Contacts of the helix formed by residues 246 - 261 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244D ALA* 3.4 3.4 - - - +
245D GLY* 1.3 84.8 - - - +
247D CYS* 1.3 65.0 + - - +
248D GLU* 3.5 15.5 + - - +
249D ASP* 3.1 30.9 + - - +
250D MET* 3.0 24.3 + - - +
276D ALA* 6.3 0.7 - - - -
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Residues in contact with CYS 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D THR* 1.3 72.8 - - - +
248D GLU* 1.3 71.9 + - - +
250D MET* 3.3 15.4 + - + +
251D MET* 3.0 31.0 + - + +
275D THR* 5.6 7.4 - - - -
276D ALA* 4.7 22.2 - - - -
279D THR* 5.4 8.1 - - + -
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Residues in contact with GLU 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D THR* 3.5 13.4 - - - +
247D CYS* 1.3 88.7 + - - +
249D ASP* 1.3 64.0 + - - +
251D MET* 3.3 6.3 + - - +
252D LYS* 3.0 28.9 + - + +
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Residues in contact with ASP 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D ALA* 3.6 18.8 - - + -
245D GLY* 4.8 3.5 + - - -
246D THR* 3.1 24.2 + - - +
248D GLU* 1.3 79.6 - - - +
250D MET* 1.3 63.9 + - - +
252D LYS* 3.3 19.5 + - - +
253D ARG* 3.3 43.1 + - - +
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Residues in contact with MET 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D ALA* 3.5 32.8 - - + +
244D ALA* 3.6 6.9 - - + +
246D THR 3.0 17.2 + - - +
247D CYS* 3.5 16.2 - - + +
248D GLU 3.3 0.2 - - - -
249D ASP* 1.3 78.7 - - - +
251D MET* 1.3 68.0 + - + +
253D ARG* 3.4 3.6 + - - +
254D ALA* 3.2 19.9 + - - +
267D HIS* 3.9 21.1 - - + -
276D ALA* 3.4 40.6 - - + +
279D THR* 4.0 21.8 - - + -
280D LEU* 4.1 19.7 - - + -
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Residues in contact with MET 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D CYS* 3.0 22.3 + - + +
248D GLU* 3.7 6.3 - - - +
250D MET* 1.3 83.9 - - + +
252D LYS* 1.3 66.0 + - - +
254D ALA* 3.2 3.0 + - - +
255D VAL* 2.9 35.9 + - + +
279D THR* 4.1 24.5 - - + +
280D LEU* 5.0 5.8 - - - -
283D TYR* 3.3 48.0 - - + -
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Residues in contact with LYS 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286C ASP* 2.9 39.1 + - - -
214D TRP* 3.9 19.0 - - + -
248D GLU* 3.0 19.5 + - + +
249D ASP* 3.3 25.0 + - - +
251D MET* 1.3 77.0 - - - +
253D ARG* 1.3 63.3 + - + +
255D VAL* 3.5 7.1 + - - +
256D PHE* 3.3 17.0 + - - +
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Residues in contact with ARG 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D ASN* 4.0 13.3 - - - +
208D SER* 3.8 20.6 - - - -
214D TRP* 3.5 64.0 - - + +
218D PHE* 3.4 21.3 - - + -
241D ASN 4.5 7.4 + - - -
242D ALA* 4.2 18.4 - - - -
243D THR 3.5 20.4 + - - -
244D ALA* 3.9 11.8 - - - +
249D ASP* 3.3 32.6 + - - +
250D MET 3.8 5.8 - - - +
251D MET 3.2 0.2 - - - -
252D LYS* 1.3 75.4 - - - +
254D ALA* 1.3 65.8 + - - +
256D PHE* 3.3 1.7 + - - +
257D ALA* 3.1 17.7 + - - +
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Residues in contact with ALA 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D ALA* 4.6 7.7 - - + +
250D MET 3.2 12.7 + - - +
251D MET* 3.2 10.3 + - - +
253D ARG* 1.3 76.3 - - - +
255D VAL* 1.3 62.0 - - - +
257D ALA* 3.2 9.0 + - - +
258D ARG* 3.0 21.5 + - - +
265D VAL* 5.0 6.1 - - + -
