Contacts of the helix formed by residues 214 - 228 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10S PHE* 3.6 20.6 - - + -
11S ILE* 4.5 10.8 - - + -
14S ASN* 3.5 44.0 - - + +
170S VAL* 3.8 14.6 - - + -
171S TYR 2.9 22.1 + - - +
172S GLY* 3.8 15.5 - - - -
173S PRO* 3.9 10.8 - - + -
212S VAL 3.6 0.4 + - - -
213S TYR* 1.3 74.9 - - + +
215S GLY* 1.3 65.1 + - - +
217S VAL* 3.1 6.3 + - + +
218S ALA* 2.9 21.8 + - - +
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Residues in contact with GLY 215 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S ASN* 5.6 2.2 - - - -
213S TYR* 3.1 18.6 + - - -
214S VAL* 1.3 84.3 - - - +
216S ASP* 1.3 63.6 + - - +
218S ALA* 3.4 7.9 + - - +
219S ASP* 3.1 29.1 + - - +
293S LYS* 5.9 1.6 - - - -
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Residues in contact with ASP 216 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212S VAL* 4.4 3.1 - - + -
213S TYR* 2.9 17.8 + - - +
215S GLY* 1.3 73.9 - - - +
217S VAL* 1.3 66.9 + - - +
219S ASP* 3.0 13.6 + - - +
220S VAL* 2.9 28.5 + - - +
288S TYR* 4.4 2.1 + - - +
291S PRO 4.7 4.1 - - - +
292S PHE* 3.4 30.5 - - + +
293S LYS* 2.8 53.5 + - - +
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Residues in contact with VAL 217 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11S ILE* 4.0 20.4 - - + -
167S TYR* 3.6 30.7 - - + -
170S VAL* 3.9 28.5 - - + -
212S VAL* 4.2 8.7 - - + -
213S TYR 3.8 10.8 - - - +
214S VAL* 3.1 10.9 + - + +
216S ASP* 1.3 77.2 - - - +
218S ALA* 1.3 64.5 + - - +
220S VAL* 3.3 3.6 + - - +
221S ASN* 3.0 32.7 + - - +
235S LEU* 4.1 24.0 - - + +
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Residues in contact with ALA 218 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S ASN* 3.9 29.8 - - + +
15S ILE* 4.6 7.4 - - - +
18S ALA* 4.0 13.2 - - + -
214S VAL 2.9 12.3 + - - +
215S GLY* 3.5 11.9 - - - +
217S VAL* 1.3 79.1 - - - +
219S ASP* 1.3 64.5 + - - +
221S ASN* 3.1 9.7 + - - +
222S LEU* 3.0 27.0 + - - +
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Residues in contact with ASP 219 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18S ALA* 5.3 5.0 - - - +
215S GLY 3.1 19.4 + - - +
216S ASP* 3.0 15.6 + - - +
218S ALA* 1.3 78.6 - - - +
220S VAL* 1.3 64.5 + - - +
222S LEU* 3.2 6.9 + - - +
223S TRP* 2.9 25.1 + - - +
288S TYR* 4.0 14.8 - - + +
290S LYS* 5.7 4.6 - - + +
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Residues in contact with VAL 220 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165S PHE* 3.6 25.8 - - + -
216S ASP 2.9 17.0 + - - +
217S VAL 3.6 7.6 - - - +
218S ALA 3.2 0.2 - - - -
219S ASP* 1.3 75.8 - - - +
221S ASN* 1.3 65.6 + - - +
223S TRP* 3.1 2.1 + - - +
224S PHE* 3.0 36.0 + - + -
235S LEU* 3.6 31.2 - - + -
283S LEU* 4.6 6.3 - - + -
288S TYR* 3.6 35.4 - - + +
292S PHE* 4.1 6.3 - - + -
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Residues in contact with ASN 221 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S ILE* 3.5 23.4 - - + +
73S PHE* 3.4 30.6 - - + -
75S GLU* 3.8 3.6 - - - +
112S LEU* 4.1 2.1 - - - +
165S PHE* 3.3 31.5 - - - -
167S TYR* 3.1 24.0 + - - -
