Contacts of the helix formed by residues 214 - 227 (chain F) in PDB entry 5IC4
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 TRP 214 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206F TRP* 3.4 48.6 + + + +
208F ASN* 4.2 10.5 - - + +
212F GLY 4.4 2.0 - - - -
213F SER* 1.3 73.7 - - - +
215F PHE* 1.3 58.6 + - - +
217F GLN* 3.5 2.8 - - - +
218F SER* 2.8 34.2 + - - -
243F VAL* 4.2 12.3 - - + -
247F PHE* 3.4 54.7 - + + -
248F GLU 3.7 5.4 - - - -
249F SER* 3.4 39.5 - - - -
259F LYS 3.7 10.8 - - - -
261F GLN* 3.7 34.5 - - + +
1K ASP* 2.9 28.3 + - - -
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Residues in contact with PHE 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159E ILE* 3.6 27.1 - - + -
160E ILE 4.3 2.9 - - - -
161E GLN* 3.4 15.4 + - + +
196F ALA* 3.7 32.8 - - + -
197F TYR 3.7 13.2 - - - -
198F SER* 3.5 30.3 - - - -
213F SER 3.3 0.6 - - - -
214F TRP* 1.3 79.3 - - - +
216F ILE* 1.3 69.9 + - + +
218F SER* 3.3 2.3 + - - -
219F LEU* 2.8 40.2 + - + +
236F LEU* 5.3 3.1 - - + -
239F VAL* 3.8 24.7 - - + -
240F ASN* 5.4 0.2 - - - -
243F VAL* 4.0 7.0 - - - -
261F GLN* 4.2 7.3 - - - +
263F PRO* 3.9 15.5 - - + -
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Residues in contact with ILE 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E ASP* 3.7 22.0 - - + +
73E ASN* 5.2 0.7 - - + -
74E LEU* 3.6 42.4 - - + -
117E VAL* 4.6 0.4 - - + -
119E LEU* 3.8 27.6 - - + -
159E ILE* 4.3 15.5 - - + -
161E GLN* 4.1 8.1 - - + -
213F SER* 3.1 19.9 + - - +
215F PHE* 1.3 88.1 - - + +
217F GLN* 1.3 67.7 + - - +
219F LEU* 4.2 4.7 - - + -
220F CYS* 3.0 29.1 + - - -
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Residues in contact with GLN 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E ASP* 4.4 2.6 + - - +
73E ASN* 4.5 12.1 + - - +
208F ASN* 4.5 1.2 - - - +
211F ASP* 3.3 42.1 + - - +
212F GLY 2.9 21.1 - - - +
213F SER 3.0 21.4 + - - +
214F TRP* 3.5 6.5 + - - +
216F ILE* 1.3 78.8 - - - +
218F SER* 1.3 61.5 + - - +
220F CYS* 3.9 2.3 - - - +
221F ALA* 3.1 22.9 + - - +
242F LYS* 5.4 1.6 - - - -
247F PHE* 3.9 28.0 - - + -
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Residues in contact with SER 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214F TRP 2.8 17.7 + - - -
215F PHE 3.8 3.1 - - - -
217F GLN* 1.3 74.4 - - - +
219F LEU* 1.3 60.0 + - - +
221F ALA* 3.3 0.7 + - - +
222F MET* 2.9 36.0 + - - +
239F VAL* 4.0 8.7 - - - -
242F LYS* 3.6 29.7 - - - +
243F VAL* 3.4 17.6 - - - +
247F PHE* 3.4 21.7 - - - -
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Residues in contact with LEU 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E LEU* 4.6 9.6 - - + -
78E PHE* 5.3 0.2 - - + -
159E ILE* 3.7 42.8 - - + -
215F PHE* 2.8 30.5 + - + +
216F ILE* 3.8 12.1 - - + +
217F GLN 3.3 0.2 - - - -
218F SER* 1.3 74.0 - - - +
220F CYS* 1.3 57.5 + - - +
222F MET* 3.9 1.0 - - - +
223F LEU* 2.9 55.4 + - + +
232F PHE* 4.7 4.9 - - + -
235F ILE* 5.3 0.4 - - + -
236F LEU* 3.7 30.3 - - + -
239F VAL* 3.7 16.7 - - + +
