Contacts of the helix formed by residues 222 - 243 (chain F) in PDB entry 4P9U
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 ASN 222 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219F TYR 3.9 12.1 - - - +
220F PHE 3.1 0.4 - - - -
221F SER* 1.3 79.3 + - - +
223F PRO* 1.3 71.3 - - - +
224F GLN* 3.1 23.8 + - - +
225F ALA* 3.0 17.0 + - + +
226F ARG* 3.1 15.8 + - - +
262F ILE* 4.4 7.5 - - - +
266F MET* 3.7 30.9 - - + +
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Residues in contact with PRO 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F LEU* 5.0 4.0 - - + +
221F SER 3.8 7.0 - - - +
222F ASN* 1.3 91.2 - - - +
224F GLN* 1.3 59.7 + - - +
226F ARG* 3.1 36.1 + - - +
227F GLU* 3.0 25.1 + - - +
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Residues in contact with GLN 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222F ASN* 3.1 15.9 + - - +
223F PRO* 1.3 79.0 - - - +
225F ALA* 1.3 60.1 + - - +
227F GLU* 4.8 6.3 - - - +
228F LEU* 3.5 28.9 + - - +
262F ILE* 4.0 19.0 - - + +
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Residues in contact with ALA 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219F TYR* 3.5 48.4 + - + +
220F PHE* 4.3 3.5 - - + -
222F ASN* 3.0 15.2 + - + +
224F GLN* 1.3 78.4 - - - +
226F ARG* 1.3 58.4 + - - +
228F LEU* 3.4 3.6 + - - +
229F ALA* 3.0 27.9 + - - +
255F TYR* 5.4 0.3 - - - -
262F ILE* 3.7 22.2 - - + +
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Residues in contact with ARG 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F LEU* 3.8 25.0 - - + +
174F GLU* 5.2 7.1 + - - -
177F ILE* 3.4 30.6 - - - +
181F PHE* 3.0 52.8 - - + -
220F PHE* 2.9 42.3 + - + +
221F SER* 4.0 13.9 + - - +
222F ASN 3.1 8.0 + - - +
223F PRO* 3.1 36.9 + - - +
225F ALA* 1.3 78.0 - - - +
227F GLU* 1.3 58.0 + - - +
229F ALA* 3.1 1.0 - - - +
230F MET* 2.9 23.1 + - - +
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Residues in contact with GLU 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F LEU* 4.8 5.3 - - + +
223F PRO 3.0 14.1 + - - +
224F GLN* 4.8 7.4 - - - +
226F ARG* 1.3 72.8 - - - +
228F LEU* 1.3 62.0 + - - +
229F ALA 3.1 0.9 - - - -
230F MET* 4.0 30.4 - - + +
231F GLU* 2.9 35.6 + - + +
234F ARG* 5.5 4.3 + - - -
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Residues in contact with LEU 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219F TYR* 5.7 0.4 - - - +
224F GLN* 3.5 27.9 + - - +
225F ALA 3.4 4.4 + - - +
226F ARG 3.4 0.2 - - - -
227F GLU* 1.3 77.5 - - - +
229F ALA* 1.3 57.7 + - - +
231F GLU* 4.7 12.6 - - + -
232F PHE* 3.0 28.0 + - + +
255F TYR* 4.1 18.4 - - + -
258F ALA* 3.4 36.3 - - + -
259F SER* 4.3 2.2 - - - +
262F ILE* 4.1 20.4 - - + -
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Residues in contact with ALA 229 (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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181F PHE* 3.5 20.4 - - + -
220F PHE* 3.9 8.7 - - + -
225F ALA 3.0 14.9 + - - +
226F ARG 3.1 13.5 - - - +
228F LEU* 1.3 78.6 - - - +
230F MET* 1.3 54.5 + - - +
232F PHE* 3.2 2.4 - - - +
233F TYR* 2.9 45.5 + - + +
255F TYR* 3.9 20.6 - - - +
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Residues in contact with MET 230 (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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132F ILE* 5.0 5.3 - - + +
135F CYS* 3.4 35.2 - - + +
136F GLU* 4.0 15.0 - - - +
138F LEU* 4.0 20.6 - - + -
139F VAL* 6.3 2.2 - - + -
181F PHE* 3.7 16.6 - - + -
226F ARG 2.9 15.2 + - - +
227F GLU* 3.2 33.8 + - - +
229F ALA* 1.3 73.3 - - - +
231F GLU* 1.3 59.5 + - - +
233F TYR* 3.1 13.3 + - + +
234F ARG* 2.9 48.7 + - - +
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Residues in contact with GLU 231 (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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227F GLU* 2.9 27.4 + - + +
228F LEU* 4.1 12.8 - - + +
230F MET* 1.3 69.1 - - - +
232F PHE* 1.3 61.6 + - - +
234F ARG* 3.3 12.5 + - + +
235F GLN* 2.9 56.1 + - + +
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Residues in contact with PHE 232 (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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113F MET* 4.8 2.7 - - + -
189F PHE* 3.9 21.8 - + - -
228F LEU* 3.0 16.5 + - + +
229F ALA 3.2 7.6 - - - +
231F GLU* 1.3 77.5 - - - +
233F TYR* 1.3 75.7 + + - +
235F GLN* 3.2 9.4 + - - +
236F LEU* 2.9 54.4 + - + +
251F VAL* 3.7 26.7 - - + -
252F ILE* 3.9 18.6 - - + -
255F TYR* 3.4 60.1 - + + -
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Residues in contact with TYR 233 (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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128F MET* 3.2 13.1 - - - +
131F VAL* 4.2 20.4 - - + -
132F ILE* 3.7 23.6 - - + -
135F CYS* 4.3 8.5 - - - -
181F PHE* 3.7 23.3 - + - -
