Contacts of the helix formed by residues 214 - 228 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10I PHE* 3.6 20.6 - - + -
11I ILE* 4.5 10.1 - - + -
14I ASN* 3.5 44.0 - - + +
170I VAL* 3.8 15.0 - - + -
171I TYR 2.9 20.9 + - - +
172I GLY* 3.8 15.7 - - - -
173I PRO* 3.9 11.0 - - + -
212I VAL 3.6 0.6 + - - -
213I TYR* 1.3 75.2 - - + +
215I GLY* 1.3 67.0 + - - +
217I VAL* 3.1 6.8 + - + +
218I ALA* 2.9 22.2 + - - +
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Residues in contact with GLY 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ASN* 5.6 1.8 - - - -
213I TYR* 3.1 20.4 + - - -
214I VAL* 1.3 84.3 - - - +
216I ASP* 1.3 59.4 + - - +
218I ALA* 3.4 8.0 + - - +
219I ASP* 3.1 33.7 + - - +
293I LYS* 5.9 0.7 - - - -
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Residues in contact with ASP 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212I VAL* 4.4 2.9 - - + -
213I TYR* 2.9 18.7 + - - +
215I GLY* 1.3 74.2 - - - +
217I VAL* 1.3 67.1 + - - +
219I ASP* 3.0 13.5 + - - +
220I VAL* 2.9 29.4 + - + +
288I TYR* 4.5 2.9 + - - +
291I PRO 4.8 3.6 - - - +
292I PHE* 3.4 30.8 - - + +
293I LYS* 2.8 54.0 + - - +
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Residues in contact with VAL 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ILE* 4.1 19.7 - - + -
167I TYR* 3.6 30.7 - - + -
170I VAL* 3.9 27.6 - - + -
212I VAL* 4.2 8.3 - - + -
213I TYR 3.8 10.5 - - - +
214I VAL* 3.3 10.3 - - + +
216I ASP* 1.3 78.0 - - - +
218I ALA* 1.3 63.5 + - - +
220I VAL* 3.3 2.9 + - - +
221I ASN* 3.0 32.5 + - - +
235I LEU* 4.1 24.2 - - + +
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Residues in contact with ALA 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I ASN* 3.9 29.8 - - + +
15I ILE* 4.7 6.5 - - - +
18I ALA* 4.0 13.0 - - + -
214I VAL* 2.9 11.6 + - - +
215I GLY* 3.5 11.9 - - - +
216I ASP 3.2 0.2 - - - -
217I VAL* 1.3 78.2 - - - +
219I ASP* 1.3 65.5 + - - +
221I ASN* 3.1 9.8 + - - +
222I LEU* 3.0 26.9 + - - +
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Residues in contact with ASP 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I ALA* 5.4 4.3 - - - +
215I GLY 3.1 19.5 + - - +
216I ASP* 3.0 16.8 + - - +
218I ALA* 1.3 78.5 - - - +
220I VAL* 1.3 64.6 + - - +
222I LEU* 3.2 7.1 + - - +
223I TRP* 2.9 24.4 + - - +
288I TYR* 4.0 14.3 + - + +
290I LYS* 5.8 3.7 - - + +
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Residues in contact with VAL 220 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165I PHE* 3.6 25.1 - - + -
216I ASP 2.9 17.7 + - - +
217I VAL 3.6 7.2 - - - +
219I ASP* 1.3 74.9 - - - +
221I ASN* 1.3 64.0 + - - +
223I TRP* 3.1 1.9 + - - +
224I PHE* 3.0 35.6 + - + -
235I LEU* 3.7 32.5 - - + -
283I LEU* 4.6 6.3 - - + -
288I TYR* 3.6 36.8 - - + +
292I PHE* 4.1 6.7 - - + -
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Residues in contact with ASN 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I ILE* 3.5 23.5 - - + +
73I PHE* 3.4 31.9 - - + -
75I GLU* 3.8 3.3 - - - +
112I LEU* 4.1 1.9 - - - +
165I PHE* 3.3 30.8 - - - -
167I TYR* 3.1 23.8 + - - -
