Contacts of the helix formed by residues 214 - 228 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10R PHE* 3.6 20.4 - - + -
11R ILE* 4.5 10.1 - - + -
14R ASN* 3.5 44.0 - - + +
170R VAL* 3.8 15.5 - - + -
171R TYR 2.9 21.7 + - - +
172R GLY* 3.8 14.8 - - - -
173R PRO* 3.9 11.4 - - + -
212R VAL 3.6 0.4 + - - -
213R TYR* 1.3 76.5 - - + +
215R GLY* 1.3 65.6 + - - +
217R VAL* 3.1 6.5 + - + +
218R ALA* 2.9 22.2 + - - +
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Residues in contact with GLY 215 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14R ASN* 5.5 2.2 - - - -
213R TYR* 3.1 19.6 - - - -
214R VAL* 1.3 84.4 - - - +
216R ASP* 1.3 64.2 + - - +
218R ALA* 3.4 7.9 + - - +
219R ASP* 3.1 28.9 + - - +
293R LYS* 5.9 1.1 - - - -
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Residues in contact with ASP 216 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212R VAL* 4.4 2.2 - - + -
213R TYR* 2.9 18.5 + - - +
215R GLY* 1.3 75.5 - - - +
217R VAL* 1.3 66.7 - - - +
219R ASP* 3.0 13.5 + - - +
220R VAL* 2.9 28.9 + - - +
288R TYR* 4.4 2.6 + - - +
291R PRO 4.7 4.4 - - - +
292R PHE* 3.4 30.4 - - + +
293R LYS* 2.8 53.7 + - - +
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Residues in contact with VAL 217 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11R ILE* 4.1 19.7 - - + -
167R TYR* 3.6 31.0 - - + -
170R VAL* 3.9 28.5 - - + -
212R VAL* 4.2 7.9 - - + -
213R TYR 3.8 10.5 - - - +
214R VAL* 3.1 10.3 + - + +
216R ASP* 1.3 77.8 - - - +
218R ALA* 1.3 63.6 + - - +
220R VAL* 3.3 3.5 + - - +
221R ASN* 3.0 32.6 + - - +
235R LEU* 4.1 24.6 - - + +
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Residues in contact with ALA 218 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14R ASN* 3.9 31.0 - - + +
15R ILE* 4.7 6.3 - - - +
18R ALA* 4.0 12.8 - - + -
214R VAL 2.9 12.0 + - - +
215R GLY* 3.5 12.1 - - - +
217R VAL* 1.3 78.2 - - - +
219R ASP* 1.3 64.6 + - - +
221R ASN* 3.1 10.4 + - - +
222R LEU* 3.0 27.1 + - - +
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Residues in contact with ASP 219 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18R ALA* 5.3 4.3 - - - +
215R GLY 3.1 19.5 + - - +
216R ASP* 3.0 15.9 + - - +
218R ALA* 1.3 79.2 - - - +
220R VAL* 1.3 64.1 + - - +
222R LEU* 3.2 7.8 + - - +
223R TRP* 2.9 24.6 + - - +
288R TYR* 4.0 14.9 + - + +
290R LYS* 5.7 4.6 - - + +
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Residues in contact with VAL 220 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165R PHE* 3.6 25.8 - - + -
216R ASP 2.9 17.7 + - - +
217R VAL 3.6 7.6 - - - +
218R ALA 3.2 0.2 - - - -
219R ASP* 1.3 75.9 - - - +
221R ASN* 1.3 64.8 + - - +
223R TRP* 3.1 1.6 + - - +
224R PHE* 3.0 36.1 + - + -
235R LEU* 3.6 30.3 - - + -
283R LEU* 4.6 6.5 - - + -
288R TYR* 3.6 35.2 - - + +
292R PHE* 4.1 7.0 - - + -
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Residues in contact with ASN 221 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15R ILE* 3.5 23.8 - - + +
73R PHE* 3.4 30.4 - - + -
75R GLU* 3.8 3.3 - - - +
112R LEU* 4.1 1.9 - - - +
165R PHE* 3.3 30.3 - - - -
167R TYR* 3.1 24.0 + - - -
217R VAL* 3.0 30.7 + - - +
218R ALA 3.1 8.7 + - - +
