Contacts of the helix formed by residues 216 - 229 (chain A) in PDB entry 5ID6
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 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A PHE* 4.6 7.4 - - + -
202A VAL* 4.0 43.1 - - + +
203A GLN* 4.5 7.7 - - - +
206A LYS* 4.2 18.8 - - + -
207A GLU* 4.8 4.9 - - + +
211A ASN* 6.3 1.6 - - - +
215A ASP* 1.3 70.4 - - - +
217A GLU* 1.3 67.7 + - - +
218A ASP 3.0 1.2 + - - -
219A PHE* 3.3 13.1 + - - +
220A PHE* 3.3 33.9 - - + -
240A ILE* 4.3 13.7 - - + -
255A LEU* 4.2 16.8 - - + -
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Residues in contact with GLU 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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190A PHE* 4.3 23.0 - - + -
202A VAL* 6.0 4.7 - - + -
215A ASP* 4.8 17.6 - - + +
216A VAL* 1.3 78.6 - - + +
218A ASP* 1.3 66.5 + - - +
220A PHE* 3.0 18.9 + - - +
221A GLU* 3.7 17.0 + - + +
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Residues in contact with ASP 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A TYR* 3.6 7.2 - - - +
215A ASP* 2.7 43.5 + - - +
216A VAL 3.0 0.8 - - - -
217A GLU* 1.3 80.1 - - - +
219A PHE* 1.3 56.7 + - - +
221A GLU* 2.9 30.3 + - - +
224A PHE* 3.2 48.8 - - + +
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Residues in contact with PHE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A TYR* 2.6 35.6 + + - -
211A ASN* 4.4 8.7 - - - -
214A TYR* 4.3 16.2 - + + -
215A ASP 3.6 18.6 - - - -
216A VAL* 3.3 9.2 + - - +
218A ASP* 1.3 70.9 - - - +
220A PHE* 1.3 67.7 + - + +
224A PHE* 3.7 21.5 - + - -
227A PHE* 3.4 42.4 - + - -
228A VAL* 5.2 4.5 - - + -
233A GLY 4.8 3.4 - - - -
236A VAL* 4.0 18.6 - - + -
237A TYR* 3.8 27.0 - + + -
240A ILE* 3.9 24.2 - - + -
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Residues in contact with PHE 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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183A TYR* 4.2 0.9 - - - -
186A ASN* 3.8 13.0 - - + -
187A MSE 3.3 29.7 - - + +
190A PHE* 3.4 59.6 - + + -
191A GLU* 6.1 1.0 - - - +
216A VAL* 3.3 39.0 - - + -
217A GLU 3.0 5.5 + - - +
218A ASP 2.9 1.2 + - - -
219A PHE* 1.3 85.1 - - + +
221A GLU* 1.3 64.8 + - - +
237A TYR* 4.1 23.8 - + - -
240A ILE* 4.6 7.6 - - + -
241A ILE* 5.8 2.9 - - + -
255A LEU* 3.8 20.2 - - + -
273A PHE* 3.9 21.3 - + - -
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Residues in contact with GLU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A TYR* 3.0 19.5 + - - -
187A MSE 3.7 2.5 - - - +
190A PHE* 6.1 0.9 - - - -
217A GLU* 3.7 18.2 - - - +
218A ASP* 2.9 22.3 + - - +
220A PHE* 1.3 84.2 - - - +
222A GLY* 1.3 65.4 + - - +
223A GLU* 4.5 4.9 - - + +
224A PHE* 3.1 13.5 + - + +
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Residues in contact with GLY 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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74A LEU* 3.7 13.7 - - - +
75A ASN* 4.6 6.3 - - - -
78A ILE* 3.5 28.3 - - - +
183A TYR* 4.5 1.6 - - - -
187A MSE 3.2 16.0 - - - +
221A GLU* 1.3 69.5 + - - +
223A GLU* 1.3 58.8 + - - +
224A PHE 3.0 9.9 + - - -
225A PHE* 3.3 14.0 + - - +
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Residues in contact with GLU 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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70A LYS* 5.8 1.7 - - - -
