Contacts of the helix formed by residues 214 - 228 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F PHE* 3.6 20.6 - - + -
11F ILE* 4.5 10.1 - - + +
14F ASN* 3.5 42.8 - - + +
170F VAL* 3.8 14.4 - - + -
171F TYR 2.9 20.4 + - - +
172F GLY* 3.8 16.2 - - - -
173F PRO* 3.9 10.5 - - + -
212F VAL 3.6 0.6 + - - -
213F TYR* 1.3 75.9 - - + +
215F GLY* 1.3 65.1 + - - +
217F VAL* 3.1 6.3 + - + +
218F ALA* 2.9 22.4 + - - +
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Residues in contact with GLY 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ASN* 5.6 2.0 - - - -
213F TYR* 3.1 19.3 - - - -
214F VAL* 1.3 83.8 - - - +
216F ASP* 1.3 58.6 + - - +
218F ALA* 3.4 6.9 + - - +
219F ASP* 3.1 33.8 + - - +
293F LYS* 5.9 1.3 - - - -
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Residues in contact with ASP 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F VAL* 4.4 2.5 - - + -
213F TYR* 2.9 17.8 + - - +
215F GLY* 1.3 75.5 - - - +
217F VAL* 1.3 67.0 + - - +
219F ASP* 3.0 13.3 + - - +
220F VAL* 2.9 29.0 + - - +
288F TYR* 4.4 2.6 + - - +
291F PRO 4.7 3.9 - - - +
292F PHE* 3.4 30.7 - - + +
293F LYS* 2.8 53.5 + - - +
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Residues in contact with VAL 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ILE* 4.0 20.0 - - + -
167F TYR* 3.6 30.7 - - + -
170F VAL* 3.9 28.0 - - + -
212F VAL* 4.2 8.3 - - + -
213F TYR 3.2 10.7 + - - +
214F VAL* 3.1 11.0 + - + +
216F ASP* 1.3 77.2 - - - +
218F ALA* 1.3 62.8 + - - +
220F VAL* 3.3 3.3 + - - +
221F ASN* 3.0 32.9 + - - +
235F LEU* 4.1 23.8 - - + -
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Residues in contact with ALA 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ASN* 3.9 30.5 - - + +
15F ILE* 4.6 6.3 - - - +
18F ALA* 4.0 13.0 - - + -
214F VAL 2.9 11.5 + - - +
215F GLY* 3.5 11.7 - - - +
217F VAL* 1.3 79.6 - - - +
219F ASP* 1.3 65.6 + - - +
221F ASN* 3.1 10.2 + - - +
222F LEU* 3.0 26.5 + - - +
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Residues in contact with ASP 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ALA* 5.3 4.9 - - - +
215F GLY 3.1 19.5 + - - +
216F ASP* 3.0 15.9 + - - +
218F ALA* 1.3 77.5 - - - +
220F VAL* 1.3 63.4 + - - +
222F LEU* 3.2 7.8 + - - +
223F TRP* 2.9 25.1 + - - +
288F TYR* 4.0 14.3 + - + +
290F LYS* 5.6 5.8 - - + +
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Residues in contact with VAL 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F PHE* 3.6 26.0 - - + -
216F ASP 2.9 17.9 + - - +
217F VAL 3.6 6.5 - - - +
219F ASP* 1.3 75.5 - - - +
221F ASN* 1.3 65.2 + - - +
223F TRP* 3.1 2.3 + - - +
224F PHE* 3.0 35.1 + - + -
235F LEU* 3.7 31.2 - - + -
283F LEU* 4.6 6.3 - - + -
288F TYR* 3.6 35.9 - - + +
292F PHE* 4.1 6.5 - - + -
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Residues in contact with ASN 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ILE* 3.5 24.2 - - + +
73F PHE* 3.4 31.7 - - + -
75F GLU* 3.8 3.3 - - - +
112F LEU* 4.1 1.9 - - - +
165F PHE* 3.3 28.6 - - - -
167F TYR* 3.1 24.6 + - - -
217F VAL* 3.0 30.1 + - - +
218F ALA 3.4 8.5 - - - +
