Contacts of the helix formed by residues 214 - 228 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A PHE* 3.6 20.4 - - + -
11A ILE* 4.5 10.1 - - + +
14A ASN* 3.5 43.3 - - + +
170A VAL* 3.8 14.6 - - + -
171A TYR 2.9 20.9 + - - +
172A GLY* 3.8 15.5 - - - -
173A PRO* 3.9 10.8 - - + -
212A VAL 3.6 0.8 + - - -
213A TYR* 1.3 74.7 - - + +
215A GLY* 1.3 64.9 + - - +
217A VAL* 3.1 6.6 + - + +
218A ALA* 2.9 22.6 + - - +
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Residues in contact with GLY 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASN* 5.6 2.0 - - - -
213A TYR* 3.1 19.3 + - - -
214A VAL* 1.3 83.6 - - - +
216A ASP* 1.3 58.6 + - - +
218A ALA* 3.4 7.5 + - - +
219A ASP* 3.1 33.8 + - - +
293A LYS* 5.9 1.1 - - - -
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Residues in contact with ASP 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A VAL* 4.4 2.5 - - + -
213A TYR* 2.9 18.6 + - - +
215A GLY* 1.3 74.9 - - - +
217A VAL* 1.3 66.1 + - - +
219A ASP* 3.0 13.3 + - - +
220A VAL* 2.9 29.3 + - - +
288A TYR* 4.4 2.6 + - - +
291A PRO 4.7 3.8 - - - +
292A PHE* 3.4 30.9 - - + +
293A LYS* 2.8 53.2 + - - +
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 4.0 20.2 - - + -
167A TYR* 3.6 30.5 - - + -
170A VAL* 3.9 27.8 - - + -
212A VAL* 4.2 8.3 - - + -
213A TYR 3.8 10.8 - - - +
214A VAL* 3.3 10.3 - - + +
216A ASP* 1.3 77.0 - - - +
218A ALA* 1.3 63.4 + - - +
220A VAL* 3.3 3.3 + - - +
221A ASN* 3.0 32.6 + - - +
235A LEU* 4.1 24.0 - - + -
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Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASN* 3.9 30.3 - - + +
15A ILE* 4.6 6.3 - - - +
18A ALA* 4.0 13.2 - - + -
214A VAL 2.9 12.3 + - - +
215A GLY* 3.5 11.7 - - - +
217A VAL* 1.3 78.8 - - - +
219A ASP* 1.3 65.3 + - - +
221A ASN* 3.1 9.8 + - - +
222A LEU* 3.0 27.2 + - - +
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Residues in contact with ASP 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ALA* 5.3 4.2 - - - +
215A GLY 3.1 20.6 + - - +
216A ASP* 3.0 15.5 + - - +
218A ALA* 1.3 77.9 - - - +
220A VAL* 1.3 63.5 + - - +
222A LEU* 3.2 7.9 + - - +
223A TRP* 2.9 25.2 + - - +
288A TYR* 4.0 14.5 + - + +
290A LYS* 5.6 5.6 - - + +
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Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PHE* 3.6 26.0 - - + -
216A ASP 2.9 16.6 + - - +
217A VAL 3.6 6.5 - - - +
219A ASP* 1.3 75.1 - - - +
221A ASN* 1.3 66.0 + - - +
223A TRP* 3.1 2.1 + - - +
224A PHE* 3.0 35.6 + - + -
235A LEU* 3.7 32.3 - - + -
283A LEU* 4.6 5.6 - - + -
288A TYR* 3.6 36.1 - - + +
292A PHE* 4.1 6.7 - - + -
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Residues in contact with ASN 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 3.5 23.4 - - + +
73A PHE* 3.4 31.2 - - + -
75A GLU* 3.8 3.6 - - - +
112A LEU* 4.1 1.9 - - - +
165A PHE* 3.3 29.9 - - - -
167A TYR* 3.1 23.7 + - - -
217A VAL* 3.0 30.3 + - - +
218A ALA* 3.4 9.0 - - - +
