Contacts of the helix formed by residues 214 - 228 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10J PHE* 3.6 21.3 - - + -
11J ILE* 4.5 10.5 - - + -
14J ASN* 3.5 43.7 - - + +
170J VAL* 3.8 14.8 - - + -
171J TYR 2.9 20.2 + - - +
172J GLY* 3.8 15.9 - - - -
173J PRO* 3.9 10.8 - - + -
212J VAL 3.6 0.4 + - - -
213J TYR* 1.3 75.3 - - + +
215J GLY* 1.3 65.9 + - - +
217J VAL* 3.1 6.7 + - + +
218J ALA* 2.9 21.9 + - - +
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Residues in contact with GLY 215 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J ASN* 5.5 2.2 - - - -
213J TYR* 3.1 20.2 + - - -
214J VAL* 1.3 84.7 - - - +
216J ASP* 1.3 63.6 + - - +
218J ALA* 3.4 7.2 + - - +
219J ASP* 3.1 29.2 + - - +
293J LYS* 5.9 1.3 - - - -
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Residues in contact with ASP 216 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212J VAL* 4.4 2.2 - - + -
213J TYR* 2.9 18.7 + - - +
215J GLY* 1.3 74.7 - - - +
217J VAL* 1.3 66.3 + - - +
219J ASP* 3.0 13.3 + - - +
220J VAL* 2.9 28.9 + - - +
288J TYR* 4.4 3.0 + - - +
291J PRO 4.7 4.8 - - - +
292J PHE* 3.4 30.4 - - + +
293J LYS* 2.8 53.9 + - - +
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Residues in contact with VAL 217 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J ILE* 4.0 20.0 - - + -
167J TYR* 3.6 31.2 - - + -
170J VAL* 3.9 28.5 - - + -
212J VAL* 4.2 9.0 - - + -
213J TYR 3.8 11.2 - - - +
214J VAL* 3.2 10.8 - - + +
216J ASP* 1.3 78.4 - - - +
218J ALA* 1.3 61.6 + - - +
220J VAL* 3.3 3.5 + - - +
221J ASN* 3.0 32.7 + - - +
235J LEU* 4.1 23.8 - - + -
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Residues in contact with ALA 218 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J ILE* 6.3 0.2 - - - -
14J ASN* 3.9 29.8 - - + +
15J ILE* 4.6 7.0 - - + +
18J ALA* 4.0 13.0 - - + -
214J VAL 2.9 12.0 + - - +
215J GLY* 3.5 11.9 - - - +
217J VAL* 1.3 79.4 - - - +
219J ASP* 1.3 66.0 + - - +
221J ASN* 3.1 10.2 + - - +
222J LEU* 3.0 26.5 + - - +
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Residues in contact with ASP 219 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J ALA* 5.3 4.9 - - - +
215J GLY 3.1 19.5 + - - +
216J ASP* 3.0 16.8 + - - +
218J ALA* 1.3 78.6 - - - +
220J VAL* 1.3 63.3 + - - +
222J LEU* 3.2 8.1 + - - +
223J TRP* 2.9 25.3 + - - +
288J TYR* 4.0 14.3 + - + +
290J LYS* 5.7 5.4 - - + +
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Residues in contact with VAL 220 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165J PHE* 3.6 24.9 - - + -
216J ASP 2.9 16.8 + - - +
217J VAL 3.6 7.0 - - - +
218J ALA 3.2 0.2 - - - -
219J ASP* 1.3 75.1 - - - +
221J ASN* 1.3 65.0 + - - +
223J TRP* 3.1 1.6 + - - +
224J PHE* 3.0 37.0 + - + -
235J LEU* 3.6 31.0 - - + -
283J LEU* 4.6 6.5 - - + -
288J TYR* 3.6 36.3 - - + +
292J PHE* 4.1 6.3 - - + -
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Residues in contact with ASN 221 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J ILE* 3.5 23.3 - - + +
73J PHE* 3.4 31.1 - - + -
75J GLU* 3.8 3.5 - - - +
112J LEU* 4.1 1.7 - - - +
165J PHE* 3.3 30.6 - - - -
