Contacts of the helix formed by residues 247 - 267 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B VAL* 5.4 1.1 - - - -
246B GLU* 1.3 120.3 + - + +
248B LEU* 1.3 61.1 + - - +
249B PRO* 3.0 8.0 - - + +
250B GLN* 3.4 24.8 - - + +
251B VAL* 2.9 33.3 + - - +
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B PRO* 3.6 24.2 - - + +
113B MET* 4.2 10.1 - - + -
114B ARG* 4.5 6.1 - - + +
117B PHE* 3.9 22.9 - - + -
236B LEU* 3.6 31.2 - - + -
239B VAL* 4.0 20.0 - - + +
245B ARG* 3.5 21.8 + - + +
246B GLU* 4.1 1.8 + - - -
247B HIS* 1.3 77.1 - - - +
249B PRO* 1.4 69.8 - - + +
251B VAL* 3.6 4.9 - - + +
252B ILE* 3.0 47.9 + - + +
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Residues in contact with PRO 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PRO* 4.3 25.7 - - + +
245B ARG 3.8 8.1 - - - +
246B GLU 3.9 6.5 - - - +
247B HIS* 3.3 10.5 - - + +
248B LEU* 1.4 97.9 - - + +
250B GLN* 1.3 62.9 + - - +
252B ILE* 3.3 2.1 + - - +
253B ARG* 2.9 26.0 + - - +
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Residues in contact with GLN 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B HIS* 3.2 27.7 + - + +
249B PRO* 1.3 77.1 - - - +
251B VAL* 1.3 66.2 + - + +
253B ARG* 3.2 5.4 + - - +
254B GLN* 2.8 63.7 + - - +
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B PHE* 3.8 19.9 - - + -
235B GLN* 3.4 37.2 - - + +
236B LEU* 4.2 11.7 - - + +
239B VAL* 4.4 16.4 - - + -
247B HIS 2.9 23.6 + - - +
248B LEU* 3.6 5.8 - - - +
250B GLN* 1.3 76.8 - - + +
252B ILE* 1.3 62.7 + - + +
254B GLN* 3.4 11.5 + - - +
255B TYR* 3.0 22.7 + - - +
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Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B THR* 3.9 22.0 - - + +
109B SER* 3.5 29.2 - - - +
110B PRO* 3.4 30.5 - - + -
113B MET* 3.7 11.0 - - + -
232B PHE* 4.0 13.7 - - + -
236B LEU* 4.3 9.9 - - + -
248B LEU* 3.0 42.8 + - + +
249B PRO 3.7 3.6 - - - +
251B VAL* 1.3 76.6 - - - +
253B ARG* 1.3 57.6 + - + +
255B TYR* 3.5 5.1 + - + +
256B GLY* 2.9 21.8 + - - -
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Residues in contact with ARG 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A TYR* 3.1 19.6 + - - -
106B THR* 3.7 31.1 + - + +
107B ASN* 2.9 30.8 + - - +
110B PRO* 5.3 4.9 - - - +
249B PRO 2.9 15.6 + - - +
250B GLN* 4.2 6.1 - - - +
252B ILE* 1.3 75.3 - - - +
254B GLN* 1.3 61.2 + - - +
256B GLY* 4.0 1.6 - - - +
257B ILE* 2.9 30.2 + - - +
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Residues in contact with GLN 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B LEU* 6.3 0.2 - - - -
235B GLN* 4.8 10.1 + - - +
250B GLN* 2.8 62.3 + - - +
251B VAL* 3.7 9.3 - - - +
253B ARG* 1.3 73.9 - - - +
255B TYR* 1.3 64.8 + - - +
257B ILE* 3.2 9.9 - - + +
258B ALA* 3.0 27.8 + - - +
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Residues in contact with TYR 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ARG* 3.9 28.5 + - - -
185B ASP* 4.2 11.0 + - - -
189B PHE* 4.6 4.3 - + - -
219B TYR* 4.6 9.5 - - - -
220B PHE* 4.5 5.9 - - - -
228B LEU* 3.8 36.3 - - + -
229B ALA* 3.8 23.1 - - - +
232B PHE* 3.4 62.4 - + + -
233B TYR* 5.7 0.2 - + - -
251B VAL 3.0 11.0 + - - +
252B ILE* 3.7 4.0 - - + +
254B GLN* 1.3 74.7 - - - +
256B GLY* 1.3 54.7 + - - +
258B ALA* 4.6 3.1 - - - -
259B SER* 2.5 55.2 + - - -
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Residues in contact with GLY 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ARG* 6.3 0.4 - - - -
106B THR* 4.0 23.5 + - - -
252B ILE 2.9 15.9 + - - -
253B ARG 3.3 4.0 + - - -
254B GLN 3.1 0.4 - - - -
255B TYR* 1.3 80.9 - - - +
257B ILE* 1.3 57.4 + - - +
259B SER* 3.2 5.8 + - - -
260B GLY* 2.9 23.9 + - - -
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Residues in contact with ILE 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B ARG 2.9 18.0 + - - +
254B GLN* 3.2 16.6 - - + +
256B GLY* 1.3 73.8 - - - +
258B ALA* 1.3 64.3 + - + +
260B GLY* 3.1 2.0 + - - +
