Contacts of the helix formed by residues 267 - 288 (chain A) in PDB entry 1NYR
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 LEU 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLU* 3.4 43.7 - - + +
252A LEU 3.1 6.8 + - - +
253A PHE* 3.9 11.7 - - - +
254A THR* 3.5 28.0 - - - +
265A LEU* 3.5 1.7 + - + +
266A TRP* 1.3 73.8 - - - +
268A PRO* 1.3 80.7 - - + +
269A ASN 3.3 0.2 - - - -
270A GLY 2.9 2.8 + - - -
271A ALA* 2.8 18.4 + - - +
293B VAL* 4.0 0.2 - - - -
342B ILE* 3.7 25.4 - - + +
345B ASN* 3.6 31.9 - - + +
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Residues in contact with PRO 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 1.3 90.9 - - + +
269A ASN* 1.3 65.9 + - - +
271A ALA* 3.1 3.3 + - - +
272A THR* 3.0 28.0 + - - -
291B ASP* 3.6 38.4 - - + +
292B HIS 3.5 13.1 - - - +
293B VAL* 3.7 14.8 - - + -
342B ILE* 4.8 5.4 - - + -
357B ILE* 4.8 7.0 - - + -
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Residues in contact with ASN 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU* 2.8 26.3 + - - +
251A GLU* 3.1 25.9 + - - +
252A LEU* 4.4 3.3 - - + +
268A PRO* 1.3 82.5 - - - +
270A GLY* 1.3 61.3 + - - +
272A THR* 3.6 6.4 + - - -
273A ILE* 3.6 6.9 + - - +
545A PRO* 3.3 46.5 - - + +
595A GLN* 6.3 1.4 - - - +
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Residues in contact with GLY 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU* 3.3 33.5 + - - +
266A TRP* 3.5 21.8 - - - -
267A LEU 2.9 4.2 + - - -
269A ASN* 1.3 77.3 - - - +
271A ALA* 1.3 64.6 + - - +
272A THR 3.1 1.1 + - - -
273A ILE* 3.3 8.1 + - - +
274A ARG 3.2 15.8 + - - -
528A VAL* 6.0 1.1 - - - -
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Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A TRP* 4.1 4.3 - - - +
267A LEU 2.8 12.6 + - - +
268A PRO 3.5 0.7 - - - +
270A GLY* 1.3 76.0 - - - +
272A THR* 1.3 58.3 + - - +
274A ARG* 3.5 2.0 + - - -
275A ARG* 2.9 31.9 + - - +
292B HIS* 3.2 28.7 - - + +
293B VAL* 3.7 7.0 - - - -
294B TYR* 3.5 35.2 - - + -
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Residues in contact with THR 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A PRO 3.0 15.0 + - - -
269A ASN* 3.9 6.7 - - - -
270A GLY 3.1 0.4 - - - -
271A ALA* 1.3 73.7 - - - +
273A ILE* 1.3 68.9 + - - +
274A ARG 3.0 1.3 - - - -
275A ARG* 3.4 28.4 + - - +
276A GLU* 3.0 24.9 + - + +
543A LEU 4.7 0.7 - - - +
544A ALA 4.4 0.7 - - - +
545A PRO* 4.3 15.4 + - + -
575A ARG* 3.7 40.1 - - - +
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Residues in contact with ILE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU* 4.2 11.9 - - + -
269A ASN 3.6 15.7 - - - +
270A GLY* 3.3 7.4 + - - +
272A THR* 1.3 76.2 - - - +
274A ARG* 1.3 59.0 + - - +
276A GLU* 3.4 5.5 + - - +
277A ILE* 2.9 39.8 + - + +
528A VAL* 4.3 15.5 - - + -
531A LEU* 4.0 25.1 - - + -
539A PHE* 3.5 38.8 - - + -
543A LEU* 3.4 31.8 - - + +
545A PRO* 3.9 8.3 - - + -
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Residues in contact with ARG 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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266A TRP* 3.0 52.9 - - + +
270A GLY 3.2 10.1 + - - +
271A ALA 3.5 7.9 - - - +
272A THR 3.0 0.4 - - - -
