Contacts of the helix formed by residues 273 - 288 (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 GLY 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B HIS* 4.2 0.9 - - - -
269B TYR 2.9 17.8 + - - +
270B LEU* 4.1 6.7 - - - -
271B THR 3.5 1.4 - - - -
272B GLY* 1.3 79.5 - - - +
274B PHE* 1.3 60.7 + - - -
275B THR 3.3 2.5 - - - -
276B ALA 3.4 3.4 + - - -
277B ASN* 2.9 28.4 + - - +
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Residues in contact with PHE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 3.8 24.0 - - + -
114B THR* 3.5 23.1 - - - +
117B PHE* 3.6 35.4 - + - -
269B TYR* 3.5 40.8 + + - -
270B LEU* 4.0 18.2 - - + -
273B GLY* 1.3 69.4 - - - -
275B THR* 1.3 65.1 + - - +
277B ASN* 3.7 3.7 - - + +
278B THR* 2.9 32.1 + - - +
314B LEU* 4.8 4.7 - - + -
317B ALA* 4.0 14.8 - - + -
321B SER* 4.5 11.0 - - - -
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Residues in contact with THR 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR* 3.2 23.9 + - - +
247B CYS* 5.6 7.9 - - - -
273B GLY* 3.3 1.0 - - - -
274B PHE* 1.3 80.7 - - - +
276B ALA* 1.3 64.2 + - - +
278B THR* 3.4 6.0 + - - -
279B THR* 3.3 23.0 + - - +
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B THR 6.3 0.4 - - - -
247B CYS* 4.7 15.7 - - - -
250B MET* 3.4 34.6 - - + +
267B HIS* 4.3 4.7 - - + +
272B GLY* 4.2 13.5 - - - +
273B GLY 3.4 7.8 + - - +
274B PHE 3.3 0.2 - - - -
275B THR* 1.3 77.7 - - - +
277B ASN* 1.3 65.5 + - - +
279B THR* 3.3 4.4 + - - -
280B LEU* 3.1 17.8 + - - +
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Residues in contact with ASN 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B HIS* 3.0 30.9 + - + +
269B TYR* 3.5 15.6 - - + +
273B GLY 2.9 16.8 + - - +
274B PHE* 3.2 8.2 + - + +
276B ALA* 1.3 78.4 - - - +
278B THR* 1.3 56.3 + - - +
280B LEU* 3.2 3.9 + - - +
281B SER* 2.8 27.2 + - - -
291B LEU* 4.7 2.6 - - - +
293B ILE* 3.3 19.2 - - - +
318B LEU* 3.9 9.1 - - - +
321B SER* 3.0 25.8 + - - +
322B GLY 3.3 20.0 + - - -
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Residues in contact with THR 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLY 4.6 15.7 + - - +
112B SER* 6.2 0.2 - - - -
113B VAL* 5.6 4.9 + - - +
148B PHE* 6.3 0.9 - - + -
274B PHE* 2.9 18.6 + - - +
275B THR* 3.8 5.8 - - - -
277B ASN* 1.3 77.1 - - - +
279B THR* 1.3 62.5 + - - +
281B SER* 3.3 3.4 + - - -
282B HIS* 3.1 52.0 + - + +
321B SER* 2.9 27.3 + - - +
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Residues in contact with THR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B CYS* 5.5 8.1 - - + -
250B MET* 4.0 8.7 - - + -
251B MET* 4.0 25.8 - - + -
275B THR* 3.3 14.7 + - - +
276B ALA* 3.5 10.8 - - - -
277B ASN 3.2 0.2 - - - -
278B THR* 1.3 80.5 - - - +
280B LEU* 1.3 62.6 + - - +
282B HIS* 3.3 8.1 + - - +
283B TYR* 3.1 19.9 + - - +
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ALA* 4.3 13.7 - - + -
250B MET* 4.1 15.9 - - + -
251B MET* 5.1 3.8 - - - -
254B ALA* 3.9 27.8 - - + -
265B VAL* 5.1 2.7 - - + -
266B MET 4.7 0.4 - - - +
267B HIS* 3.6 39.7 - - + -
276B ALA 3.1 12.6 + - - +
277B ASN* 3.6 8.1 - - - +
279B THR* 1.3 75.7 - - - +
281B SER* 1.3 61.0 + - - +
283B TYR* 3.1 9.6 + - + +
284B CYS* 2.8 51.2 + - - -
291B LEU* 3.9 13.0 - - + -
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Residues in contact with SER 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLN* 3.2 23.5 + - - -
