Contacts of the helix formed by residues 214 - 228 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10P PHE* 3.6 20.9 - - + -
11P ILE* 4.5 10.3 - - + -
14P ASN* 3.5 44.4 - - + +
170P VAL* 3.8 15.3 - - + -
171P TYR 2.9 20.4 + - - +
172P GLY* 3.8 15.5 - - - -
173P PRO* 3.9 10.8 - - + -
212P VAL 3.6 0.4 + - - -
213P TYR* 1.3 75.9 - - + +
215P GLY* 1.3 66.3 + - - +
217P VAL* 3.1 6.5 + - + +
218P ALA* 2.9 21.9 + - - +
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Residues in contact with GLY 215 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P ASN* 5.6 1.8 - - - -
213P TYR* 3.1 19.3 + - - -
214P VAL* 1.3 83.6 - - - +
216P ASP* 1.3 64.1 + - - +
218P ALA* 3.4 7.7 + - - +
219P ASP* 3.1 29.3 + - - +
293P LYS* 5.9 1.1 - - - -
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Residues in contact with ASP 216 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212P VAL* 4.4 2.7 - - + -
213P TYR* 2.9 18.3 + - - +
215P GLY* 1.3 74.9 - - - +
217P VAL* 1.3 67.4 + - - +
219P ASP* 3.0 13.6 + - - +
220P VAL* 2.9 28.9 + - - +
288P TYR* 4.4 2.4 + - - +
291P PRO 4.7 5.1 - - - +
292P PHE* 3.4 30.6 - - + +
293P LYS* 2.8 54.4 + - - +
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Residues in contact with VAL 217 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P ILE* 4.0 20.2 - - + -
167P TYR* 3.6 30.5 - - + -
170P VAL* 3.9 27.8 - - + -
212P VAL* 4.2 15.7 - - + -
213P TYR 3.8 11.0 - - - +
214P VAL* 3.1 10.5 + - + +
216P ASP* 1.3 78.0 - - - +
218P ALA* 1.3 63.0 + - - +
220P VAL* 3.3 4.0 + - - +
221P ASN* 3.0 33.6 + - - +
235P LEU* 4.2 17.5 - - + +
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Residues in contact with ALA 218 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P ASN* 3.9 29.8 - - + +
15P ILE* 4.6 7.4 - - - +
18P ALA* 4.0 13.5 - - + -
214P VAL* 2.9 12.0 + - - +
215P GLY* 3.5 11.7 - - - +
217P VAL* 1.3 79.0 - - - +
219P ASP* 1.3 64.2 + - - +
221P ASN* 3.1 8.9 + - - +
222P LEU* 3.0 27.2 + - - +
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Residues in contact with ASP 219 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P ALA* 5.3 4.9 - - - +
215P GLY 3.1 19.0 + - - +
216P ASP* 3.0 16.5 + - - +
218P ALA* 1.3 78.8 - - - +
220P VAL* 1.3 63.6 + - - +
222P LEU* 3.2 8.1 + - - +
223P TRP* 2.9 24.6 + - - +
288P TYR* 4.0 14.8 + - + +
290P LYS* 5.7 5.5 - - + +
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Residues in contact with VAL 220 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165P PHE* 3.6 26.0 - - + -
216P ASP 2.9 16.2 + - - +
217P VAL 3.6 7.2 - - - +
219P ASP* 1.3 74.6 - - - +
221P ASN* 1.3 65.0 + - - +
223P TRP* 3.1 2.3 + - - +
224P PHE* 3.0 35.8 + - + -
235P LEU* 3.6 31.6 - - + -
283P LEU* 4.6 6.3 - - + -
288P TYR* 3.6 36.8 - - + +
292P PHE* 4.1 6.1 - - + -
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Residues in contact with ASN 221 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P ILE* 3.5 22.4 - - + +
73P PHE* 3.4 31.1 - - + -
75P GLU* 3.8 3.3 - - - +
112P LEU* 4.1 1.9 - - - +
165P PHE* 3.3 31.1 - - - -
167P TYR* 3.1 23.8 + - - -
217P VAL* 3.0 31.1 + - - +