220A VAL* 1.3 78.4 - - - +
222A LEU* 1.3 65.1 + - + +
224A PHE* 3.3 3.5 + - - +
225A LEU* 3.1 20.4 + - - +
235A LEU* 4.7 0.4 - - - +
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Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 4.4 9.9 - - + -
18A ALA* 3.8 36.8 - - + +
19A LEU* 3.9 29.6 - - + +
22A LYS* 3.8 27.8 - - + -
73A PHE* 4.1 13.7 - - + -
218A ALA 3.0 17.3 + - - +
219A ASP* 3.9 7.6 - - - +
221A ASN* 1.3 78.3 - - - +
223A TRP* 1.3 63.0 + - - +
225A LEU* 3.2 8.2 + - + +
226A GLU* 3.0 37.1 + - - +
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Residues in contact with TRP 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ASP 2.9 17.5 + - - +
220A VAL 3.4 4.3 - - - +
222A LEU* 1.3 76.5 - - - +
224A PHE* 1.3 92.5 + + - +
226A GLU* 3.2 6.6 + - - -
227A ASN* 2.7 74.0 + - + +
229A VAL* 4.5 3.8 - - + -
286A ALA 3.6 15.0 - - - -
287A GLY* 3.5 32.7 + - - -
288A TYR* 3.5 35.3 - + + +
289A ASP* 5.8 1.2 + - - +
290A LYS* 4.1 23.0 - - - +
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Residues in contact with PHE 224 (chain A).
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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112A LEU* 4.0 7.2 - - + -
161A GLN* 2.9 12.3 + - - +
163A VAL* 4.1 7.2 - - + -
165A PHE* 3.5 33.4 - + + -
220A VAL* 3.0 25.8 + - + +
221A ASN 3.8 2.0 - - - +
223A TRP* 1.3 98.5 - + - +
225A LEU* 1.3 66.3 + - - +
227A ASN* 4.4 0.7 - - - +
228A GLY 2.9 21.1 + - - -
229A VAL* 3.8 35.0 - - + -
233A PHE* 3.6 37.9 - + - -
283A LEU* 3.7 26.5 - - + -
286A ALA* 4.2 12.6 - - + -
288A TYR* 4.5 2.2 - - + -
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ILE* 4.2 19.3 - - + -
19A LEU* 5.0 5.4 - - + -
24A ILE* 6.1 1.3 - - + -
70A GLU* 4.5 14.4 - - + +
71A ALA* 3.6 23.3 - - + -
73A PHE* 3.7 29.2 - - + -
110A PRO* 4.4 7.4 - - + -
112A LEU* 3.9 11.7 - - + +
161A GLN* 4.2 11.6 - - - +
221A ASN 3.1 12.7 + - - +
222A LEU* 3.5 10.8 - - + +
224A PHE* 1.3 78.1 - - - +
226A GLU* 1.3 66.1 + - + +
227A ASN 3.3 0.2 + - - -
228A GLY* 3.8 5.0 + - - -
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Residues in contact with GLU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LYS* 3.1 36.3 + - - +
222A LEU* 3.0 23.4 + - - +
223A TRP* 3.7 10.2 - - - +
225A LEU* 1.3 81.0 - - + +
227A ASN* 1.3 67.2 + - - +
228A GLY 3.6 0.2 - - - -
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Residues in contact with ASN 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A TRP* 2.7 81.6 + - + +
224A PHE 4.3 0.7 - - - +
225A LEU 3.2 0.2 - - - -
226A GLU* 1.3 90.3 + - - +
228A GLY* 1.3 57.4 + - - +
229A VAL* 3.2 16.9 + - + +
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Residues in contact with GLY 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A GLN* 3.2 31.0 + - - +
224A PHE 2.9 7.9 + - - -
225A LEU 3.8 3.2 + - - -
226A GLU 3.6 2.0 + - - -
227A ASN* 1.3 76.4 - - - +
229A VAL* 1.3 62.7 + - - +
230A 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