72A LYS* 5.4 7.0 + - - -
74A LEU* 4.6 7.2 - - - -
75A ASN* 2.4 45.3 + - - +
221A GLU* 3.3 4.4 - - + +
222A GLY* 1.3 75.6 - - - +
224A PHE* 1.3 60.5 + - - +
225A PHE 3.3 0.9 - - - -
226A ASN* 2.9 22.8 + - - +
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Residues in contact with PHE 224 (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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183A TYR* 3.4 6.9 + - - +
214A TYR* 3.5 31.0 - + - -
218A ASP* 3.2 51.6 - - + +
219A PHE* 3.7 38.5 - + - -
221A GLU* 3.1 18.3 + - + +
222A GLY 3.0 1.4 - - - -
223A GLU* 1.3 79.6 - - + +
225A PHE* 1.3 65.0 + - - +
226A ASN* 3.3 4.9 - - - +
227A PHE* 3.2 32.2 + + + +
228A VAL* 4.0 2.4 + - - +
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Residues in contact with PHE 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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71A LEU* 4.5 12.3 - - + -
74A LEU* 4.3 18.2 - - + -
78A ILE* 5.4 0.2 - - + -
175A CYS 3.4 23.8 - - - -
176A ILE* 4.7 2.5 - - + -
179A ASN* 4.0 9.2 - - + -
180A LEU* 3.5 33.7 - - + -
183A TYR* 3.3 48.7 + + + -
222A GLY 3.3 12.9 + - - +
223A GLU 3.3 1.8 - - - -
224A PHE* 1.3 78.3 - - - +
226A ASN* 1.3 54.8 + - - +
228A VAL* 2.6 58.0 + - + +
229A LEU* 3.5 25.9 + - + -
276A LEU* 5.2 0.2 - - + -
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Residues in contact with ASN 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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66A LEU 4.4 6.6 - - - +
69A ILE 3.3 25.9 - - - +
70A LYS* 4.3 22.5 - - + +
71A LEU* 4.0 14.7 + - + +
74A LEU* 3.8 18.7 - - - +
223A GLU 2.9 27.1 + - - +
224A PHE* 3.9 2.6 - - - +
225A PHE* 1.3 75.0 - - - +
227A PHE* 1.3 68.2 + - - +
229A LEU* 3.1 34.2 + - + +
230A THR* 4.8 1.4 + - - +
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Residues in contact with PHE 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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214A TYR* 3.1 47.1 - + - -
219A PHE* 3.4 33.0 - + - -
224A PHE* 3.2 30.1 + + + +
225A PHE 2.9 0.6 + - - -
226A ASN* 1.3 80.7 - - - +
228A VAL* 1.3 58.6 + - - +
229A LEU 3.3 3.3 + - - -
230A THR* 3.8 10.2 + - - +
233A GLY* 3.6 32.1 - - - -
236A VAL* 4.8 8.3 - - + -
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Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASN* 4.1 6.4 + - - -
183A TYR* 4.0 9.6 - - + -
219A PHE* 5.2 2.7 - - + -
224A PHE 4.7 2.0 - - - +
225A PHE* 2.6 54.3 + - + +
227A PHE* 1.3 75.7 - - + +
229A LEU* 1.3 61.6 + - - +
230A THR 3.4 3.4 - - - -
233A GLY* 3.2 29.8 - - - +
234A ILE* 3.3 18.1 - - - +
237A TYR* 3.7 13.7 - - + -
276A LEU* 3.5 30.1 - - + -
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Residues in contact with LEU 229 (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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66A LEU* 3.3 44.9 - - + +
69A ILE* 4.1 22.9 - - + +
71A LEU* 4.8 11.0 - - + -
105A ILE* 5.3 3.1 - - + -
175A CYS* 4.3 22.5 - - + -
179A ASN* 5.6 1.2 + - - +
225A PHE* 3.5 37.7 - - + -
226A ASN* 3.1 32.5 - - + +
227A PHE 3.3 0.8 - - - -
228A VAL* 1.3 80.1 - - - +
230A THR* 1.3 61.6 + - - +
231A GLN 4.2 0.2 + - - -
234A ILE* 4.0 4.5 - - - +
279A GLN* 4.0 14.4 + - - +
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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