Contacts of the helix formed by residues 247 - 267 (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 HIS 247 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239F VAL* 5.5 0.7 - - - -
246F GLU* 1.3 111.0 + - + +
248F LEU* 1.3 60.6 + - - +
249F PRO* 3.1 8.3 - - + -
250F GLN* 3.3 26.0 - - + +
251F VAL* 3.0 32.3 + - - +
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Residues in contact with LEU 248 (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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110F PRO* 3.7 23.8 - - + +
113F MET* 4.1 10.5 - - + -
114F ARG* 4.4 7.9 - - + +
117F PHE* 3.8 23.8 - - + -
236F LEU* 3.5 31.6 - - + -
239F VAL* 4.0 23.0 - - + +
245F ARG* 3.7 16.3 + - + +
246F GLU* 3.7 1.2 + - - -
247F HIS* 1.3 75.6 - - - +
249F PRO* 1.4 69.0 - - + +
251F VAL* 3.3 6.0 + - + +
252F ILE* 2.9 48.2 + - + +
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Residues in contact with PRO 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F PRO* 4.3 26.2 - - + +
245F ARG 3.9 7.9 - - - +
246F GLU 3.9 6.7 - - - +
247F HIS* 3.3 11.0 - - + -
248F LEU* 1.4 97.0 - - + +
250F GLN* 1.3 62.1 + - - +
252F ILE* 3.4 0.9 + - - +
253F ARG* 3.0 40.9 + - - +
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Residues in contact with GLN 250 (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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247F HIS* 3.1 31.0 + - + +
249F PRO* 1.3 79.5 - - - +
251F VAL* 1.3 65.6 + - + +
253F ARG* 2.6 42.2 + - - +
254F GLN* 2.9 59.0 + - - +
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Residues in contact with VAL 251 (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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232F PHE* 3.7 20.4 - - + -
235F GLN* 3.4 38.1 - - + +
236F LEU* 4.1 11.2 - - + +
239F VAL* 4.3 18.6 - - + -
247F HIS* 3.0 19.6 + - - +
248F LEU* 3.5 8.1 - - - +
250F GLN* 1.3 76.8 - - + +
252F ILE* 1.3 64.0 + - + +
254F GLN* 3.3 13.5 + - - +
255F TYR* 3.0 22.7 + - - +
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Residues in contact with ILE 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F THR* 3.9 20.8 - - + +
109F SER* 3.5 29.6 - - - +
110F PRO* 3.4 30.7 - - + -
113F MET* 3.7 10.5 - - - -
189F PHE* 6.3 0.2 - - + -
232F PHE* 3.9 14.6 - - + -
236F LEU* 4.2 9.2 - - + -
248F LEU* 2.9 43.7 + - + +
249F PRO 3.8 3.4 - - - +
251F VAL* 1.3 76.8 - - - +
253F ARG* 1.3 58.0 + - + +
255F TYR* 3.5 6.1 + - + +
256F GLY* 2.9 21.0 + - - -
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Residues in contact with ARG 253 (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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106F THR* 4.1 16.4 - - + +
249F PRO* 3.0 30.6 + - - +
250F GLN* 2.6 32.3 + - - +
252F ILE* 1.3 75.0 - - + +
254F GLN* 1.3 65.6 + - + +
255F TYR 3.2 0.7 - - - -
256F GLY 3.4 1.6 - - - +
257F ILE* 2.9 29.8 + - + +
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Residues in contact with GLN 254 (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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235F GLN* 5.4 4.1 + - - +
250F GLN* 2.9 65.4 + - - +
251F VAL* 3.9 11.8 - - - +
253F ARG* 1.3 78.2 - - + +
255F TYR* 1.3 63.2 + - - +
257F ILE* 3.2 11.6 - - + +
258F ALA* 2.9 27.0 + - - +
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Residues in contact with TYR 255 (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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105F ARG* 3.9 27.6 + - - -
185F ASP* 4.2 10.7 + - - -
189F PHE* 4.7 4.0 - + - -
219F TYR* 4.6 7.6 - - - -
220F PHE* 4.6 5.7 - - - -
225F ALA 5.4 0.2 - - - -
228F LEU* 3.8 36.6 - - + -
229F ALA* 3.9 21.7 - - - +
232F PHE* 3.4 60.3 - + + -
251F VAL 3.0 8.4 + - - +
252F ILE* 3.6 7.9 - - + +
254F GLN* 1.3 77.2 - - - +
256F GLY* 1.3 53.1 + - - +
258F ALA* 4.5 3.1 - - - -
259F SER* 2.6 54.4 + - - -
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Residues in contact with GLY 256 (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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105F ARG* 6.2 0.4 - - - -
106F THR* 4.0 24.2 + - - -
252F ILE 2.9 15.1 + - - -
253F ARG 3.2 4.2 + - - -
254F GLN 3.2 0.6 - - - -
255F TYR* 1.3 80.1 - - - +
257F ILE* 1.3 56.6 + - - +
259F SER* 3.1 6.4 + - - -
260F GLY* 2.9 23.7 + - - -
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Residues in contact with ILE 257 (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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253F ARG* 2.9 17.2 + - + +
254F GLN* 3.2 18.4 - - + +
