Contacts of the helix formed by residues 214 - 228 (chain D) in PDB entry 2X86
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 VAL 214 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D PHE* 3.6 20.2 - - + -
11D ILE* 4.5 10.1 - - + -
14D ASN* 3.5 44.9 - - + +
170D VAL* 3.8 15.7 - - + -
171D TYR 2.9 21.5 + - - +
172D GLY* 3.8 15.7 - - - -
173D PRO* 3.9 10.5 - - + -
212D VAL 3.6 0.6 + - - -
213D TYR* 1.3 75.0 - - + +
215D GLY* 1.3 67.4 + - - +
217D VAL* 3.1 6.4 + - + +
218D ALA* 2.9 22.0 + - - +
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Residues in contact with GLY 215 (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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14D ASN* 5.6 2.0 - - - -
213D TYR* 3.1 20.2 + - - -
214D VAL* 1.3 84.2 - - - +
216D ASP* 1.3 59.2 + - - +
218D ALA* 3.4 7.8 + - - +
219D ASP* 3.1 33.3 + - - +
293D LYS* 5.9 0.7 - - - -
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Residues in contact with ASP 216 (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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212D VAL* 4.4 3.1 - - + +
213D TYR* 2.9 18.1 + - - +
215D GLY* 1.3 74.5 - - - +
217D VAL* 1.3 67.2 + - - +
219D ASP* 3.0 13.8 + - - +
220D VAL* 2.9 29.0 + - + +
288D TYR* 4.5 2.9 + - - +
291D PRO 4.8 3.8 - - - +
292D PHE* 3.4 30.7 - - + +
293D LYS* 2.8 54.2 + - - +
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Residues in contact with VAL 217 (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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11D ILE* 4.0 19.7 - - + -
167D TYR* 3.6 30.5 - - + -
170D VAL* 3.9 28.3 - - + -
212D VAL* 4.2 8.5 - - + -
213D TYR 3.8 10.8 - - - +
214D VAL* 3.2 10.5 - - + +
216D ASP* 1.3 78.3 - - - +
218D ALA* 1.3 63.4 + - - +
220D VAL* 3.3 2.9 + - - +
221D ASN* 3.0 32.8 + - - +
235D LEU* 4.1 24.4 - - + +
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Residues in contact with ALA 218 (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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14D ASN* 3.9 29.6 - - + +
15D ILE* 4.7 7.0 - - - +
18D ALA* 4.0 13.5 - - + -
214D VAL* 2.9 11.6 + - - +
215D GLY* 3.5 12.1 - - - +
216D ASP 3.2 0.2 - - - -
217D VAL* 1.3 78.2 - - - +
219D ASP* 1.3 65.6 + - - +
221D ASN* 3.1 9.7 + - - +
222D LEU* 3.0 27.1 + - - +
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Residues in contact with ASP 219 (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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18D ALA* 5.4 4.3 - - - +
215D GLY 3.1 19.1 + - - +
216D ASP* 3.0 17.2 + - - +
218D ALA* 1.3 78.4 - - - +
220D VAL* 1.3 64.8 + - - +
222D LEU* 3.2 7.3 + - - +
223D TRP* 2.9 24.0 + - - +
288D TYR* 4.0 14.3 + - + +
290D LYS* 5.8 4.3 - - + +
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Residues in contact with VAL 220 (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 PHE* 3.6 25.4 - - + -
216D ASP 2.9 18.1 + - - +
217D VAL 3.6 7.0 - - - +
219D ASP* 1.3 74.5 - - - +
221D ASN* 1.3 63.8 + - - +
223D TRP* 3.1 1.9 + - - +
224D PHE* 3.0 35.8 + - + -
235D LEU* 3.6 32.1 - - + -
283D LEU* 4.6 6.5 - - + -
288D TYR* 3.6 36.1 - - + +
292D PHE* 4.1 6.7 - - + -
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Residues in contact with ASN 221 (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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15D ILE* 3.5 23.1 - - + +
73D PHE* 3.4 31.8 - - + -
75D GLU* 3.8 3.3 - - - +
112D LEU* 4.1 2.1 - - - +
