - +
285D LYS* 3.1 49.1 + - - +
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Residues in contact with LYS 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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130D TYR* 4.8 4.7 - - - +
278D ASP 2.6 22.7 + - - +
279D ALA* 3.8 5.6 - - - +
281D GLN* 1.3 70.1 - - - +
283D ALA* 1.3 65.3 + - - +
285D LYS* 3.2 8.9 + - - +
286D ASP* 2.9 43.4 + - - +
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Residues in contact with ALA 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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127D LEU* 3.5 23.6 - - + -
130D TYR* 3.5 40.7 + - + -
131D PHE* 3.6 7.9 - - + -
279D ALA 3.0 16.9 + - - +
280D ARG 3.2 0.6 + - - +
282D LYS* 1.3 76.8 - - - +
284D LEU* 1.3 61.6 + - - +
286D ASP* 3.4 1.6 + - - +
287D LEU* 3.0 27.5 + - - +
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Residues in contact with LEU 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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106D LEU* 4.0 18.2 - - + -
122D VAL* 3.8 24.5 - - + +
123D GLY* 4.2 0.9 - - - +
127D LEU* 3.7 29.6 - - + -
280D ARG* 2.9 51.6 + - + +
281D GLN* 3.7 14.4 - - - +
282D LYS 3.2 0.2 - - - -
283D ALA* 1.3 77.0 - - - +
285D LYS* 1.3 57.3 + - - +
287D LEU* 3.2 7.0 + - + +
288D LEU* 2.9 28.8 + - - +
1331D EDO 3.8 34.1 - - - +
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Residues in contact with LYS 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D LEU* 4.4 11.2 - - + -
108D GLU* 3.5 38.7 + - + +
281D GLN* 3.1 42.5 + - - +
282D LYS* 3.6 9.9 - - + +
284D LEU* 1.3 72.8 - - - +
286D ASP* 1.3 63.5 + - - +
288D LEU* 3.4 3.5 + - - +
289D LYS* 2.9 30.7 + - - +
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Residues in contact with ASP 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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130D TYR* 2.6 36.1 + - + -
282D LYS* 2.9 28.7 + - - +
283D ALA 3.6 7.0 - - - +
285D LYS* 1.3 75.9 - - - +
287D LEU* 1.3 58.2 + - - +
289D LYS* 3.4 16.1 + - - +
290D TRP* 2.9 54.7 + - + -
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Residues in contact with LEU 287 (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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121D THR* 3.4 28.0 - - + +
122D VAL* 4.2 9.4 - - + -
126D GLY 3.6 28.7 - - - +
127D LEU* 3.8 18.8 - - + +
130D TYR* 4.2 9.9 - - + -
157D VAL* 4.3 3.6 - - + -
161D ILE* 4.1 15.9 - - + -
283D ALA 3.0 21.7 + - - +
284D LEU* 3.2 6.7 + - + +
286D ASP* 1.3 77.7 - - - +
288D LEU* 1.3 57.7 + - - +
290D TRP* 3.4 5.4 + - + +
291D VAL* 2.9 32.4 + - - +
296D ILE* 3.9 22.5 - - + +
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Residues in contact with LEU 288 (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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106D LEU* 4.1 20.0 - - + -
108D GLU* 4.1 21.8 - - + +
109D TRP* 4.3 7.6 - - + -
110D PRO* 4.0 20.2 - - + -
113D ILE* 3.6 31.2 - - + -
122D VAL* 4.0 18.7 - - + +
284D LEU 2.9 16.4 + - - +
285D LYS* 3.9 4.0 - - - +
287D LEU* 1.3 75.3 - - - +
289D LYS* 1.3 57.6 + - - +
291D VAL* 3.1 3.8 + - + -
292D LEU* 2.8 49.5 + - + +
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Residues in contact with LYS 289 (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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285D LYS 2.9 20.8 + - - +
286D ASP* 3.7 14.4 + - - +
288D LEU* 1.3 70.8 - - - +
290D TRP* 1.3 79.8 + - - +
292D LEU* 2.9 10.1 + - - +
293D GLU* 2.8 63.3 + - + +
295D LYS* 5.8 0.9 - - - +
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Residues in contact with TRP 290 (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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130D TYR* 3.8 28.5 - + - -
134D LEU* 4.7 5.2 - - + -
161D ILE* 3.8 27.6 - - + -
164D LEU* 4.2 23.1 - - + +
165D LYS* 4.3 23.8 - - - -
286D ASP* 2.9 38.2 + - + +
287D LEU* 3.8 4.7 - - + +
289D LYS* 1.3 89.5 - - - +
291D VAL* 1.3 63.3 + - - +
293D GLU* 3.6 17.4 + - - -
294D GLY 3.1 2.8 + - - -
295D LYS* 3.0 47.8 + - + +
296D ILE* 3.1 35.0 + - + -
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Residues in contact with VAL 291 (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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113D ILE* 4.2 18.2 - - + -
117D LEU* 4.1 12.6 - - + -
121D THR* 3.7 29.2 - - + -
122D VAL* 3.9 10.5 - - + -
287D LEU 2.9 18.3 + - - +
288D LEU* 3.5 9.2 - - + +
290D TRP* 1.3 77.7 - - - +
292D LEU* 1.3 64.5 + - + +
294D GLY* 3.1 13.3 + - - -
296D ILE* 3.5 18.4 - - + +
298D TYR* 4.0 27.4 - - + -
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Residues in contact with LEU 292 (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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108D GLU 5.6 1.3 - - - +
110D PRO* 3.9 31.4 - - + -
112D THR* 4.0 12.6 - - - +
113D ILE* 4.3 13.0 - - + -
288D LEU* 2.8 38.6 + - + +
289D LYS* 3.5 10.5 - - - +
291D VAL* 1.3 72.5 - - - +
293D GLU* 1.3 62.9 + - + +
294D GLY 3.4 0.5 + - - -
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Residues in contact with GLU 293 (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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289D LYS* 2.8 44.8 + - + +
290D TRP* 3.9 19.7 - - - +
292D LEU* 1.3 73.8 - - + +
294D GLY* 1.3 58.4 + - - +
295D LYS* 3.0 38.4 + - + +
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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