185F ASP* 2.6 45.0 + - - +
188F LEU* 3.7 31.9 - - + -
189F PHE* 5.0 1.8 - + - -
229F ALA* 2.9 35.7 + - + +
230F MET* 3.1 15.0 + - + +
232F PHE* 1.3 90.9 - + - +
234F ARG* 1.3 58.5 + - - +
236F LEU* 3.3 5.0 + - - -
237F LEU* 2.9 24.1 + - - +
255F TYR* 5.4 0.2 - - - -
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Residues in contact with ARG 234 (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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132F ILE* 4.0 33.4 - - + +
136F GLU* 4.5 14.1 + - - -
227F GLU* 5.5 4.0 + - - -
230F MET* 2.9 33.9 + - - +
231F GLU* 3.8 10.7 - - + +
232F PHE 3.2 0.2 - - - -
233F TYR* 1.3 72.8 - - - +
235F GLN* 1.3 60.9 + - - +
237F LEU* 3.3 10.8 + - + +
238F ALA* 2.9 28.2 + - - +
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Residues in contact with GLN 235 (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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231F GLU* 2.9 51.3 + - + +
232F PHE* 3.6 9.5 - - - +
234F ARG* 1.3 75.8 - - - +
236F LEU* 1.3 58.7 + - - +
238F ALA* 3.2 9.6 + - - +
239F VAL* 2.9 32.0 + - - +
251F VAL* 3.4 35.5 - - + +
254F GLN* 5.4 4.0 + - - +
255F TYR* 6.0 0.2 - - - +
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Residues in contact with LEU 236 (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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113F MET* 3.9 27.1 - - + -
117F PHE* 3.7 11.6 - - + -
128F MET* 3.4 17.3 - - + -
188F LEU* 4.4 13.0 - - + -
192F LEU* 4.9 1.6 - - + -
232F PHE* 2.9 59.3 + - + +
233F TYR* 3.5 4.3 - - - +
235F GLN* 1.3 76.8 - - - +
237F LEU* 1.3 55.8 + - - +
239F VAL* 3.0 7.7 + - - +
240F CYS 2.9 24.4 + - - -
248F LEU* 3.5 28.9 - - + -
251F VAL* 4.1 6.7 - - + -
252F ILE* 4.2 2.0 - - + -
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Residues in contact with LEU 237 (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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125F GLU* 3.6 43.7 - - + +
128F MET* 3.3 15.4 - - + +
129F ILE* 3.7 19.7 - - + -
132F ILE* 3.9 16.2 - - + -
233F TYR 2.9 14.9 + - - +
234F ARG* 3.5 11.4 - - + +
236F LEU* 1.3 75.4 - - - +
238F ALA* 1.3 57.8 + - - +
240F CYS* 3.3 1.8 + - + +
241F GLN* 2.9 57.6 + - - +
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Residues in contact with ALA 238 (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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234F ARG 2.9 14.0 + - - +
235F GLN* 3.2 13.0 + - - +
237F LEU* 1.3 76.9 - - - +
239F VAL* 1.3 56.8 + - + +
241F GLN* 4.0 9.9 - - - +
242F SER* 2.9 32.3 + - - -
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Residues in contact with VAL 239 (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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117F PHE* 3.9 20.4 - - + -
235F GLN 2.9 21.8 + - - +
236F LEU* 3.3 10.8 - - - +
238F ALA* 1.3 76.4 - - + +
240F CYS* 1.3 57.9 + - - +
242F SER* 3.3 6.0 + - - -
243F GLY* 3.0 27.2 + - - -
244F GLU 3.8 18.9 + - - +
245F ARG* 4.3 4.7 - - - -
246F GLU* 5.8 1.1 - - - +
247F HIS 5.5 0.4 - - - -
248F LEU* 4.0 27.6 - - + +
251F VAL* 4.3 20.6 - - + -
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Residues in contact with CYS 240 (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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117F PHE* 3.6 48.5 - - + +
121F LYS* 3.4 54.1 - - - +
124F ALA* 4.0 0.2 - - - -
125F GLU* 4.0 15.0 - - + -
128F MET* 4.8 2.7 - - - -
236F LEU 2.9 11.6 + - - +
237F LEU* 3.8 6.5 - - - +
239F VAL* 1.3 77.1 - - - +
241F GLN* 1.3 61.8 + - - +
243F GLY* 3.5 7.5 + - - -
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Residues in contact with GLN 241 (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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121F LYS* 4.0 11.3 - - - +
125F GLU* 3.2 23.6 + - - +
129F ILE* 4.5 11.5 - - - +
237F LEU* 2.9 50.2 + - + +
238F ALA* 4.0 7.3 - - - +
240F CYS* 1.3 75.7 - - - +
242F SER* 1.3 66.0 + - - +
243F GLY* 3.4 0.5 + - - -
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Residues in contact with SER 242 (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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238F ALA 2.9 21.3 + - - -
239F VAL* 3.6 5.8 - - - -
241F GLN* 1.3 77.2 - - - +
243F GLY* 1.3 60.7 + - - +
244F GLU* 3.5 15.5 + - - +
246F GLU* 5.7 1.0 + - - -
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Residues in contact with GLY 243 (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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117F PHE 6.1 1.1 - - - -
121F LYS* 5.6 4.5 - - - -
239F VAL 3.0 10.7 + - - -
240F CYS* 3.5 8.9 + - - -
241F GLN 3.2 2.9 - - - -
242F SER* 1.3 77.3 - - - +
244F GLU* 1.3 59.6 + - - +
245F ARG* 3.9 15.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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