167J TYR* 3.1 24.4 + - - -
217J VAL* 3.0 29.9 + - - +
218J ALA 3.4 8.7 - - - +
220J VAL* 1.3 78.5 - - - +
222J LEU* 1.3 65.1 + - + +
224J PHE* 3.3 3.6 + - - +
225J LEU* 3.1 19.4 + - - +
235J LEU* 4.7 0.4 - - - +
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Residues in contact with LEU 222 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J ILE* 4.4 10.1 - - + -
18J ALA* 3.8 35.2 - - + +
19J LEU* 3.9 31.0 - - + +
22J LYS* 3.8 29.2 - - + -
73J PHE* 4.1 13.7 - - + -
218J ALA 3.0 17.3 + - - +
219J ASP* 3.9 8.1 - - - +
221J ASN* 1.3 78.3 - - - +
223J TRP* 1.3 62.6 + - - +
225J LEU* 3.2 7.7 + - + +
226J GLU* 3.0 37.4 + - - +
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Residues in contact with TRP 223 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219J ASP 2.9 17.4 + - - +
220J VAL 3.1 4.5 + - - +
222J LEU* 1.3 77.0 - - - +
224J PHE* 1.3 92.3 + + - +
226J GLU* 3.2 7.2 + - - -
227J ASN* 2.7 73.1 + - + +
229J VAL* 4.5 3.4 - - + -
286J ALA 3.6 15.5 - - - -
287J GLY* 3.5 33.1 + - - -
288J TYR* 3.5 36.4 - + + +
289J ASP* 5.8 1.2 + - - +
290J LYS* 4.1 23.1 - - - +
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Residues in contact with PHE 224 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J LEU* 4.0 7.4 - - + -
161J GLN* 2.9 12.1 + - - +
163J VAL* 4.1 7.2 - - + -
165J PHE* 3.5 32.3 - + + -
220J VAL* 3.0 25.7 + - + +
221J ASN 3.8 2.2 - - - +
223J TRP* 1.3 98.6 - + + +
225J LEU* 1.3 65.3 + - - +
227J ASN* 4.8 0.4 - - - -
228J GLY 2.9 21.5 + - - -
229J VAL* 3.8 35.4 + - + -
233J PHE* 3.6 37.2 - + - -
283J LEU* 3.7 26.5 - - + -
286J ALA* 4.2 12.1 - - + -
288J TYR* 4.5 1.6 - - + -
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Residues in contact with LEU 225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J ILE* 4.2 18.4 - - + -
19J LEU* 5.0 5.4 - - + -
24J ILE* 6.2 1.1 - - + -
70J GLU* 4.5 15.0 - - + +
71J ALA* 3.6 22.9 - - + -
73J PHE* 3.7 30.1 - - + -
110J PRO* 4.4 7.9 - - + -
112J LEU* 3.9 11.8 - - + +
161J GLN* 4.2 11.6 - - - +
221J ASN 3.1 13.1 + - - +
222J LEU* 3.2 10.7 + - + +
224J PHE* 1.3 79.3 - - - +
226J GLU* 1.3 65.4 + - + +
228J GLY* 3.8 5.4 + - - -
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Residues in contact with GLU 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J LYS* 3.1 36.4 + - - +
222J LEU* 3.0 23.1 + - - +
223J TRP* 3.7 9.8 - - - +
225J LEU* 1.3 80.4 - - + +
227J ASN* 1.3 69.1 + - - +
228J GLY 3.6 0.4 + - - -
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Residues in contact with ASN 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223J TRP* 2.7 80.1 + - + +
224J PHE 4.3 0.7 - - - +
225J LEU 3.2 0.2 - - - -
226J GLU* 1.3 90.4 + - - +
228J GLY* 1.3 56.9 + - - +
229J VAL* 3.2 16.6 + - + +
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Residues in contact with GLY 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161J GLN* 3.2 30.3 + - - +
224J PHE 2.9 8.3 + - - -
225J LEU 3.8 3.5 + - - -
226J GLU 3.6 1.8 - - - -
227J ASN* 1.3 76.0 - - - +
229J VAL* 1.3 62.3 + - - +
230J 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