Contacts of the helix formed by residues 273 - 288 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A HIS* 4.2 0.9 - - - -
269A TYR 2.9 19.5 + - - +
270A LEU 3.6 7.2 + - - -
271A THR 3.4 1.6 - - - -
272A GLY* 1.3 80.0 - - - +
274A PHE* 1.3 60.4 + - - -
275A THR 3.4 3.1 - - - -
276A ALA 3.5 2.6 + - - -
277A ASN* 2.9 25.6 + - - +
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Residues in contact with PHE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A VAL* 3.8 24.5 - - + -
114A THR* 3.5 23.3 - - - +
117A PHE* 3.4 36.1 - + - -
269A TYR* 3.6 39.7 + + - -
270A LEU* 4.1 18.2 - - + -
273A GLY* 1.3 69.7 - - - -
275A THR* 1.3 57.8 + - - +
277A ASN* 3.7 4.1 - - + +
278A THR* 2.7 39.1 + - - +
314A LEU* 4.8 4.0 - - + -
317A ALA* 4.0 14.1 - - + -
321A SER* 4.1 11.8 + - - -
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Residues in contact with THR 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 3.2 23.5 + - - +
247A CYS* 5.6 7.9 - - - -
273A GLY 3.4 0.6 - - - -
274A PHE* 1.3 79.3 - - - +
276A ALA* 1.3 64.4 + - - +
278A THR* 3.5 5.0 + - - -
279A THR* 3.3 24.6 + - - +
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Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A THR 6.4 0.2 - - - -
247A CYS* 4.9 16.1 - - - -
250A MET* 3.4 33.1 - - + +
267A HIS* 4.4 5.6 - - + +
272A GLY* 4.1 14.6 - - - +
273A GLY* 3.5 7.9 + - - +
274A PHE 3.3 0.4 - - - -
275A THR* 1.3 79.5 - - - +
277A ASN* 1.3 63.4 + - - +
279A THR* 3.2 5.0 + - - -
280A LEU* 3.1 17.3 + - - +
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Residues in contact with ASN 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A HIS* 2.9 31.0 + - + +
269A TYR* 3.5 15.9 - - + +
273A GLY 2.9 19.2 + - - +
274A PHE* 3.7 7.6 - - + +
275A THR 3.3 0.2 - - - -
276A ALA* 1.3 77.3 - - - +
278A THR* 1.3 56.7 + - - +
280A LEU* 3.2 3.5 + - - +
281A SER* 2.8 25.8 + - - -
291A LEU* 4.7 2.6 - - - +
293A ILE* 3.3 18.9 - - - +
318A LEU* 3.9 10.7 - - - +
321A SER* 3.0 22.5 + - - +
322A GLY 3.2 22.4 + - - -
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Residues in contact with THR 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLY 4.6 15.7 + - - +
113A VAL* 5.6 4.7 + - - +
148A PHE* 6.3 1.3 - - + -
274A PHE* 2.7 23.9 + - - +
275A THR* 3.9 5.3 - - - -
277A ASN* 1.3 73.1 - - - +
279A THR* 1.3 65.8 + - - +
281A SER* 3.3 4.7 + - - -
282A HIS* 3.0 49.7 + - + +
321A SER* 3.0 27.7 + - - +
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Residues in contact with THR 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A CYS* 5.7 8.2 - - + -
250A MET* 3.9 17.3 - - + -
251A MET* 4.1 18.2 - - + -
275A THR* 3.3 13.9 + - - +
276A ALA* 3.2 10.8 + - - -
278A THR* 1.3 80.3 - - - +
280A LEU* 1.3 62.4 + - - +
282A HIS* 3.4 7.0 + - - +
283A TYR* 3.1 19.8 + - - +
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ALA* 4.4 12.1 - - + -
250A MET* 4.1 19.1 - - + -
251A MET* 4.9 2.7 - - - -
254A ALA* 3.9 27.8 - - + -
265A VAL* 5.1 3.4 - - + -
266A MET 4.6 0.7 - - - +
267A HIS* 3.6 39.9 - - + -
276A ALA 3.1 13.3 + - - +
277A ASN* 3.7 7.9 - - - +
279A THR* 1.3 75.1 - - - +
281A SER* 1.3 61.6 + - - +
283A TYR* 3.2 9.0 + - + +
284A CYS* 2.9 44.0 + - - -
291A LEU* 3.9 14.6 - - + -
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Residues in contact with SER 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A GLN* 3.2 24.9 + - - -
