Contacts of the helix formed by residues 214 - 228 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10N PHE* 3.6 20.4 - - + -
11N ILE* 4.5 10.1 - - + -
14N ASN* 3.5 43.7 - - + +
170N VAL* 3.8 16.2 - - + -
171N TYR 2.9 22.2 + - - +
172N GLY* 3.8 16.2 - - - -
173N PRO* 3.9 10.1 - - + -
212N VAL 3.6 0.6 + - - -
213N TYR* 1.3 74.4 - - + +
215N GLY* 1.3 64.9 + - - +
217N VAL* 3.1 5.9 + - + +
218N ALA* 2.9 22.6 + - - +
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Residues in contact with GLY 215 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N ASN* 5.6 2.2 - - - -
213N TYR* 3.1 19.7 - - - -
214N VAL* 1.3 83.8 - - - +
216N ASP* 1.3 63.5 + - - +
218N ALA* 3.4 7.6 + - - +
219N ASP* 3.1 28.6 + - - +
293N LYS* 5.9 0.9 - - - -
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Residues in contact with ASP 216 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212N VAL* 4.4 3.4 - - + -
213N TYR* 2.9 17.1 + - - +
215N GLY* 1.3 76.0 - - - +
217N VAL* 1.3 66.9 + - - +
219N ASP* 3.0 13.6 + - - +
220N VAL* 2.9 29.1 + - - +
288N TYR* 4.5 3.0 + - - +
291N PRO 4.7 4.4 - - - +
292N PHE* 3.4 30.1 - - + +
293N LYS* 2.8 54.5 + - - +
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Residues in contact with VAL 217 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N ILE* 4.0 21.3 - - + -
167N TYR* 3.6 31.0 - - + -
170N VAL* 3.9 27.4 - - + -
212N VAL* 4.2 8.5 - - + -
213N TYR 3.2 10.7 + - - +
214N VAL* 3.1 9.8 + - + +
216N ASP* 1.3 77.6 - - - +
218N ALA* 1.3 63.5 + - - +
220N VAL* 3.3 2.6 + - - +
221N ASN* 3.0 33.2 + - - +
235N LEU* 4.1 24.2 - - + +
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Residues in contact with ALA 218 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N ASN* 3.9 29.4 - - + +
15N ILE* 4.6 7.4 - - + +
18N ALA* 4.0 13.7 - - + -
214N VAL 2.9 12.3 + - - +
215N GLY* 3.5 11.9 - - - +
217N VAL* 1.3 79.7 - - - +
219N ASP* 1.3 64.1 + - - +
221N ASN* 3.1 10.0 + - - +
222N LEU* 3.0 26.6 + - - +
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Residues in contact with ASP 219 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18N ALA* 5.3 4.9 - - - +
215N GLY 3.1 19.4 + - - +
216N ASP* 3.0 16.1 + - - +
218N ALA* 1.3 78.0 - - - +
220N VAL* 1.3 64.1 + - - +
222N LEU* 3.2 7.4 + - - +
223N TRP* 2.9 24.6 + - - +
288N TYR* 4.0 14.1 - - + +
290N LYS* 5.7 4.6 - - + +
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Residues in contact with VAL 220 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165N PHE* 3.6 25.6 - - + -
216N ASP 2.9 16.4 + - - +
217N VAL 3.6 7.4 - - - +
219N ASP* 1.3 74.8 - - - +
221N ASN* 1.3 64.7 + - - +
223N TRP* 3.1 1.9 + - - +
224N PHE* 3.0 36.8 + - + -
235N LEU* 3.6 31.4 - - + -
283N LEU* 4.6 6.1 - - + -
288N TYR* 3.6 36.1 - - + +
292N PHE* 4.1 6.3 - - + -
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Residues in contact with ASN 221 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15N ILE* 3.6 24.5 - - + +
73N PHE* 3.4 30.8 - - + -
75N GLU* 3.8 3.6 - - - +
112N LEU* 4.1 1.7 - - - +
165N PHE* 3.3 31.4 - - - -
167N TYR* 3.1 24.0 + - - -
217N VAL* 3.0 29.7 + - - +
218N ALA* 3.1 9.2 + - - +
220N VAL* 1.3 79.1 - - - +