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Residues in contact with CYS 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E ASN* 3.4 46.4 - - - +
74E LEU* 3.7 22.7 - - - -
77E THR* 3.4 27.4 + - - +
216F ILE* 3.0 24.0 + - - +
217F GLN 3.9 0.2 - - - +
219F LEU* 1.3 75.0 - - - +
221F ALA* 1.3 56.8 + - - +
223F LEU* 3.7 5.5 - - - +
224F LYS* 2.7 37.2 + - - +
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Residues in contact with ALA 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F GLN 3.1 17.7 + - - +
218F SER 3.6 4.9 - - - +
220F CYS* 1.3 76.4 - - - +
222F MET* 1.3 70.9 + - + +
224F LYS* 3.2 10.8 + - - +
225F GLN* 2.8 30.7 + - - +
242F LYS* 4.4 12.3 - - - -
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Residues in contact with MET 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F SER 2.9 18.6 + - - +
221F ALA* 1.3 80.0 - - + +
223F LEU* 1.3 58.0 + - - +
225F GLN* 3.8 17.7 - - - +
226F TYR* 2.7 63.8 + - + +
235F ILE* 3.9 13.3 - - + +
238F ARG* 4.0 16.2 - - - +
239F VAL* 3.7 35.2 - - + +
242F LYS* 3.8 28.3 - - + +
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Residues in contact with LEU 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E THR* 3.7 29.6 - - + -
78E PHE* 4.0 26.9 - - + -
81E LEU* 4.5 7.4 - - + +
159E ILE* 5.7 0.2 - - + -
219F LEU* 2.9 41.5 + - + +
220F CYS* 3.7 0.7 - - - +
222F MET* 1.3 76.3 - - - +
224F LYS* 1.3 62.5 + - - +
227F ALA* 3.0 31.8 + - + +
232F PHE* 4.1 8.5 - - + -
235F ILE* 4.0 20.2 - - + -
275F PHE* 3.8 30.1 - - + -
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Residues in contact with LYS 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E THR* 4.7 6.9 - - + +
80E ASN* 6.1 0.7 - - - -
220F CYS 2.7 22.1 + - - +
221F ALA* 3.4 9.4 - - - +
223F LEU* 1.3 73.2 - - - +
225F GLN* 1.3 59.8 + - + +
227F ALA 4.9 0.5 + - - -
228F ASP* 5.1 2.1 - - - +
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Residues in contact with GLN 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221F ALA* 2.8 16.1 + - - +
222F MET* 3.8 18.5 - - - +
224F LYS* 1.3 78.3 - - - +
226F TYR* 1.3 97.6 + - + +
227F ALA 3.8 0.4 - - - -
228F ASP* 3.6 4.6 - - - +
229F LYS* 3.5 24.7 + - - +
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Residues in contact with TYR 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F MET* 2.7 51.1 + - + +
225F GLN* 1.3 110.8 + - + +
227F ALA* 1.3 56.2 + - - +
228F ASP* 3.0 7.2 - - - -
229F LYS* 2.8 21.2 + - + -
230F LEU* 2.8 58.7 + - + +
235F ILE* 3.9 9.4 - - + +
238F ARG* 3.3 45.7 + - - -
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Residues in contact with ALA 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E LEU* 3.7 28.9 - - + -
222F MET 4.0 1.0 + - - -
223F LEU* 3.0 26.2 + - + +
224F LYS 4.8 0.4 - - - -
225F GLN 3.8 0.6 - - - -
226F TYR* 1.3 75.9 - - - +
228F ASP* 1.3 58.0 + - + +
229F LYS 3.4 1.1 + - - -
230F LEU 4.4 3.4 - - - +
235F ILE* 4.0 11.9 - - - -
275F PHE* 3.8 24.0 + - + +
276F TYR* 3.5 17.5 - - - -
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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