Contacts of the helix formed by residues 275 - 287 (chain A) in PDB entry 2IBI
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 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A ARG 3.8 4.9 + - - -
271A ASN* 3.3 9.3 + - - -
272A LEU* 2.9 42.6 + - + +
273A GLY 3.5 14.8 - - - +
274A ASN* 1.3 75.7 - - - +
276A CYS* 1.3 59.6 + - - +
277A PHE* 3.2 12.3 - - + -
278A MET* 2.8 34.0 + - - +
279A ASN* 2.9 19.6 + - - -
340A LYS* 4.0 23.6 - - + -
353A TYR* 6.0 0.2 - - - -
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Residues in contact with CYS 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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271A ASN* 4.5 1.6 + - - +
275A THR* 1.3 77.0 + - - +
277A PHE* 1.3 63.7 + - - +
279A ASN* 3.7 0.4 - - - +
280A SER* 2.8 36.6 + - - -
557A HIS* 3.7 9.6 - - + -
558A TYR* 3.2 35.5 - - - +
575A ASP* 3.3 23.8 + - - +
75B GLY 3.5 1.8 - - - -
76B NEH 1.8 55.4 - - + +
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Residues in contact with PHE 277 (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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274A ASN 3.2 27.8 - - - -
275A THR* 4.2 8.5 - - + -
276A CYS* 1.3 81.1 - - - +
278A MET* 1.3 76.6 + - + +
280A SER* 4.1 0.2 - - - -
281A ILE* 3.4 26.7 + - - +
340A LYS* 6.3 1.6 - - - -
350A PHE* 3.7 18.6 - + + -
354A ASN 3.7 3.1 - - - -
356A GLN* 3.3 54.5 - - + +
357A ASP 4.3 1.1 - - - -
358A ALA* 3.7 9.0 - - + +
361A PHE* 3.7 37.0 - + + -
558A TYR* 3.6 23.3 - - + -
75B GLY 3.5 10.3 - - - +
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Residues in contact with MET 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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272A LEU* 5.0 1.6 - - + -
275A THR* 2.8 26.2 + - - +
277A PHE* 1.3 96.9 - - + +
279A ASN* 1.3 60.9 + - - +
281A ILE* 3.4 4.9 + - - +
282A LEU* 2.9 45.5 + - + +
336A PRO* 4.1 15.3 - - + -
339A PHE* 3.7 28.0 - - + -
340A LYS* 4.1 30.5 - - + -
343A ILE* 4.4 3.1 - - - -
350A PHE* 6.4 0.7 - - - -
361A PHE* 3.2 40.4 - - + -
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Residues in contact with ASN 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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269A LEU* 3.5 45.4 + - + +
270A ARG 3.7 10.3 + - - +
275A THR* 2.9 22.7 + - - +
276A CYS 3.7 2.7 - - - +
278A MET* 1.3 76.8 - - - +
280A SER* 1.3 66.4 + - - +
282A LEU* 3.2 4.3 + - - +
283A GLN* 3.0 30.7 + - + +
336A PRO* 3.8 15.1 - - - +
575A ASP* 2.6 36.6 + - - +
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Residues in contact with SER 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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276A CYS 2.8 21.0 + - - -
277A PHE 4.1 4.0 - - - -
279A ASN* 1.3 73.7 - - - +
281A ILE* 1.3 62.8 + - - +
283A GLN* 3.3 0.6 + - - -
284A CYS* 3.1 27.9 + - - -
547A SER* 3.0 22.2 + - - -
558A TYR* 3.8 14.6 - - - -
559A THR* 2.7 32.6 + - - +
560A ALA* 3.7 11.5 - - - +
573A PHE 5.6 1.3 - - - -
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Residues in contact with ILE 281 (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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277A PHE 3.4 14.1 + - - +
278A MET 3.4 7.5 + - - +
279A ASN 3.3 0.4 - - - -
280A SER* 1.3 73.1 - - - +
282A LEU* 1.3 67.6 + - - +
283A GLN 3.1 0.2 + - - -
284A CYS* 3.2 4.7 + - + +
285A LEU* 2.9 43.0 + - + +
358A ALA* 3.3 33.9 - - + +
361A PHE* 4.0 19.1 - - + -
362A LEU* 4.0 22.9 - - + -
365A LEU* 4.4 1.1 - - + -