222N LEU* 1.3 65.9 + - + +
224N PHE* 3.3 3.3 + - - +
225N LEU* 3.1 20.3 + - - +
235N LEU* 4.7 0.2 - - - +
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Residues in contact with LEU 222 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15N ILE* 4.5 9.9 - - + -
18N ALA* 3.8 36.6 - - + +
19N LEU* 3.9 29.8 - - + +
22N LYS* 3.8 28.3 - - + -
73N PHE* 4.1 14.6 - - + -
218N ALA 3.0 17.1 + - - +
219N ASP* 3.9 7.9 - - - +
221N ASN* 1.3 77.8 - - + +
223N TRP* 1.3 64.3 + - - +
225N LEU* 3.2 8.4 + - + +
226N GLU* 3.0 38.0 + - + +
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Residues in contact with TRP 223 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219N ASP 2.9 17.0 + - - +
220N VAL 3.1 4.2 + - - +
222N LEU* 1.3 76.8 - - - +
224N PHE* 1.3 92.5 + + - +
226N GLU* 3.2 6.4 + - - -
227N ASN* 2.7 74.3 + - + +
229N VAL* 4.5 4.3 - - + -
286N ALA 3.6 15.9 - - - -
287N GLY* 3.5 32.5 + - - -
288N TYR* 3.5 36.7 - + + +
289N ASP* 5.9 1.0 + - - -
290N LYS* 4.0 22.4 - - - +
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Residues in contact with PHE 224 (chain N).
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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112N LEU* 4.0 6.7 - - + -
161N GLN* 2.9 12.1 + - - +
163N VAL* 4.1 7.4 - - + -
165N PHE* 3.5 33.2 - + + -
220N VAL* 3.0 24.9 + - + +
221N ASN 3.8 2.0 - - - +
223N TRP* 1.3 97.4 - + - +
225N LEU* 1.3 65.7 + - - +
227N ASN* 4.4 0.4 - - - +
228N GLY 2.9 21.3 + - - -
229N VAL* 3.8 35.0 - - + -
233N PHE* 3.6 37.5 - + - -
283N LEU* 3.7 26.2 - - + -
286N ALA* 4.2 12.8 - - + -
288N TYR* 4.5 2.5 - - + -
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Residues in contact with LEU 225 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2N ILE* 4.2 15.9 - - + -
19N LEU* 5.1 4.9 - - + -
24N ILE* 6.3 0.7 - - + -
70N GLU* 4.5 15.3 - - + +
71N ALA* 3.6 26.9 - - + -
73N PHE* 3.7 29.8 - - + -
110N PRO* 4.4 11.7 - - + -
112N LEU* 3.9 11.7 - - + +
161N GLN* 4.2 7.6 - - - +
221N ASN 3.1 12.6 + - - +
222N LEU* 3.5 11.4 - - + +
224N PHE* 1.3 78.9 - - - +
226N GLU* 1.3 66.1 + - + +
227N ASN 3.3 0.2 + - - -
228N GLY* 3.8 5.5 + - - -
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Residues in contact with GLU 226 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22N LYS* 3.1 37.3 + - - +
222N LEU* 3.0 22.8 + - - +
223N TRP* 3.7 10.6 - - - +
225N LEU* 1.3 80.5 - - + +
227N ASN* 1.3 67.6 + - - +
228N GLY 3.6 0.2 - - - -
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Residues in contact with ASN 227 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223N TRP* 2.7 79.7 + - + +
224N PHE 4.3 1.1 - - - +
226N GLU* 1.3 90.8 + - - +
228N GLY* 1.3 56.8 + - - +
229N VAL* 3.2 17.0 + - + +
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Residues in contact with GLY 228 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161N GLN* 3.2 30.8 + - - +
224N PHE 2.9 8.1 + - - -
225N LEU 3.8 3.7 + - - -
226N GLU 3.6 1.8 - - - -
227N ASN* 1.3 76.1 - - - +
229N VAL* 1.3 62.8 + - - +
230N SER* 3.7 2.9 + - - -
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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