152B PRO* 3.6 7.7 - - - +
277B ASN 2.8 16.5 + - - -
278B THR 3.5 5.2 - - - -
279B THR 3.3 0.2 - - - -
280B LEU* 1.3 77.8 - - - +
282B HIS* 1.3 62.4 + - - +
284B CYS 3.4 0.5 + - - -
285B ARG 3.2 17.2 + - - -
291B LEU* 3.9 12.1 - - - +
321B SER 3.1 25.6 + - - -
322B GLY* 3.2 22.0 - - - -
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Residues in contact with HIS 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLN* 3.2 44.4 + - + +
278B THR* 3.1 35.8 + - + +
279B THR* 3.7 9.4 - - - +
281B SER* 1.3 74.4 - - - +
283B TYR* 1.3 67.0 + - - +
285B ARG* 3.3 3.8 + - - +
286B ASP* 3.1 31.1 + - - +
321B SER 4.8 4.9 - - - -
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Residues in contact with TYR 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B MET* 3.4 29.8 - - + -
254B ALA* 3.8 27.4 - - + -
255B VAL* 3.6 22.6 - - + +
258B ARG* 3.6 24.6 - - - +
279B THR 3.1 13.4 + - - +
280B LEU* 3.1 14.8 + - + +
282B HIS* 1.3 77.9 - - - +
284B CYS* 1.3 65.9 + - - +
286B ASP* 3.2 4.4 + - - -
287B ASN* 3.0 56.6 + - - +
289B LEU* 4.1 19.7 - - + -
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Residues in contact with CYS 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B PRO* 4.1 11.2 - - + -
153B HIS* 3.6 1.4 - - - -
265B VAL* 3.9 27.1 - - - -
280B LEU* 2.8 32.3 + - - +
281B SER 3.7 5.2 - - - +
283B TYR* 1.3 79.8 - - - +
285B ARG* 1.3 57.7 + - - +
287B ASN* 5.0 0.2 - - - -
288B GLY* 3.0 25.3 + - - -
289B LEU* 3.0 44.5 + - - +
291B LEU* 4.1 12.8 - - + -
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Residues in contact with ARG 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLN* 3.3 53.4 + - - +
151B PRO 3.0 22.8 + - - -
152B PRO* 2.7 29.9 + - + +
153B HIS* 4.6 5.4 + - - -
281B SER 3.2 9.2 + - - +
282B HIS 3.5 4.9 - - - +
283B TYR 3.2 0.2 - - - -
284B CYS* 1.3 78.6 - - - +
286B ASP* 1.3 68.2 + - - +
287B ASN 3.4 0.7 + - - -
288B GLY* 3.8 2.6 + - - -
372B PRO* 5.1 7.3 - - - +
213C ARG* 3.8 48.5 - - - +
215C ARG* 3.7 18.2 - - - +
216C ASP* 6.0 0.9 - - - -
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Residues in contact with ASP 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ARG* 5.3 0.5 + - - -
282B HIS* 3.1 23.4 + - - +
283B TYR* 3.8 5.5 - - + +
285B ARG* 1.3 83.0 - - - +
287B ASN* 1.3 70.0 + - - +
214C TRP* 4.8 14.8 + - - -
215C ARG* 3.0 20.0 + - - +
252C LYS* 3.7 32.8 + - - -
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Residues in contact with ASN 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ARG* 3.1 37.1 + - + +
283B TYR* 3.0 63.5 + - + +
284B CYS 4.6 0.4 - - - +
286B ASP* 1.3 89.4 + - - +
288B GLY* 1.3 63.9 + - - +
289B LEU* 3.4 5.7 + - + +
215C ARG* 3.5 16.8 + - - +
59T PRO* 3.8 19.1 - - - +
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Residues in contact with GLY 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B HIS* 3.8 17.8 + - - -
161B LYS* 4.7 8.3 + - - -
263B PRO 4.5 2.3 - - - +
284B CYS 3.0 6.5 + - - -
285B ARG 3.8 3.5 + - - -
286B ASP 3.7 0.8 - - - -
287B ASN* 1.3 78.5 - - - +
289B LEU* 1.3 60.0 + - - +
290B LEU* 4.0 2.8 + - - +
215C ARG* 3.5 19.5 - - - +
59T PRO* 3.6 22.5 - - - +
60T GLY* 4.3 3.6 + - - -
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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
------------------------------------------------------------
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