165D PHE* 3.3 30.6 - - - -
167D TYR* 3.1 24.0 + - - -
217D VAL* 3.0 30.5 + - - +
218D ALA 3.1 8.7 + - - +
220D VAL* 1.3 78.0 - - - +
222D LEU* 1.3 65.7 + - + +
224D PHE* 3.3 3.3 + - - +
225D LEU* 3.1 19.8 + - - +
235D LEU* 4.7 0.2 - - - +
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Residues in contact with LEU 222 (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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15D ILE* 4.5 9.9 - - + -
18D ALA* 3.8 35.2 - - + +
19D LEU* 3.9 29.4 - - + +
22D LYS* 3.8 28.0 - - + -
73D PHE* 4.1 14.6 - - + -
218D ALA 3.0 17.8 + - - +
219D ASP* 3.9 7.4 - - - +
221D ASN* 1.3 78.3 - - - +
223D TRP* 1.3 63.8 + - - +
225D LEU* 3.2 8.0 + - + +
226D GLU* 3.0 37.2 + - - +
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Residues in contact with TRP 223 (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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219D ASP 2.9 16.8 + - - +
220D VAL 3.1 4.5 + - - +
222D LEU* 1.3 77.2 - - - +
224D PHE* 1.3 92.5 + + - +
226D GLU* 3.2 6.6 + - - -
227D ASN* 2.7 75.5 + - + +
229D VAL* 4.5 3.4 - - + -
286D ALA 3.6 15.5 - - - -
287D GLY* 3.5 32.9 + - - -
288D TYR* 3.5 35.1 - + + +
289D ASP* 5.9 0.6 + - - -
290D LYS* 4.0 22.1 - - - +
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Residues in contact with PHE 224 (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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112D LEU* 4.0 7.2 - - + -
161D GLN* 2.9 11.5 + - - +
163D VAL* 4.1 7.4 - - + -
165D PHE* 3.5 33.9 - + + -
220D VAL* 3.0 25.3 + - + +
221D ASN 3.8 2.0 - - - +
223D TRP* 1.3 98.3 - + - +
225D LEU* 1.3 64.6 + - - +
227D ASN* 4.4 0.9 - - - +
228D GLY 2.9 21.7 + - - -
229D VAL* 3.8 34.3 + - + -
233D PHE* 3.6 37.2 - + - -
283D LEU* 3.7 26.5 - - + -
286D ALA* 4.2 13.2 - - + -
288D TYR* 4.5 2.5 - - + -
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Residues in contact with LEU 225 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D ILE* 4.2 15.3 - - + -
19D LEU* 5.1 5.2 - - + -
24D ILE* 6.2 1.1 - - + -
70D GLU* 4.5 14.8 - - + +
71D ALA* 3.7 25.6 - - + -
73D PHE* 3.7 30.3 - - + -
110D PRO* 4.4 7.6 - - + -
112D LEU* 3.9 12.6 - - + +
161D GLN* 4.2 12.0 - - - +
221D ASN 3.1 12.7 + - - +
222D LEU* 3.2 11.4 + - + +
224D PHE* 1.3 78.8 - - - +
226D GLU* 1.3 65.0 + - + +
227D ASN 3.3 0.2 + - - -
228D GLY* 3.8 5.2 + - - -
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Residues in contact with GLU 226 (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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22D LYS* 3.1 37.5 + - - +
222D LEU* 3.0 22.8 + - - +
223D TRP* 3.2 10.7 + - - +
225D LEU* 1.3 81.5 - - + +
227D ASN* 1.3 68.7 + - - +
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Residues in contact with ASN 227 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223D TRP* 2.7 81.4 + - + +
224D PHE 4.3 0.9 - - - +
225D LEU 3.2 0.2 - - - -
226D GLU* 1.3 90.8 + - - +
228D GLY* 1.3 56.1 + - - +
229D VAL* 3.2 16.7 + - + +
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Residues in contact with GLY 228 (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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161D GLN* 3.2 31.0 + - - +
224D PHE 2.9 8.6 + - - -
225D LEU 3.8 3.9 + - - -
226D GLU 3.6 1.6 + - - -
227D ASN* 1.3 76.7 - - - +
229D VAL* 1.3 62.5 + - - +
230D SER* 3.7 2.6 + - - -
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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