Contacts of the helix formed by residues 246 - 261 (chain B) in PDB entry 1IR1
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 THR 246 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244B ALA* 3.4 3.3 - - - +
245B GLY* 1.3 83.5 - - - +
247B CYS* 1.3 64.5 + - - +
248B GLU* 3.4 16.4 + - - +
249B ASP* 3.2 32.0 + - - +
250B MET* 3.1 23.4 + - - +
276B ALA* 6.3 0.9 - - - -
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Residues in contact with CYS 247 (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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246B THR* 1.3 73.2 - - - +
248B GLU* 1.3 66.0 + - - +
250B MET* 3.3 14.8 + - + +
251B MET* 3.0 37.3 + - + +
275B THR* 5.6 7.2 - - - -
276B ALA* 4.7 21.8 - - - -
279B THR* 5.5 8.5 - - + -
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Residues in contact with GLU 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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246B THR* 3.4 21.6 - - - +
247B CYS* 1.3 83.2 + - - +
249B ASP* 1.3 59.7 + - - +
251B MET* 3.5 6.6 + - - +
252B LYS* 3.0 30.1 + - - +
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Residues in contact with ASP 249 (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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244B ALA* 3.6 18.8 - - + -
245B GLY* 4.8 3.1 + - - -
246B THR* 3.2 24.2 + - - +
248B GLU* 1.3 78.3 - - - +
250B MET* 1.3 67.8 + - - +
252B LYS* 3.2 19.5 + - - +
253B ARG* 3.2 42.7 + - - +
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Residues in contact with MET 250 (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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242B ALA* 3.4 27.3 - - + +
244B ALA* 3.6 7.1 - - + +
246B THR 3.1 13.9 + - - +
247B CYS* 3.5 19.5 - - + +
249B ASP* 1.3 77.7 - - - +
251B MET* 1.3 67.2 + - - +
253B ARG* 3.3 5.5 + - - +
254B ALA* 3.1 19.9 + - - +
267B HIS* 3.8 21.1 - - + -
276B ALA* 3.4 41.3 - - + +
279B THR* 4.0 20.4 - - + -
280B LEU* 4.1 26.2 - - + -
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Residues in contact with MET 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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247B CYS* 3.0 22.2 + - + +
248B GLU* 3.8 6.5 - - - +
250B MET* 1.3 83.5 - - + +
252B LYS* 1.3 60.0 + - - +
254B ALA* 3.2 3.2 + - + +
255B VAL* 2.8 42.6 + - + +
279B THR* 4.0 26.2 - - + +
280B LEU* 5.1 5.8 - - - -
283B TYR* 3.4 48.2 - - + -
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Residues in contact with LYS 252 (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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286A ASP* 3.5 37.5 + - - +
214B TRP* 3.7 23.9 - - + -
248B GLU 3.0 15.5 + - - +
249B ASP* 3.2 24.9 + - - +
251B MET* 1.3 75.4 - - - +
253B ARG* 1.3 62.0 + - - +
255B VAL* 3.6 8.5 + - - +
256B PHE* 3.3 16.6 + - - +
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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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207B ASN* 3.9 14.3 - - - +
208B SER* 3.8 20.6 - - - -
214B TRP* 3.6 61.9 - - + +
218B PHE* 3.4 22.7 - - + -
241B ASN 4.4 8.9 + - - -
242B ALA* 4.2 19.5 - - - -
243B THR 3.4 20.0 + - - -
244B ALA* 3.8 14.5 - - - +
245B GLY 5.7 0.2 - - - +
249B ASP* 3.2 30.3 + - - +
250B MET 3.7 5.6 - - - +
251B MET 3.2 0.6 - - - -
252B LYS* 1.3 75.7 - - - +
254B ALA* 1.3 65.5 + - - +
256B PHE* 3.3 1.9 + - - +
257B ALA* 3.2 17.3 + - - +
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Residues in contact with ALA 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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242B ALA* 4.5 6.9 - - + +
250B MET 3.1 13.4 + - - +
251B MET* 3.6 10.1 - - + +
253B ARG* 1.3 76.6 - - - +
255B VAL* 1.3 62.9 + - - +
257B ALA* 3.2 9.1 + - - +
258B ARG* 3.1 21.1 + - - +