220R VAL* 1.3 79.0 - - - +
222R LEU* 1.3 65.8 + - + +
224R PHE* 3.3 3.5 + - - +
225R LEU* 3.1 19.8 + - - +
235R LEU* 4.7 0.6 - - - +
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Residues in contact with LEU 222 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15R ILE* 4.4 10.5 - - + -
18R ALA* 3.8 37.7 - - + +
19R LEU* 3.9 30.5 - - + +
22R LYS* 3.8 27.8 - - + -
73R PHE* 4.1 13.5 - - + -
218R ALA 3.0 17.2 + - - +
219R ASP* 3.9 8.3 - - - +
221R ASN* 1.3 78.9 - - - +
223R TRP* 1.3 62.7 + - - +
225R LEU* 3.2 7.5 + - + +
226R GLU* 3.0 37.1 + - + +
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Residues in contact with TRP 223 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219R ASP 2.9 17.4 + - - +
220R VAL 3.1 4.5 + - - +
222R LEU* 1.3 76.4 - - - +
224R PHE* 1.3 90.2 + + - +
226R GLU* 3.2 7.7 + - - -
227R ASN* 2.7 75.8 + - + +
229R VAL* 4.5 3.8 - - + -
286R ALA 3.6 14.8 - - - -
287R GLY* 3.5 32.9 + - - -
288R TYR* 3.5 34.4 - + + +
289R ASP* 5.9 0.8 + - - -
290R LYS* 4.1 22.4 - - - +
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Residues in contact with PHE 224 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112R LEU* 4.0 7.2 - - + -
161R GLN* 2.9 11.4 + - - +
163R VAL* 4.1 7.4 - - + -
165R PHE* 3.5 32.1 - + + -
220R VAL* 3.0 25.2 + - + +
221R ASN 3.7 2.2 - - - +
222R LEU 3.2 0.2 - - - -
223R TRP* 1.3 97.0 - + + +
225R LEU* 1.3 64.6 + - - +
227R ASN* 4.4 0.4 - - - +
228R GLY 2.9 21.3 + - - -
229R VAL* 3.8 34.3 - - + -
233R PHE* 3.6 37.2 - + - -
283R LEU* 3.7 27.6 - - + -
286R ALA* 4.2 13.9 - - + -
288R TYR* 4.5 1.6 - - + -
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Residues in contact with LEU 225 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2R ILE* 4.2 19.1 - - + -
19R LEU* 4.9 6.1 - - + -
24R ILE* 6.1 1.3 - - + -
70R GLU* 4.6 13.5 - - + +
71R ALA* 3.6 23.8 - - + -
73R PHE* 3.7 29.6 - - + -
110R PRO* 4.4 7.4 - - + -
112R LEU* 3.9 7.5 - - + +
161R GLN* 4.2 16.7 - - - +
221R ASN 3.1 13.9 + - - +
222R LEU* 3.2 11.4 + - + +
224R PHE* 1.3 78.4 - - - +
226R GLU* 1.3 65.8 + - + +
227R ASN 3.3 0.2 + - - -
228R GLY* 3.8 5.2 + - - -
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Residues in contact with GLU 226 (chain R).
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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22R LYS* 3.1 36.6 + - - +
222R LEU* 3.0 22.3 + - - +
223R TRP* 3.2 11.1 + - - +
225R LEU* 1.3 81.3 - - + +
227R ASN* 1.3 68.2 + - - +
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Residues in contact with ASN 227 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223R TRP* 2.7 78.6 + - + +
224R PHE 4.3 0.9 - - - +
226R GLU* 1.3 91.0 + - - +
228R GLY* 1.3 57.2 + - - +
229R VAL* 3.2 17.5 + - + +
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Residues in contact with GLY 228 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161R GLN* 3.2 30.8 + - - +
224R PHE 2.9 7.9 + - - -
225R LEU 3.8 3.7 + - - -
226R GLU 3.6 1.8 - - - -
227R ASN* 1.3 75.1 - - - +
229R VAL* 1.3 62.5 + - - +
230R SER* 3.7 3.1 + - - -
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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