220F VAL* 1.3 78.8 - - - +
222F LEU* 1.3 65.5 + - + +
224F PHE* 3.3 3.6 + - - +
225F LEU* 3.1 20.1 + - - +
235F LEU* 4.7 0.4 - - - +
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Residues in contact with LEU 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ILE* 4.4 9.6 - - + -
18F ALA* 3.8 36.8 - - + +
19F LEU* 3.8 30.3 - - + +
22F LYS* 3.8 28.3 - - + -
73F PHE* 4.1 13.7 - - + -
218F ALA 3.0 17.1 + - - +
219F ASP* 3.9 7.6 - - - +
221F ASN* 1.3 79.4 - - + +
223F TRP* 1.3 63.0 + - - +
225F LEU* 3.2 9.6 + - + +
226F GLU* 3.0 37.1 + - + +
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Residues in contact with TRP 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F ASP 2.9 17.0 + - - +
220F VAL 3.4 4.3 - - - +
222F LEU* 1.3 76.3 - - - +
224F PHE* 1.3 92.0 + + - +
226F GLU* 3.2 7.0 + - - -
227F ASN* 2.7 73.6 + - + +
229F VAL* 4.5 4.3 - - + -
286F ALA 3.6 15.0 - - - -
287F GLY* 3.5 32.2 + - - -
288F TYR* 3.5 35.0 - + + +
289F ASP* 5.8 1.2 + - - +
290F LYS* 4.1 22.4 - - - +
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Residues in contact with PHE 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F LEU* 4.0 7.2 - - + -
161F GLN* 2.9 12.1 + - - +
163F VAL* 4.1 7.2 - - + -
165F PHE* 3.5 32.1 - + + -
220F VAL* 3.0 26.2 + - + +
221F ASN 3.8 2.0 - - - +
223F TRP* 1.3 97.9 - + - +
225F LEU* 1.3 65.2 + - - +
227F ASN* 4.4 0.4 - - - +
228F GLY 2.9 21.3 + - - -
229F VAL* 3.8 34.8 - - + -
233F PHE* 3.6 37.9 - + - -
283F LEU* 3.7 26.2 - - + -
286F ALA* 4.2 13.5 - - + -
288F TYR* 4.5 2.0 - - + -
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Residues in contact with LEU 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F ILE* 4.2 19.7 - - + -
19F LEU* 5.0 5.6 - - + -
24F ILE* 6.1 1.6 - - + -
70F GLU* 4.5 14.4 - - + +
71F ALA* 3.6 23.1 - - + -
73F PHE* 3.7 30.1 - - + -
110F PRO* 4.5 7.4 - - + -
112F LEU* 3.9 12.4 - - + +
161F GLN* 4.2 11.7 - - - +
221F ASN 3.1 12.6 + - - +
222F LEU* 3.5 10.5 - - + +
224F PHE* 1.3 78.3 - - - +
226F GLU* 1.3 66.5 + - + +
227F ASN 3.3 0.2 + - - -
228F GLY* 3.8 5.2 + - - -
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Residues in contact with GLU 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F LYS* 3.1 36.8 + - - +
222F LEU* 3.0 22.7 + - - +
223F TRP* 3.7 10.4 - - - +
225F LEU* 1.3 81.7 - - + +
227F ASN* 1.3 68.8 + - - +
228F GLY 3.6 0.4 + - - -
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Residues in contact with ASN 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F TRP* 2.7 81.6 + - + +
224F PHE 4.3 0.9 - - - +
225F LEU 3.2 0.2 - - - -
226F GLU* 1.3 91.0 + - - +
228F GLY* 1.3 57.2 + - - +
229F VAL* 3.2 17.7 + - + +
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Residues in contact with GLY 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161F GLN* 3.2 31.5 + - - +
224F PHE 2.9 8.3 + - - -
225F LEU 3.8 3.2 + - - -
226F GLU 3.6 1.8 - - - -
227F ASN* 1.3 76.4 - - - +
229F VAL* 1.3 62.2 + - - +
230F SER* 3.7 2.8 + - - -
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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