265B VAL* 5.0 6.5 - - + -
280B LEU* 3.9 23.6 - - + -
283B TYR* 3.8 22.7 + - + -
289B LEU* 4.1 6.9 - - + +
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Residues in contact with VAL 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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251B MET* 2.8 33.6 + - + +
252B LYS* 3.7 8.5 - - - +
254B ALA* 1.3 77.4 - - - +
256B PHE* 1.3 63.0 + - - +
258B ARG* 3.2 5.4 + - + +
259B GLU* 3.0 22.5 + - + +
283B TYR* 3.6 26.5 - - + +
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Residues in contact with PHE 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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258A ARG* 5.1 0.2 - - - -
214B TRP* 3.9 24.7 - + + -
215B ARG* 3.3 57.0 - - + -
218B PHE* 3.9 22.7 - + + -
219B LEU* 4.3 8.3 - - + -
252B LYS 3.3 5.5 + - - +
253B ARG 3.3 8.5 + - - +
255B VAL* 1.3 77.2 - - - +
257B ALA* 1.3 66.1 + - - +
259B GLU* 3.1 31.2 + - - -
260B LEU* 3.0 51.4 + - + +
58S SER* 4.8 7.0 - - - -
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Residues in contact with ALA 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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218B PHE* 4.5 3.9 - - + -
240B LEU* 4.4 8.1 - - + -
253B ARG 3.2 12.9 + - - +
254B ALA 3.2 10.1 + - - +
256B PHE* 1.3 76.0 - - - +
258B ARG* 1.3 62.1 + - - +
260B LEU* 3.2 9.1 + - - +
261B GLY 3.2 15.9 + - - -
262B VAL* 3.3 27.8 + - + +
265B VAL* 3.6 30.1 - - + -
289B LEU* 4.7 4.3 - - + -
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Residues in contact with ARG 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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254B ALA 3.1 7.9 + - - +
255B VAL* 3.3 10.3 - - + +
256B PHE 3.2 0.2 - - - -
257B ALA* 1.3 76.9 - - - +
259B GLU* 1.3 62.0 + - - +
261B GLY* 3.1 13.7 + - - -
283B TYR* 3.6 23.6 - - + +
286B ASP 5.3 0.4 + - - -
287B ASN* 3.1 34.8 + - + +
289B LEU* 4.5 7.4 - - + +
215C ARG* 3.5 22.7 - - - +
256C PHE* 4.8 0.8 - - - -
259C GLU* 3.2 39.2 + - - -
58T SER* 4.0 13.6 - - - +
59T PRO* 3.9 23.9 - - + +
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Residues in contact with GLU 259 (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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258A ARG* 3.2 38.9 + - - -
255B VAL* 3.0 14.9 + - + +
256B PHE* 3.1 25.1 + - + +
258B ARG* 1.3 79.1 - - - +
260B LEU* 1.3 60.5 + - - +
261B GLY* 3.3 1.2 + - - -
56S HIS* 3.2 39.4 + - - +
58S SER* 4.0 1.2 - - - -
57T ASN* 5.9 0.7 + - - -
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Residues in contact with LEU 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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218B PHE* 3.8 25.6 - - + +
219B LEU* 5.0 3.8 - - + -
222B ALA* 4.3 15.9 - - + -
226B TYR* 2.8 25.2 + - + -
240B LEU* 4.8 4.9 - - + -
256B PHE* 3.0 56.0 + - + +
257B ALA* 3.2 12.3 + - - +
259B GLU* 1.3 76.0 - - - +
261B GLY* 1.3 58.5 + - - +
262B VAL* 3.4 10.7 + - + -
55S HIS 4.9 1.9 - - - +
56S HIS* 4.0 32.3 - - + +
58S SER* 5.2 0.2 - - - +
61S TYR* 5.0 9.4 - - + -
53T ARG* 4.7 0.3 + - - -
57T ASN* 5.0 3.0 + - - -
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Residues in contact with GLY 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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226B TYR* 3.3 3.8 + - - -
257B ALA 3.2 1.4 + - - -
258B ARG 3.1 12.9 + - - -
259B GLU 3.1 5.2 - - - -
260B LEU* 1.3 78.6 - - - +
262B VAL* 1.3 64.1 + - - +
263B PRO* 3.9 1.7 - - - +
53T ARG* 2.9 28.8 + - - -
57T ASN* 3.4 21.8 - - - -
59T PRO* 3.9 10.6 - - - +
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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
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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