280D LEU* 4.0 22.9 - - + -
283D TYR* 3.8 23.1 - - + -
289D LEU* 4.0 8.1 - - + +
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Residues in contact with VAL 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D MET* 2.9 29.3 + - + +
252D LYS* 3.6 7.6 - - - +
254D ALA* 1.3 77.5 - - - +
256D PHE* 1.3 58.9 + - - +
258D ARG* 3.1 5.6 - - + +
259D GLU* 2.9 28.3 + - + +
283D TYR* 3.6 28.7 - - + +
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Residues in contact with PHE 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C ARG* 5.1 0.4 - - - -
214D TRP* 3.8 30.7 - + + -
215D ARG* 3.3 57.0 - - + -
218D PHE* 3.8 18.8 - + + -
219D LEU* 4.3 8.1 - - + -
252D LYS 3.3 7.8 + - - +
253D ARG 3.3 7.2 + - - +
254D ALA 3.3 0.2 - - - -
255D VAL* 1.3 76.5 - - - +
257D ALA* 1.3 66.1 + - - +
259D GLU* 3.1 27.3 + - - -
260D LEU* 3.0 56.5 + - + +
58U SER* 4.9 6.5 - - - -
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Residues in contact with ALA 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D PHE* 4.4 5.8 - - + -
240D LEU* 4.3 8.1 - - + -
253D ARG 3.1 12.9 + - - +
254D ALA 3.2 10.1 + - - +
256D PHE* 1.3 76.5 - - - +
258D ARG* 1.3 61.7 + - - +
260D LEU* 3.3 7.6 + - - +
261D GLY 3.2 15.6 + - - -
262D VAL* 3.4 28.2 + - + +
265D VAL* 3.6 29.8 - - + -
289D LEU* 4.8 3.8 - - + -
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Residues in contact with ARG 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ARG* 3.7 21.2 - - - +
256A PHE* 4.8 0.8 - - - -
259A GLU* 3.2 38.8 + - - -
254D ALA 3.0 12.6 + - - +
255D VAL* 3.1 10.5 - - + +
257D ALA* 1.3 77.8 - - - +
259D GLU* 1.3 63.4 + - - +
261D GLY* 3.0 14.9 + - - -
283D TYR* 3.6 17.9 - - - +
286D ASP 5.4 0.4 + - - -
287D ASN* 3.2 33.4 + - + +
289D LEU* 4.5 6.4 - - + +
57V ASN 5.3 0.2 - - - +
58V SER* 3.9 14.0 - - - +
59V PRO* 3.9 22.2 - - + +
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Residues in contact with GLU 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C ARG* 3.2 40.1 + - - -
255D VAL* 2.9 16.1 + - + +
256D PHE* 3.1 24.3 + - + +
258D ARG* 1.3 79.8 - - - +
260D LEU* 1.3 58.6 + - - +
261D GLY* 3.3 1.2 + - - -
56U HIS* 3.0 37.2 + - + +
58U SER* 4.1 1.2 - - - -
57V ASN* 5.5 3.8 + - - +
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Residues in contact with LEU 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D PHE* 3.7 29.6 - - + +
219D LEU* 5.2 2.7 - - + -
222D ALA* 4.1 16.2 - - + -
226D TYR* 2.8 24.8 + - + -
240D LEU* 4.9 5.4 - - + -
256D PHE* 3.0 53.0 + - + +
257D ALA* 3.7 9.0 - - - +
258D ARG 3.2 0.4 - - - -
259D GLU* 1.3 75.0 - - - +
261D GLY* 1.3 58.3 + - - +
262D VAL* 3.4 9.8 + - + -
55U HIS 5.0 1.7 - - - +
56U HIS* 3.8 40.4 - - + +
58U SER* 5.0 0.7 - - - +
61U TYR* 5.1 6.7 - - + -
53V ARG* 4.7 0.3 + - - -
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Residues in contact with GLY 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D TYR* 3.3 5.7 + - - -
257D ALA 3.2 1.6 + - - -
258D ARG 3.0 16.5 + - - -
259D GLU 3.1 1.4 - - - -
260D LEU* 1.3 78.6 - - - +
262D VAL* 1.3 65.2 + - - +
263D PRO* 3.9 1.2 - - - +
53V ARG* 2.9 25.5 + - - -
57V ASN 3.4 22.9 - - - -
59V PRO* 3.9 9.0 - - - +
62V TYR* 4.9 0.3 + - - -
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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