Contacts of the helix formed by residues 286 - 305 (chain A) in PDB entry 1NRX
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 286 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ARG* 3.6 31.9 - - + +
187A GLU* 3.7 23.6 - - - +
190A ASN* 3.2 33.4 - - + +
278A GLU* 4.2 2.7 - - - -
283A PRO 4.8 7.4 - - - +
285A ILE* 1.3 75.6 - - - +
287A HIS* 1.3 63.9 + - - +
289A GLU* 3.1 33.2 + - - +
290A CYS* 3.0 29.6 + - - -
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Residues in contact with HIS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 4.4 14.1 - - + -
190A ASN* 3.7 6.6 + - - +
194A GLU* 4.4 1.6 - - - -
271A HIS* 3.6 7.1 + - - -
274A GLY 6.3 0.2 - - - -
275A HIS* 3.5 29.6 - + - -
278A GLU* 2.5 34.9 + - - +
286A LEU* 1.3 71.9 - - - +
288A GLY* 1.3 62.5 + - - +
289A GLU 2.9 1.3 - - - -
290A CYS* 2.8 21.7 + - - +
291A VAL* 2.8 27.0 + - + +
400A NAD 5.4 10.2 - + - +
600A ZN 2.8 33.8 - - - -
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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
----------------------------------------------------------
142A LEU* 5.3 2.4 - - - +
190A ASN* 2.7 35.9 + - - -
193A ALA* 3.4 16.7 - - - +
194A GLU* 5.4 1.6 - - - -
287A HIS* 1.3 80.2 - - - +
289A GLU* 1.3 51.4 + - - -
291A VAL* 3.7 5.8 - - - -
292A ALA* 2.7 35.5 + - - +
325A LEU* 4.1 2.6 - - - +
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Residues in contact with GLU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ARG* 3.0 42.5 + - - +
189A ILE* 5.6 3.5 - - + +
190A ASN* 3.4 6.2 + - - +
285A ILE* 3.5 19.3 - - + +
286A LEU* 3.1 29.2 + - - +
287A HIS 2.9 0.8 + - - -
288A GLY* 1.3 79.2 - - - +
290A CYS* 1.3 63.3 + - - +
292A ALA* 3.4 9.2 + - - +
293A ILE* 3.4 19.7 + - - +
325A LEU* 4.7 5.4 - - + +
326A PRO* 3.8 23.8 - - + +
333A ARG* 2.9 32.6 + - - +
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Residues in contact with CYS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A GLY* 3.5 24.1 - - - +
277A ILE* 3.8 20.4 - - + +
278A GLU* 3.6 30.5 - - + +
281A LEU* 4.4 2.9 - - - -
285A ILE* 3.8 20.4 - - - -
286A LEU 3.0 20.6 - - - -
287A HIS* 2.8 12.1 + - - +
289A GLU* 1.3 71.8 - - - +
291A VAL* 1.3 53.9 + - + +
293A ILE* 3.1 9.7 + - - +
294A GLY* 2.7 32.6 + - - -
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Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ALA* 4.6 1.3 - - + -
194A GLU* 3.9 6.3 - - - +
197A LYS* 5.3 1.1 - - + -
269A TRP 4.4 0.7 - - - +
270A GLY 4.3 2.0 - - - -
271A HIS* 3.8 34.8 - - + +
274A GLY* 4.2 13.2 - - - -
287A HIS* 2.8 54.4 + - + +
288A GLY* 3.7 7.6 - - - +
290A CYS* 1.3 70.5 - - + +
292A ALA* 1.3 56.5 + - - +
294A GLY 3.5 1.3 - - - +
295A MET* 2.6 62.0 + - + +
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Residues in contact with ALA 292 (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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288A GLY 2.7 22.1 + - - +
289A GLU 3.4 6.1 - - - +
290A CYS 3.2 0.2 - - - -
291A VAL* 1.3 74.1 - - - +
293A ILE* 1.3 61.6 + - - +
295A MET* 3.1 13.4 + - - +