256F GLY* 1.3 74.0 - - - +
258F ALA* 1.3 63.9 + - + +
260F GLY* 3.1 4.1 + - - +
261F HIS* 2.9 54.1 + - + +
264F ASN* 6.3 0.2 - - - +
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Residues in contact with ALA 258 (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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228F LEU* 3.4 29.2 - - + -
254F GLN 2.9 19.1 + - - +
255F TYR* 3.9 2.7 - - - +
257F ILE* 1.3 74.6 - - + +
259F SER* 1.3 62.2 + - - +
260F GLY 3.0 4.5 - - - -
261F HIS* 3.0 19.9 + - - +
262F ILE* 3.0 16.3 + - - +
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Residues in contact with SER 259 (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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102F LEU* 5.2 7.6 - - - +
105F ARG* 4.6 8.5 + - - -
219F TYR* 3.2 29.4 - - - -
228F LEU* 4.3 2.7 - - - +
255F TYR* 2.6 45.0 + - - -
256F GLY* 3.1 10.7 + - - -
258F ALA* 1.3 76.0 - - - +
260F GLY* 1.3 56.0 + - - +
262F ILE* 3.8 5.0 - - - +
263F TRP* 2.9 30.5 + - - +
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Residues in contact with GLY 260 (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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102F LEU* 5.5 5.6 - - - -
256F GLY 2.9 17.4 + - - -
257F ILE* 3.3 10.1 - - - -
258F ALA 3.0 0.8 - - - -
259F SER* 1.3 77.0 - - - +
261F HIS* 1.3 55.9 + - - +
263F TRP* 3.4 5.0 + - - +
264F ASN* 2.8 41.6 + - - +
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Residues in contact with HIS 261 (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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257F ILE* 2.9 38.8 + - + +
258F ALA* 3.0 9.3 + - - +
260F GLY* 1.3 74.2 - - - +
262F ILE* 1.3 66.9 + - + +
264F ASN* 3.1 16.2 + - + +
265F GLN* 3.0 24.3 + - - +
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Residues in contact with ILE 262 (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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219F TYR* 3.6 25.6 - - + +
222F ASN* 4.4 7.0 - - - +
224F GLN* 4.0 21.1 - - + +
225F ALA* 3.7 29.6 - - + +
228F LEU* 4.1 19.3 - - + -
258F ALA 3.0 15.8 + - - +
259F SER 3.8 6.7 - - - +
261F HIS* 1.3 77.5 - - + +
263F TRP* 1.3 56.6 + - - +
265F GLN* 3.4 3.7 + - - +
266F MET* 3.0 50.0 + - + +
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Residues in contact with TRP 263 (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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95F THR* 4.9 5.8 + - - +
98F VAL* 3.5 40.2 - - + +
99F GLU* 4.4 17.1 + - + +
102F LEU* 3.9 23.3 - - + -
215F VAL* 4.5 12.1 - - + -
218F TYR* 3.8 25.8 - + - -
219F TYR* 4.2 24.0 - + + -
259F SER 2.9 18.5 + - - +
260F GLY* 3.6 3.6 - - - +
262F ILE* 1.3 77.1 - - - +
264F ASN* 1.3 69.3 + - - +
266F MET* 3.1 7.2 + - + -
267F LYS* 2.9 50.6 + - + +
270F LEU* 4.3 20.2 - - + -
274F PHE* 4.3 15.7 - + - -
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Residues in contact with ASN 264 (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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99F GLU* 5.6 2.4 - - - +
260F GLY* 2.8 28.8 + - - +
261F HIS* 3.1 19.7 + - + +
263F TRP* 1.3 90.7 - - - +
265F GLN* 1.3 59.3 + - - +
267F LYS* 3.1 31.8 + - + +
268F MET* 4.3 8.3 - - - +
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Residues in contact with GLN 265 (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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261F HIS 3.0 14.1 + - - +
262F ILE* 4.1 3.8 - - - +
264F ASN* 1.3 77.1 - - - +
266F MET* 1.3 65.7 + - + +
267F LYS 3.3 1.5 + - - -
268F MET* 3.5 32.4 + - - +
269F THR* 4.6 2.3 + - - +
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Residues in contact with MET 266 (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 TYR* 2.3 84.7 + - + +
219F TYR* 3.8 20.2 - - - +
221F SER* 4.3 2.0 - - - +
222F ASN* 3.7 32.1 - - + +
262F ILE* 3.0 39.6 + - + +
263F TRP* 3.1 6.7 + - + +
265F GLN* 1.3 77.5 - - + +
267F LYS* 1.3 62.4 + - - +
268F MET 3.2 0.8 + - - -
269F THR* 3.7 7.0 + - - +
270F LEU* 3.8 0.3 - - - +
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Residues in contact with LYS 267 (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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95F THR* 4.3 21.0 - - + +
99F GLU* 3.7 18.5 + - - +
263F TRP* 2.9 35.5 + - + +
264F ASN* 3.1 43.9 + - + +
266F MET* 1.3 71.4 - - - +
268F MET* 1.3 78.7 + - - +
270F LEU* 3.0 32.1 - - + +
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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