217S VAL* 3.0 30.1 + - - +
218S ALA 3.4 9.2 - - - +
220S VAL* 1.3 79.1 - - - +
222S LEU* 1.3 66.4 + - + +
224S PHE* 3.3 3.3 + - - +
225S LEU* 3.1 20.1 + - - +
235S LEU* 4.7 0.4 - - - +
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Residues in contact with LEU 222 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S ILE* 4.5 10.3 - - + -
18S ALA* 3.8 35.7 - - + +
19S LEU* 3.9 29.4 - - + +
22S LYS* 3.8 29.4 - - + -
73S PHE* 4.1 13.9 - - + -
218S ALA 3.0 17.4 + - - +
219S ASP* 3.9 7.6 - - - +
221S ASN* 1.3 78.8 - - - +
223S TRP* 1.3 63.7 + - - +
225S LEU* 3.2 8.5 + - + +
226S GLU* 3.0 36.6 + - - +
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Residues in contact with TRP 223 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219S ASP 2.9 17.0 + - - +
220S VAL 3.1 4.7 + - - +
222S LEU* 1.3 77.0 - - - +
224S PHE* 1.3 92.9 + + - +
226S GLU* 3.2 7.2 + - - -
227S ASN* 2.7 76.5 + - + +
229S VAL* 4.5 3.4 - - + -
286S ALA 3.6 15.9 - - - -
287S GLY* 3.5 32.5 + - - -
288S TYR* 3.5 36.2 - + + +
289S ASP* 5.9 0.8 + - - -
290S LYS* 4.1 23.5 - - - +
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Residues in contact with PHE 224 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112S LEU* 4.0 6.7 - - + -
161S GLN* 2.9 12.1 + - - +
163S VAL* 4.1 7.4 - - + -
165S PHE* 3.4 33.2 - + + -
220S VAL* 3.0 25.6 + - + +
221S ASN 3.8 1.8 - - - +
223S TRP* 1.3 97.3 - + - +
225S LEU* 1.3 65.7 + - - +
227S ASN* 4.8 0.4 - - - -
228S GLY 2.9 21.1 + - - -
229S VAL* 3.8 35.2 - - + -
233S PHE* 3.6 37.0 - + - -
283S LEU* 3.7 26.2 - - + -
286S ALA* 4.2 13.0 - - + -
288S TYR* 4.5 2.0 - - + -
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Residues in contact with LEU 225 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2S ILE* 4.2 19.5 - - + -
19S LEU* 5.0 5.4 - - + -
24S ILE* 6.1 1.1 - - + -
70S GLU* 4.5 14.1 - - + +
71S ALA* 3.6 23.6 - - + -
73S PHE* 3.7 29.6 - - + -
110S PRO* 4.4 7.9 - - + -
112S LEU* 3.9 12.0 - - + +
161S GLN* 4.2 12.2 - - - +
221S ASN 3.1 12.9 + - - +
222S LEU* 3.2 11.4 + - + +
224S PHE* 1.3 78.9 - - - +
226S GLU* 1.3 66.7 + - + +
227S ASN 3.3 0.2 + - - -
228S GLY* 3.8 5.2 + - - -
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Residues in contact with GLU 226 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22S LYS* 3.1 36.9 + - - +
222S LEU* 3.0 23.0 + - - +
223S TRP* 3.2 11.1 + - - +
225S LEU* 1.3 81.1 - - + +
227S ASN* 1.3 68.1 + - - +
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Residues in contact with ASN 227 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223S TRP* 2.7 78.9 + - + +
224S PHE 4.3 1.1 - - - +
225S LEU 3.2 0.2 - - - -
226S GLU* 1.3 90.6 + - - +
228S GLY* 1.3 56.8 + - - +
229S VAL* 3.2 18.0 + - + +
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Residues in contact with GLY 228 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161S GLN* 3.2 31.0 + - - +
224S PHE 2.9 8.7 + - - -
225S LEU 3.8 3.7 + - - -
226S GLU 3.6 1.8 - - - -
227S ASN* 1.3 75.2 - - - +
229S VAL* 1.3 61.9 + - - +
230S 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