296A VAL* 3.1 17.3 + - - +
320A LEU* 3.2 17.5 - - + +
325A LEU* 3.8 28.7 - - + -
326A PRO* 3.4 18.8 - - + +
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Residues in contact with ILE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ILE* 3.7 21.8 - - + -
281A LEU* 5.2 2.7 - - + -
285A ILE* 6.0 0.7 - - + -
289A GLU 3.5 15.9 - - - +
290A CYS* 3.1 10.0 + - - +
292A ALA* 1.3 71.5 - - - +
294A GLY* 1.3 66.9 + - - +
296A VAL* 3.2 8.7 + - - +
297A LYS* 2.9 36.5 + - + +
326A PRO* 3.8 27.8 - - + +
327A THR 4.5 1.3 - - - -
328A SER* 3.6 36.3 - - - +
329A LEU* 4.2 17.3 - - + +
334A ILE* 4.7 11.4 - - + -
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Residues in contact with GLY 294 (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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270A GLY 3.4 22.4 - - - -
273A ILE* 4.1 11.9 - - - -
274A GLY* 3.8 10.5 - - - -
277A ILE* 4.3 0.6 - - - +
290A CYS 2.7 17.6 + - - -
291A VAL 3.1 1.5 + - - -
293A ILE* 1.3 73.9 - - - +
295A MET* 1.3 55.8 + - - +
297A LYS* 3.6 1.1 - - - +
298A GLU* 2.8 35.2 + - - +
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Residues in contact with MET 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ALA* 3.4 29.8 - - + +
196A ILE* 4.9 1.1 - - - -
197A LYS* 4.0 16.2 - - + -
269A TRP* 3.5 40.9 - - + +
270A GLY* 3.6 18.8 - - - -
291A VAL* 2.6 34.3 + - + +
292A ALA* 3.2 31.6 - - - +
294A GLY* 1.3 70.3 - - - +
296A VAL* 1.3 55.1 + - - +
298A GLU* 3.0 2.6 + - - +
299A ALA* 2.6 39.0 + - - +
316A ILE* 4.9 1.1 - - + -
320A LEU* 4.0 20.0 - - + -
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ALA 3.1 4.9 + - - +
293A ILE 3.4 6.5 - - - +
295A MET* 1.3 76.1 - - - +
297A LYS* 1.3 65.7 + - - +
299A ALA* 2.9 9.2 + - - +
300A GLU* 2.7 38.6 + - + +
313A VAL* 5.3 3.0 - - + +
316A ILE* 5.0 3.6 - - + +
317A VAL* 4.1 23.3 - - + -
320A LEU* 3.6 17.0 - - + +
327A THR* 3.1 48.7 - - + +
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Residues in contact with LYS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ILE* 3.8 24.7 - - + -
277A ILE* 5.5 1.8 - - + -
293A ILE* 2.9 34.2 + - + +
294A GLY 3.6 3.6 - - - +
296A VAL* 1.3 88.9 - - - +
298A GLU* 1.3 57.5 + - - +
300A GLU* 3.0 30.5 + - - -
301A LEU* 2.9 24.8 + - - +
327A THR 4.9 4.0 - - - -
328A SER* 5.8 3.1 - - - +
329A LEU* 5.6 7.4 - - + +
390A VAL* 3.0 48.2 + - + +
391A LEU* 5.2 4.9 - - + +
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Residues in contact with GLU 298 (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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268A ASN 4.1 1.6 - - - +
269A TRP* 3.5 21.4 + - - +
270A GLY* 2.4 34.8 + - - -
272A SER* 2.7 38.1 + - - -
273A ILE* 2.7 27.8 + - + -
294A GLY 2.8 19.7 + - - +
295A MET 3.7 3.1 - - - +
297A LYS* 1.3 73.3 - - - +
299A ALA* 1.3 60.0 + - - +
301A LEU* 3.3 10.4 - - - +
302A ALA* 3.3 19.8 + - - +
365A ILE* 3.7 21.1 - - + +
366A VAL 4.4 0.3 + - - +
367A LEU* 4.4 5.2 - - - +
368A LEU 5.7 0.2 + - - -
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A TRP* 4.1 7.4 - - + +