547A SER* 4.5 7.6 - - - -
593A LEU* 3.9 22.2 - - + -
595A PHE* 4.4 13.0 - - + -
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Residues in contact with LEU 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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269A LEU* 3.7 20.9 - - + -
278A MET* 2.9 47.7 + - + +
279A ASN* 3.2 9.8 + - - +
281A ILE* 1.3 74.8 - - - +
283A GLN* 1.3 52.9 + - - +
285A LEU* 3.6 4.4 + - - +
286A SER* 2.8 33.0 + - - -
318A PHE* 4.2 19.7 - - + -
321A LEU* 3.8 29.2 - - + -
322A ILE* 4.2 6.5 - - + +
325A ILE* 5.0 3.2 - - + +
336A PRO* 4.2 2.2 - - + -
339A PHE* 3.8 27.4 - - + -
361A PHE* 5.2 1.1 - - + -
365A LEU* 4.5 6.1 - - + -
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Residues in contact with GLN 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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265A GLY 4.6 1.9 - - - +
267A ALA 3.1 24.3 + - - +
268A GLY* 4.1 4.8 - - - -
269A LEU* 3.6 27.2 - - + +
279A ASN* 3.0 22.6 + - + +
280A SER* 3.8 4.5 - - - +
281A ILE 3.1 0.2 - - - -
282A LEU* 1.3 74.8 - - - +
284A CYS* 1.3 61.5 + - - +
285A LEU 3.2 0.2 - - - -
286A SER* 3.4 14.1 + - - -
287A ASN* 2.8 38.2 + - - +
325A ILE* 4.4 5.8 - - - +
560A ALA* 4.2 5.2 - - + -
562A CYS* 3.7 15.4 - - - -
573A PHE* 3.4 39.5 - - + +
575A ASP 4.9 1.8 + - - -
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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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280A SER 3.1 19.0 + - - -
281A ILE* 3.7 6.7 - - - +
283A GLN* 1.3 76.5 - - - +
285A LEU* 1.3 53.3 + - - +
287A ASN* 3.5 3.0 + - - +
288A THR* 2.7 32.3 + - - -
544A TYR* 3.7 6.6 - - - -
545A ALA* 3.8 20.6 - - + -
546A VAL 4.1 0.4 - - - -
547A SER* 4.1 15.7 - - - -
560A ALA* 4.1 14.4 - - - -
562A CYS* 4.2 0.7 - - - -
595A PHE* 3.4 45.3 - - + -
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Residues in contact with LEU 285 (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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281A ILE* 2.9 30.5 + - + +
282A LEU* 3.9 3.6 - - - +
284A CYS* 1.3 74.8 - - + +
286A SER* 1.3 64.9 + - - +
287A ASN 3.1 1.3 - - - -
288A THR* 3.0 25.0 + - - +
291A LEU* 4.0 18.7 - - + +
292A ARG* 4.3 3.6 + - - -
318A PHE* 4.1 17.5 - - + -
322A ILE* 4.4 3.7 - - - +
362A LEU* 4.1 15.0 - - + -
365A LEU* 3.7 30.1 - - + -
366A LEU* 4.2 14.6 - - + -
415A PHE* 3.7 30.5 - - + -
595A PHE* 4.7 4.5 - - + -
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Residues in contact with SER 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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265A GLY 4.8 0.5 + - - -
282A LEU 2.8 23.4 + - - -
283A GLN* 3.5 17.3 + - - -
285A LEU* 1.3 71.3 - - - +
287A ASN* 1.3 61.9 + - - +
288A THR 3.3 0.2 - - - -
292A ARG* 3.4 18.5 - - - +
322A ILE* 3.5 22.6 - - - +
325A ILE* 3.7 15.0 - - - +
326A TRP* 2.9 37.5 + - - +
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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
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265A GLY 4.9 3.2 + - - +
266A LEU* 6.1 1.0 - - - +
283A GLN* 2.8 29.9 + - - +
284A CYS* 3.5 6.3 + - - +
285A LEU 3.1 0.2 - - - -
286A SER* 1.3 83.3 + - - +
288A THR* 1.3 59.0 + - - +
289A ARG* 3.3 6.6 + - - +
326A TRP* 3.6 10.0 - - - -
544A TYR* 3.5 18.0 - - + -
562A CYS* 3.5 31.0 - - + +
563A ARG 4.1 8.7 - - - +
564A SER* 3.8 8.8 + - - -
565A PRO* 3.5 32.2 - - - +
573A PHE* 4.1 15.9 - - - -
597A GLU* 5.6 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