261B HIS* 2.9 55.0 + - + +
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Residues in contact with ALA 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B LEU* 3.4 27.6 - - + -
254B GLN 3.0 19.3 + - - +
255B TYR* 4.1 1.1 - - - +
257B ILE* 1.3 76.2 - - + +
259B SER* 1.3 64.8 + - - +
261B HIS* 3.1 7.1 + - - +
262B ILE* 3.0 24.8 + - - +
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Residues in contact with SER 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 5.3 7.1 - - - +
105B ARG* 4.7 7.9 + - - -
219B TYR* 3.2 30.3 - - - -
228B LEU* 4.0 3.0 - - - +
255B TYR* 2.5 45.5 + - - -
256B GLY* 3.2 8.1 + - - -
258B ALA* 1.3 77.0 - - - +
260B GLY* 1.3 56.8 + - - +
262B ILE* 3.7 5.6 - - - +
263B TRP* 2.9 29.6 + - - +
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Residues in contact with GLY 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 5.4 6.7 - - - -
256B GLY 2.9 21.2 + - - -
257B ILE* 3.3 6.1 - - - -
258B ALA 3.0 1.0 - - - -
259B SER* 1.3 78.3 - - - +
261B HIS* 1.3 56.6 + - - +
263B TRP* 3.4 7.8 + - - +
264B ASN* 2.8 33.6 + - - +
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Residues in contact with HIS 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B ILE* 2.9 44.7 + - + +
258B ALA* 3.1 4.7 + - - +
260B GLY* 1.3 71.7 - - - +
262B ILE* 1.3 66.2 + - - +
263B TRP 3.1 1.3 - - - -
264B ASN* 2.9 34.2 + - + +
265B GLN* 2.9 14.0 + - - +
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Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B TYR* 3.7 25.4 - - + +
222B ASN* 4.4 7.4 - - - +
224B GLN* 3.9 28.7 - - + +
225B ALA* 3.7 29.6 - - + +
228B LEU* 4.1 17.9 - - + -
258B ALA 3.0 17.2 + - - +
259B SER 3.7 6.5 - - - +
261B HIS* 1.3 74.1 - - - +
263B TRP* 1.3 63.4 + - - +
265B GLN* 3.2 6.0 + - - +
266B MET* 3.0 38.8 + - + +
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Residues in contact with TRP 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B THR* 4.8 5.8 + - - +
98B VAL* 3.5 38.8 - - + +
99B GLU* 4.3 18.4 + - + +
102B LEU* 3.8 23.6 - - + -
215B VAL* 4.6 11.2 - - + -
218B TYR* 3.8 26.7 - + - -
219B TYR* 4.3 22.9 - + + -
259B SER 2.9 18.1 + - - +
260B GLY 3.5 4.9 - - - +
262B ILE* 1.3 77.1 - - - +
264B ASN* 1.3 65.6 + - - +
266B MET* 4.4 7.9 - - + +
267B LYS* 2.9 49.3 + - + +
270B LEU* 4.3 20.0 - - + -
274B PHE* 4.3 15.7 - + - -
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Residues in contact with ASN 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B GLY 2.8 24.2 + - - +
261B HIS* 2.9 41.0 + - + +
263B TRP* 1.3 81.4 - - - +
265B GLN* 1.3 60.2 + - - +
267B LYS* 3.1 37.5 + - + +
268B MET* 4.4 9.5 - - - +
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Residues in contact with GLN 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B HIS 2.9 11.2 + - - +
262B ILE* 4.0 5.2 - - - +
264B ASN* 1.3 80.2 + - - +
266B MET* 1.3 66.0 + - + +
267B LYS 3.2 1.7 + - - -
268B MET* 3.5 25.1 + - - +
269B THR* 4.6 2.8 + - - +
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Residues in contact with MET 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B TYR* 2.4 79.4 + - + +
219B TYR* 3.7 24.0 - - - +
221B SER* 4.4 2.0 - - - +
222B ASN* 3.7 37.9 - - + +
262B ILE* 3.0 33.6 + - + +
263B TRP* 3.2 7.2 + - + +
265B GLN* 1.3 76.7 - - + +
267B LYS* 1.3 63.7 + - - +
268B MET 3.2 0.6 + - - -
269B THR* 3.9 6.1 - - - +
270B LEU* 3.8 1.2 - - - +
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Residues in contact with LYS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B THR* 4.6 15.9 - - + +
99B GLU* 3.7 22.7 + - - -
263B TRP* 2.9 35.1 + - + +
264B ASN* 3.1 46.9 + - + +
266B MET* 1.3 75.0 - - - +
268B MET* 1.3 82.2 + - + +
270B LEU* 3.1 31.6 - - + +
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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
------------------------------------------------------------
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