218P ALA* 3.1 9.2 + - - +
220P VAL* 1.3 77.4 - - - +
222P LEU* 1.3 65.6 + - + +
224P PHE* 3.3 3.5 + - - +
225P LEU* 3.1 19.6 + - - +
235P LEU* 4.7 0.4 - - - +
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Residues in contact with LEU 222 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P ILE* 4.4 10.3 - - + -
18P ALA* 3.8 35.7 - - + +
19P LEU* 3.9 29.8 - - + +
22P LYS* 3.8 29.2 - - + -
73P PHE* 4.1 13.9 - - + -
218P ALA 3.0 17.8 + - - +
219P ASP* 3.9 7.2 - - - +
221P ASN* 1.3 79.3 - - - +
223P TRP* 1.3 63.1 + - - +
225P LEU* 3.2 7.7 + - + +
226P GLU* 3.0 37.8 + - - +
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Residues in contact with TRP 223 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219P ASP 2.9 17.4 + - - +
220P VAL 3.1 4.9 + - - +
222P LEU* 1.3 77.4 - - - +
224P PHE* 1.3 92.0 + + - +
226P GLU* 3.2 7.2 + - - -
227P ASN* 2.7 73.7 + - + +
229P VAL* 4.5 3.4 - - + -
286P ALA 3.6 16.4 - - - -
287P GLY* 3.5 33.3 + - - -
288P TYR* 3.5 35.8 - + + +
289P ASP* 5.9 1.2 + - - -
290P LYS* 4.0 22.8 - - - +
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Residues in contact with PHE 224 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112P LEU* 4.0 7.2 - - + -
161P GLN* 2.9 12.4 + - - +
163P VAL* 4.1 7.6 - - + -
165P PHE* 3.5 33.0 - + + -
220P VAL* 3.0 25.4 + - + +
221P ASN 3.8 1.8 - - - +
223P TRP* 1.3 97.4 - + - +
225P LEU* 1.3 64.7 + - - +
227P ASN* 4.4 0.7 - - - +
228P GLY 2.9 21.3 + - - -
229P VAL* 3.8 34.7 + - + -
233P PHE* 3.6 37.0 - + - -
283P LEU* 3.7 25.6 - - + -
286P ALA* 4.2 13.9 - - + -
288P TYR* 4.5 2.2 - - + -
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Residues in contact with LEU 225 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2P ILE* 4.2 19.1 - - + -
19P LEU* 5.1 4.9 - - + -
24P ILE* 6.2 0.9 - - + -
70P GLU* 4.5 14.1 - - + +
71P ALA* 3.6 24.5 - - + -
73P PHE* 3.7 29.6 - - + -
110P PRO* 4.4 7.6 - - + -
112P LEU* 3.9 11.1 - - + +
161P GLN* 4.2 11.8 - - - +
221P ASN 3.1 13.7 + - - +
222P LEU* 3.2 10.7 + - + +
224P PHE* 1.3 78.4 - - - +
226P GLU* 1.3 66.4 + - + +
228P GLY* 3.8 5.5 + - - -
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Residues in contact with GLU 226 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H ASP* 6.0 1.6 - - - +
22P LYS* 3.1 36.4 + - - +
222P LEU* 3.0 23.6 + - - +
223P TRP* 3.7 10.7 - - - +
225P LEU* 1.3 80.3 - - + +
227P ASN* 1.3 66.2 + - - +
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Residues in contact with ASN 227 (chain P).
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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223P TRP* 2.7 80.2 + - + +
224P PHE 4.3 0.9 - - - +
226P GLU* 1.3 90.0 + - - +
228P GLY* 1.3 57.0 + - - +
229P VAL* 3.2 16.3 + - + +
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Residues in contact with GLY 228 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161P GLN* 3.2 30.6 + - - +
224P PHE 2.9 8.5 + - - -
225P LEU 3.8 3.5 + - - -
226P GLU 3.6 1.4 - - - -
227P ASN* 1.3 75.9 - - - +
229P VAL* 1.3 61.9 + - - +
230P 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