217I VAL* 3.0 30.7 + - - +
218I ALA 3.1 8.9 + - - +
220I VAL* 1.3 77.8 - - - +
222I LEU* 1.3 65.9 + - + +
224I PHE* 3.3 3.3 + - - +
225I LEU* 3.1 19.9 + - - +
235I LEU* 4.7 0.2 - - - +
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Residues in contact with LEU 222 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I ILE* 4.5 9.9 - - + -
18I ALA* 3.8 35.2 - - + +
19I LEU* 3.9 29.8 - - + +
22I LYS* 3.8 28.5 - - + -
73I PHE* 4.1 14.4 - - + -
218I ALA 3.0 17.8 + - - +
219I ASP* 3.9 7.4 - - - +
221I ASN* 1.3 78.9 - - + +
223I TRP* 1.3 63.2 + - - +
225I LEU* 3.2 8.3 + - + +
226I GLU* 3.0 38.0 + - - +
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Residues in contact with TRP 223 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219I ASP 2.9 17.0 + - - +
220I VAL 3.1 4.5 + - - +
222I LEU* 1.3 77.0 - - - +
224I PHE* 1.3 91.6 + + - +
226I GLU* 3.2 7.2 + - - -
227I ASN* 2.7 74.4 + - + +
229I VAL* 4.5 3.6 - - + -
286I ALA 3.6 15.5 - - - -
287I GLY* 3.5 32.6 + - - -
288I TYR* 3.5 35.8 - + + +
289I ASP* 6.0 0.2 + - - -
290I LYS* 4.0 22.3 - - - +
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Residues in contact with PHE 224 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112I LEU* 4.0 7.2 - - + -
161I GLN* 2.9 11.3 + - - +
163I VAL* 4.1 7.4 - - + -
165I PHE* 3.5 33.0 - + + -
220I VAL* 3.0 25.4 + - + +
221I ASN 3.8 2.2 - - - +
223I TRP* 1.3 98.1 - + - +
225I LEU* 1.3 64.5 + - - +
227I ASN* 4.4 0.9 - - - +
228I GLY 2.9 21.5 + - - -
229I VAL* 3.8 33.9 - - + -
233I PHE* 3.6 37.7 - + - -
283I LEU* 3.7 26.5 - - + -
286I ALA* 4.2 12.6 - - + -
288I TYR* 4.5 2.2 - - + -
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Residues in contact with LEU 225 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I ILE* 4.2 18.4 - - + -
19I LEU* 5.0 5.2 - - + -
24I ILE* 6.2 1.1 - - + -
70I GLU* 4.5 14.1 - - + +
71I ALA* 3.7 22.9 - - + -
73I PHE* 3.7 30.1 - - + -
110I PRO* 4.4 7.4 - - + -
112I LEU* 3.9 13.1 - - + +
161I GLN* 4.2 12.7 - - - +
221I ASN 3.1 12.6 + - - +
222I LEU* 3.2 11.4 + - + +
224I PHE* 1.3 79.0 - - - +
226I GLU* 1.3 65.0 + - + +
227I ASN 3.3 0.2 + - - -
228I GLY* 3.8 5.5 + - - -
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Residues in contact with GLU 226 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I LYS* 3.1 37.2 + - - +
222I LEU* 3.0 22.8 + - - +
223I TRP* 3.2 10.5 + - - +
225I LEU* 1.3 81.8 - - + +
227I ASN* 1.3 68.3 + - - +
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Residues in contact with ASN 227 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223I TRP* 2.7 81.2 + - + +
224I PHE 4.3 0.9 - - - +
225I LEU 3.2 0.2 - - - -
226I GLU* 1.3 89.8 + - - +
228I GLY* 1.3 55.5 + - - +
229I VAL* 3.2 16.8 + - + +
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Residues in contact with GLY 228 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161I GLN* 3.2 31.0 + - - +
224I PHE 2.9 8.6 + - - -
225I LEU 3.8 3.7 + - - -
226I GLU 3.6 1.6 + - - -
227I ASN* 1.3 76.4 - - - +
229I VAL* 1.3 62.9 + - - +
230I 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