Contacts of the helix formed by residues 246 - 261 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244C ALA* 4.0 3.9 - - - +
245C GLY* 1.3 82.1 - - - +
247C CYS* 1.3 64.8 + - - +
248C GLU* 3.4 16.6 + - - +
249C ASP* 3.2 30.3 + - - +
250C MET* 3.1 23.4 + - - +
276C ALA* 6.4 0.4 - - - -
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Residues in contact with CYS 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C THR* 1.3 74.5 - - - +
248C GLU* 1.3 66.9 + - + +
250C MET* 3.2 15.2 + - + +
251C MET* 2.9 36.5 + - + +
275C THR* 5.7 7.0 - - - -
276C ALA* 5.0 19.5 - - - -
279C THR* 5.8 7.2 - - + -
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Residues in contact with GLU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C THR* 3.4 20.6 - - - +
247C CYS* 1.3 81.4 + - + +
249C ASP* 1.3 63.1 + - - +
251C MET* 3.4 6.9 + - - +
252C LYS* 3.1 28.2 + - + +
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Residues in contact with ASP 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C ALA* 3.6 19.7 - - + -
245C GLY* 5.0 3.1 + - - -
246C THR* 3.2 22.1 + - - +
248C GLU* 1.3 77.4 - - - +
250C MET* 1.3 65.9 + - - +
252C LYS* 3.4 22.5 + - - +
253C ARG* 3.3 43.5 + - - +
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Residues in contact with MET 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C ALA* 3.4 33.6 - - + +
244C ALA* 3.6 7.5 - - + +
246C THR 3.1 12.9 + - - +
247C CYS* 3.5 15.3 - - + +
249C ASP* 1.3 78.0 - - - +
251C MET* 1.3 73.1 + - + +
253C ARG* 3.3 5.9 + - - +
254C ALA* 3.2 19.4 + - - +
267C HIS* 3.9 21.1 - - + -
276C ALA* 3.4 38.1 - - + +
279C THR* 3.9 22.9 - - + -
280C LEU* 3.9 20.2 - - + -
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Residues in contact with MET 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C CYS* 2.9 23.0 + - + +
248C GLU* 3.7 6.7 - - - +
249C ASP 3.3 0.2 - - - -
250C MET* 1.3 88.7 - - + +
252C LYS* 1.3 56.1 + - - +
254C ALA* 3.1 3.1 + - - +
255C VAL* 2.8 42.0 + - + +
279C THR* 4.0 26.2 - - + -
280C LEU* 4.9 5.4 - - - -
283C TYR* 3.4 47.6 - - + -
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Residues in contact with LYS 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ASP* 3.7 33.0 + - - -
214C TRP* 3.7 22.7 - - + -
248C GLU* 3.1 16.4 + - + +
249C ASP* 3.5 25.5 + - - +
251C MET* 1.3 76.5 - - - +
253C ARG* 1.3 61.1 + - - +
255C VAL* 3.6 7.8 + - - +
256C PHE* 3.3 17.5 + - - +
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Residues in contact with ARG 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C ASN* 4.0 13.7 - - - +
208C SER* 3.8 20.4 - - - -
214C TRP* 3.6 59.0 - - + +
218C PHE* 3.3 27.0 - - + -
241C ASN 4.5 8.2 + - - -
242C ALA* 4.2 19.1 - - - -
243C THR 3.3 20.2 + - - -
244C ALA* 3.8 12.1 - - - +
249C ASP* 3.3 31.9 + - - +
250C MET 3.3 6.7 + - - +
251C MET 3.1 0.4 - - - -
252C LYS* 1.3 73.9 - - - +
254C ALA* 1.3 65.3 + - - +
256C PHE* 3.5 1.4 + - - +
257C ALA* 3.2 17.2 + - - +
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Residues in contact with ALA 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C ALA* 4.6 7.3 - - + +
250C MET 3.2 11.6 + - - +
251C MET* 3.1 10.4 + - - +
253C ARG* 1.3 75.4 - - - +
255C VAL* 1.3 63.8 + - - +
257C ALA* 3.3 9.3 + - - +
258C ARG* 3.1 20.8 + - - +
265C VAL* 5.0 6.5 - - + -
280C LEU* 3.8 23.3 - - + -
283C TYR* 3.8 22.0 - - + -