150A GLY 3.6 0.3 + - - -
152A PRO* 3.5 8.1 - - - +
277A ASN 2.8 17.7 + - - -
278A THR 3.3 4.5 + - - -
280A LEU* 1.3 77.7 - - - +
282A HIS* 1.3 61.9 + - - +
284A CYS 3.4 0.3 + - - -
285A ARG 3.2 17.2 + - - -
291A LEU* 4.0 12.5 - - - +
321A SER 3.0 26.5 + - - -
322A GLY* 3.4 19.7 - - - -
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Residues in contact with HIS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLY 6.1 0.2 - - - -
149A GLN* 3.3 41.8 + - + +
278A THR* 3.0 42.6 + - + +
279A THR* 3.8 6.7 - - - +
281A SER* 1.3 77.0 - - - +
283A TYR* 1.3 64.0 + - - +
285A ARG* 3.3 3.6 + - - +
286A ASP* 3.1 32.8 + - - +
321A SER 5.1 1.0 + - - -
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Residues in contact with TYR 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A MET* 3.3 29.8 - - + -
254A ALA* 3.8 29.2 - - + -
255A VAL* 3.6 22.8 - - + +
258A ARG* 3.5 25.5 - - - +
279A THR* 3.1 14.3 + - + +
280A LEU* 3.6 12.8 - - + +
282A HIS* 1.3 75.8 - - - +
284A CYS* 1.3 65.9 + - - +
286A ASP* 3.2 4.8 + - - +
287A ASN* 2.9 58.3 + - - +
289A LEU* 3.9 19.3 - - + -
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Residues in contact with CYS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A PRO* 4.1 11.7 - - + -
153A HIS* 3.8 1.2 - - - -
265A VAL* 3.9 27.1 - - - -
280A LEU* 2.9 32.9 + - - +
281A SER 3.7 4.9 - - - +
283A TYR* 1.3 79.7 - - - +
285A ARG* 1.3 55.5 + - - +
288A GLY* 3.0 26.9 + - - -
289A LEU* 3.0 43.8 + - - +
291A LEU* 4.0 13.0 - - + -
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Residues in contact with ARG 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A GLN* 3.3 58.7 + - - +
151A PRO 3.1 22.8 + - - -
152A PRO* 2.7 29.0 + - + +
153A HIS* 4.7 5.5 + - - -
281A SER 3.2 5.3 + - - -
282A HIS 3.6 4.0 - - - +
283A TYR 3.2 0.2 - - - -
284A CYS* 1.3 76.8 - - - +
286A ASP* 1.3 68.3 + - - +
287A ASN 3.4 0.9 + - - -
288A GLY* 3.9 2.1 + - - -
372A PRO* 5.2 6.3 - - - +
213B ARG* 3.8 46.3 - - - +
215B ARG* 3.6 19.4 - - - +
216B ASP* 5.8 2.0 + - - -
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Residues in contact with ASP 286 (chain A).
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* 5.5 0.2 + - - -
282A HIS* 3.1 24.8 + - - +
283A TYR* 3.2 6.3 + - + +
285A ARG* 1.3 83.6 - - - +
287A ASN* 1.3 69.6 + - - +
214B TRP* 5.0 11.9 + - - -
215B ARG* 2.9 19.5 + - - +
252B LYS* 3.5 36.0 + - - +
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Residues in contact with ASN 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ARG* 3.2 34.9 + - + +
283A TYR* 2.9 66.0 + - + +
284A CYS 4.6 0.2 - - - +
286A ASP* 1.3 89.9 - - - +
288A GLY* 1.3 62.9 + - - +
289A LEU* 3.3 6.4 + - + +
215B ARG* 3.5 16.8 + - - +
59S PRO* 3.7 19.1 - - - +
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Residues in contact with GLY 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A HIS* 3.8 16.9 + - - -
161A LYS* 4.7 8.7 + - - -
263A PRO 4.5 2.3 - - - +
284A CYS 3.0 6.9 + - - -
285A ARG 3.9 3.1 + - - -
286A ASP 3.7 0.4 - - - -
287A ASN* 1.3 77.6 - - - +
289A LEU* 1.3 59.0 + - - +
290A LEU* 4.0 2.9 + - - +
215B ARG* 3.6 20.9 - - - +
219B LEU* 5.8 0.2 - - - -
59S PRO* 3.6 24.0 - - - +
60S GLY* 4.2 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
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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