295A MET 2.6 17.0 + - - +
296A VAL* 3.1 14.1 - - - +
298A GLU* 1.3 71.6 - - - +
300A GLU* 1.3 66.1 + - - +
302A ALA* 3.2 11.5 + - - -
303A ARG* 3.4 4.2 + - - +
308A LEU* 3.3 28.7 - - + +
313A VAL* 4.6 11.2 - - + +
316A ILE* 4.0 27.1 - - + -
368A LEU* 5.7 0.7 - - - -
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Residues in contact with GLU 300 (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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296A VAL* 2.7 18.8 + - + +
297A LYS* 3.0 39.6 + - - +
299A ALA* 1.3 72.6 - - - +
301A LEU* 1.3 56.9 + - - +
303A ARG* 3.4 21.6 + - - +
304A HIS* 3.0 27.6 + - + +
313A VAL* 4.6 18.6 - - + +
389A VAL 5.0 1.4 - - - +
390A VAL* 4.2 18.8 - - + +
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Residues in contact with LEU 301 (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* 5.1 3.6 - - + -
297A LYS 2.9 9.0 + - - +
298A GLU* 3.3 12.1 - - - +
300A GLU* 1.3 75.5 - - - +
302A ALA* 1.3 64.7 + - - +
304A HIS* 3.2 4.1 + - + +
305A LEU* 3.0 49.8 + - + +
365A ILE* 3.3 43.7 - - + -
367A LEU* 4.3 8.7 - - + -
382A VAL* 4.1 14.6 - - + -
386A ASP 4.1 13.5 - - - +
387A ILE* 4.3 9.0 - - + -
390A VAL* 3.6 28.0 - - + +
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Residues in contact with ALA 302 (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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298A GLU 3.3 8.0 + - - +
299A ALA* 3.2 7.7 + - - +
301A LEU* 1.3 79.2 - - - +
303A ARG* 1.3 63.7 + - - +
305A LEU* 3.1 10.9 + - - +
307A ILE* 3.0 27.9 + - + +
308A LEU* 3.4 24.7 - - + +
367A LEU* 4.2 13.9 - - + +
368A LEU 3.6 25.4 - - - +
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Residues in contact with ARG 303 (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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299A ALA 3.4 2.2 + - - +
300A GLU* 3.4 30.4 + - - +
301A LEU 3.3 0.2 - - - -
302A ALA* 1.3 78.3 - - - +
304A HIS* 1.3 69.2 + - - +
306A GLY* 2.7 26.0 + - - -
308A LEU* 3.1 28.1 - - - +
310A GLY* 3.4 29.8 - - - +
313A VAL* 3.9 21.9 - - + +
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Residues in contact with HIS 304 (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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300A GLU* 3.0 14.3 + - + +
301A LEU* 3.4 13.0 - - + +
302A ALA 3.2 0.4 - - - -
303A ARG* 1.3 92.3 + - - +
305A LEU* 1.3 79.9 + - + +
306A GLY 3.0 2.8 + - - -
386A ASP* 2.8 25.8 + - + -
389A VAL* 3.5 37.8 - - + +
390A VAL* 5.3 0.7 - - + -
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Residues in contact with LEU 305 (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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301A LEU* 3.0 37.9 - - + +
302A ALA 3.1 8.3 + - - +
304A HIS* 1.3 95.2 - - + +
306A GLY* 1.3 58.3 + - - +
307A ILE* 3.2 16.1 + - + +
367A LEU* 3.7 29.4 - - + -
382A VAL* 4.0 18.4 - - + -
386A ASP* 4.2 12.6 - - + +
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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