273A ILE* 1.3 79.3 - - - +
275A ARG* 1.3 53.8 + - - +
277A ILE* 2.9 5.6 + - - +
278A GLU* 2.7 60.5 + - - +
382A THR* 3.6 25.2 + - - +
524A MET* 3.6 30.9 - - + +
525A GLU* 4.2 5.1 + - - -
528A VAL* 4.9 0.7 - - - -
294B TYR* 3.2 45.8 - - + +
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Residues in contact with ARG 275 (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 ALA* 2.9 21.1 + - - +
272A THR* 3.2 42.2 + - - +
274A ARG* 1.3 71.3 - - - +
276A GLU* 1.3 67.4 + - + +
278A GLU* 3.2 5.4 + - + +
279A ARG* 2.8 63.1 + - + +
575A ARG* 5.4 3.2 - - - +
282B VAL* 4.1 24.0 - - + +
283B ASP* 5.2 1.3 - - - -
286B VAL* 4.2 25.4 - - - +
292B HIS* 3.6 29.3 + - - +
294B TYR* 3.9 17.0 + - - +
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Residues in contact with GLU 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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272A THR* 3.0 17.3 + - + +
273A ILE 3.4 8.5 - - - +
275A ARG* 1.3 86.7 + - + +
277A ILE* 1.3 60.7 + - - +
279A ARG* 4.1 9.6 + - - +
280A TYR* 3.2 23.6 + - - +
542A TRP* 3.0 32.8 - - + +
543A LEU* 3.7 16.8 - - + -
575A ARG* 2.8 28.4 + - - +
639A ILE* 6.0 0.9 - - - +
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Residues in contact with ILE 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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273A ILE* 2.9 26.7 + - + +
274A ARG 2.9 8.2 + - - +
276A GLU* 1.3 74.4 - - - +
278A GLU* 1.3 65.3 + - - +
280A TYR* 3.2 7.3 + - + +
281A ILE* 3.1 21.9 + - + +
413A PHE* 4.2 11.7 - - + -
521A VAL* 4.1 30.5 - - + -
524A MET* 3.3 19.1 - - + -
527A PHE* 3.9 23.1 - - + -
528A VAL* 4.0 23.3 - - + -
531A LEU* 4.4 8.7 - - + -
542A TRP* 4.8 0.9 - - - -
543A LEU* 4.0 13.0 - - + -
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Residues in contact with GLU 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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274A ARG* 2.7 56.4 + - - +
275A ARG* 3.7 5.5 - - - +
277A ILE* 1.3 74.2 - - - +
279A ARG* 1.3 65.6 + - + +
281A ILE* 3.4 6.4 - - - +
282A VAL* 3.0 30.7 + - + +
360A LEU* 4.6 22.2 - - + +
382A THR* 4.8 1.9 - - - +
524A MET* 3.9 18.0 - - + +
294B TYR* 2.8 26.9 + - - -
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Residues in contact with ARG 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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275A ARG* 2.8 43.8 + - + +
276A GLU* 4.1 10.2 + - - +
278A GLU* 1.3 73.2 - - + +
280A TYR* 1.3 58.2 + - - +
283A ASP* 2.9 41.6 + - - +
279B ARG* 3.2 62.9 + - - +
282B VAL* 3.9 18.4 - - - +
283B ASP* 3.0 31.3 + - - -
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Residues in contact with TYR 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 GLU 3.2 17.2 + - - +
277A ILE* 3.3 7.6 - - + +
278A GLU 3.2 0.2 - - - -
279A ARG* 1.3 80.8 - - - +
281A ILE* 1.3 83.1 + - + +
283A ASP* 3.6 5.5 - - - +
284A LYS* 3.0 48.8 + - - +
409A VAL* 3.6 18.3 - - + +
412A ASP* 2.5 39.3 + - + +
413A PHE* 3.6 30.1 - + - -
521A VAL* 5.1 1.1 - - + -
542A TRP* 3.8 14.6 - + + -
642A LYS* 3.7 31.0 - - + +
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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 ILE* 3.1 8.9 + - + +