289C LEU* 4.0 7.8 - - + +
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Residues in contact with VAL 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C MET* 2.8 28.0 + - + +
252C LYS* 3.8 8.1 - - - +
253C ARG 3.3 0.2 - - - -
254C ALA* 1.3 77.2 - - - +
256C PHE* 1.3 57.7 + - - +
258C ARG* 3.1 6.7 - - + +
259C GLU* 3.0 27.6 + - + +
283C TYR* 3.6 27.4 - - + +
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Residues in contact with PHE 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B ARG* 5.1 0.7 - - - -
214C TRP* 3.9 21.3 - + + -
215C ARG* 3.3 56.1 - - + -
218C PHE* 3.8 27.6 - + + -
219C LEU* 4.3 8.3 - - + -
252C LYS 3.3 14.1 + - - +
253C ARG 3.9 1.1 - - - +
254C ALA 3.3 0.4 - - - -
255C VAL* 1.3 77.1 - - - +
257C ALA* 1.3 66.3 + - - +
259C GLU* 3.1 29.0 + - - -
260C LEU* 2.9 52.3 + - + +
58T SER* 5.0 7.0 - - - -
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Residues in contact with ALA 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C PHE* 4.4 9.3 - - + -
240C LEU* 4.6 2.7 - - + -
253C ARG 3.2 10.7 + - - +
254C ALA 3.5 9.4 - - - +
255C VAL 3.3 0.2 - - - -
256C PHE* 1.3 77.8 - - - +
258C ARG* 1.3 61.8 + - - +
260C LEU* 3.2 16.3 + - - -
261C GLY 3.3 3.8 + - - -
262C VAL* 3.3 33.7 + - + +
265C VAL* 3.6 29.4 - - + -
289C LEU* 4.7 3.8 - - + -
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Residues in contact with ARG 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C ALA 3.1 7.7 + - - +
255C VAL* 3.1 12.1 - - + +
257C ALA* 1.3 77.1 - - - +
259C GLU* 1.3 64.1 + - - +
261C GLY* 3.0 15.1 + - - -
283C TYR* 3.6 20.9 - - - +
286C ASP 5.4 0.2 + - - -
287C ASN* 3.2 33.7 + - + +
289C LEU* 4.5 5.8 - - + +
215D ARG* 3.5 22.4 - - - +
256D PHE* 4.8 0.4 - - - -
259D GLU* 3.2 38.8 + - - -
58U SER* 3.8 15.0 - - - +
59U PRO* 3.7 25.2 - - + +
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Residues in contact with GLU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B ARG* 3.2 40.6 + - - -
255C VAL* 3.0 15.4 + - + +
256C PHE* 3.4 26.2 - - + +
258C ARG* 1.3 78.4 - - - +
260C LEU* 1.3 61.0 + - - +
261C GLY* 3.4 0.9 + - - -
56T HIS* 3.2 36.7 + - - +
58T SER* 4.1 1.7 - - - -
57U ASN* 5.5 4.5 + - - -
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Residues in contact with LEU 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C PHE* 3.9 24.7 - - + +
219C LEU* 5.0 3.4 - - + -
222C ALA* 4.3 17.9 - - + -
226C TYR* 2.7 29.7 + - + -
240C LEU* 5.2 3.1 - - + -
256C PHE* 2.9 55.3 + - + +
257C ALA* 3.6 14.1 - - - +
258C ARG 3.2 0.6 - - - -
259C GLU* 1.3 76.2 - - - +
261C GLY* 1.3 52.6 + - - +
262C VAL* 4.0 13.5 - - + -
55T HIS 5.0 1.6 - - - +
56T HIS* 4.0 33.0 - - + +
58T SER* 5.2 0.2 - - - +
61T TYR* 5.0 7.0 - - + -
53U ARG* 4.7 0.5 + - - -
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Residues in contact with GLY 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C TYR* 3.3 3.9 + - - -
257C ALA 3.3 0.6 + - - -
258C ARG 3.0 16.0 + - - -
259C GLU 3.2 1.8 - - - -
260C LEU* 1.3 78.9 - - - +
262C VAL* 1.3 64.4 + - - +
263C PRO* 4.0 1.6 - - - +
53U ARG* 2.9 29.4 + - - -
57U ASN* 3.3 22.9 - - - -
59U PRO* 3.9 8.3 - - - +
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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
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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