278A GLU* 3.4 14.6 - - - +
280A TYR* 1.3 97.3 - - + +
282A VAL* 1.3 72.4 + - + +
284A LYS* 3.3 11.8 + - + +
285A GLU* 2.8 38.6 + - - +
360A LEU* 4.7 6.1 - - + -
384A ASN* 3.6 40.2 - - - +
405A MET* 4.5 6.3 - - + -
409A VAL* 4.1 19.3 - - + -
520A VAL* 4.3 8.3 - - + -
521A VAL* 4.2 15.0 - - + -
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Residues in contact with VAL 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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278A GLU* 3.0 16.4 + - + +
279A ARG 4.2 1.3 - - - +
281A ILE* 1.3 80.6 - - + +
283A ASP* 1.3 65.4 + - - +
285A GLU* 3.9 0.7 - - - +
286A VAL* 3.1 27.6 + - + +
292A HIS* 4.0 30.3 - - + -
360A LEU* 2.9 37.5 - - + -
275B ARG* 4.2 19.3 - - + +
279B ARG* 4.0 17.3 - - - +
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Residues in contact with ASP 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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279A ARG* 2.9 26.6 + - - +
280A TYR* 3.6 5.7 - - - +
282A VAL* 1.3 76.9 - - - +
284A LYS* 1.3 64.7 + - - +
286A VAL* 3.5 6.4 + - - +
287A SER* 3.0 23.7 + - - -
279B ARG* 3.1 28.5 + - - -
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Residues in contact with LYS 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 TYR* 3.0 49.3 + - + +
281A ILE* 3.6 9.4 - - + +
283A ASP* 1.3 74.7 - - - +
285A GLU* 1.3 65.0 + - - +
287A SER* 2.7 24.7 + - - +
288A MET* 3.2 27.1 + - + +
405A MET* 4.0 22.9 - - + -
408A ASP* 6.4 0.7 - - - -
409A VAL* 4.1 14.8 - - + +
412A ASP* 4.3 5.9 + - - -
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Residues in contact with GLU 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* 2.8 28.2 + - + +
282A VAL* 3.4 2.9 + - - +
284A LYS* 1.3 72.1 - - - +
286A VAL* 1.3 63.4 + - - +
288A MET* 2.9 13.8 + - - -
289A GLY 3.3 0.3 + - - -
290A TYR* 3.0 41.1 + - + +
292A HIS* 2.6 39.4 + - - +
358A ALA* 3.8 7.6 - - - +
384A ASN* 3.0 25.9 + - - +
385A ASP 4.9 1.0 - - - +
405A MET* 4.0 10.1 - - + -
518A ARG* 2.5 36.7 + - - +
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A VAL* 3.1 23.3 + - + +
283A ASP* 3.8 6.1 - - - +
285A GLU* 1.3 76.6 - - - +
287A SER* 1.3 60.5 + - - +
288A MET 3.4 0.5 + - - -
289A GLY* 3.6 8.7 + - - -
290A TYR 4.1 13.8 + - - +
292A HIS* 4.0 19.3 - - + +
275B ARG* 4.3 27.1 - - - +
575B ARG* 6.1 6.7 - - + -
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Residues in contact with SER 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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283A ASP 3.0 14.2 + - - -
284A LYS* 2.7 21.0 + - - +
285A GLU 3.1 0.2 - - - -
286A VAL* 1.3 78.0 - - - +
288A MET* 1.3 62.1 + - - +
289A GLY 3.4 2.4 + - - -
570B LYS* 6.1 1.1 - - - +
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Residues in contact with MET 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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284A LYS* 3.2 38.1 + - + +
285A GLU 2.9 6.5 + - - +
287A SER* 1.3 83.6 - - - +
289A GLY* 1.3 60.4 + - - +
290A TYR* 3.5 16.9 + - + +
356A ARG* 4.0 12.6 + - - -
401A ARG* 5.0 7.6 - - + +
405A MET* 3.7 41.7 - - + -
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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