Contacts of the helix formed by residues 372 - 391 (chain A) in PDB entry 6NIY
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 ILE 372 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A PHE* 3.6 40.4 - - + -
214A VAL* 4.9 13.3 - - + +
221A MET* 4.7 10.1 - - + -
370A GLU 3.2 11.5 - - - +
371A ASN* 1.3 76.9 - - - +
373A ARG* 1.3 68.2 + - + +
374A ARG 3.2 0.4 - - - -
375A VAL* 3.4 18.6 + - + +
376A PHE* 3.3 17.8 + - - +
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Residues in contact with ARG 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A VAL* 3.8 25.3 - - - +
215A ASP* 3.4 28.3 + - - -
370A GLU* 3.3 18.1 + - - +
372A ILE* 1.3 81.8 - - + +
374A ARG* 1.3 59.7 + - + +
376A PHE* 3.2 18.0 + - - +
377A ASN* 2.8 48.8 + - - +
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Residues in contact with ARG 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ILE* 5.0 0.7 - - - +
290A PHE* 4.4 3.8 - - + -
362A HIS* 4.2 34.6 + - + +
363A PHE 3.7 24.5 + - - +
365A CYS 3.2 31.7 + - - -
370A GLU* 3.5 18.6 + - - +
371A ASN* 3.1 35.0 + - - +
372A ILE 3.2 0.6 - - - -
373A ARG* 1.3 79.3 - - + +
375A VAL* 1.3 57.3 + - - +
377A ASN* 4.0 7.2 - - - +
378A ASP* 3.2 32.9 + - - +
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Residues in contact with VAL 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.7 30.3 - - + -
212A PHE* 5.8 1.8 - - + -
219A PHE* 5.0 4.2 - - + -
243A ALA* 6.0 0.2 - - + -
245A ILE* 3.7 17.3 - - + -
288A ILE* 4.3 16.4 - - + +
290A PHE* 3.7 24.0 - - + -
371A ASN 3.4 18.2 - - - +
372A ILE* 3.4 20.8 + - + +
373A ARG 3.2 0.6 - - - -
374A ARG* 1.3 75.6 - - - +
376A PHE* 1.3 63.5 + - - +
378A ASP 4.2 0.2 - - - -
379A CYS* 3.2 25.6 + - + +
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Residues in contact with PHE 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A VAL* 3.9 19.1 - - + -
215A ASP* 3.8 31.9 - - + -
217A VAL* 3.8 11.7 - - + -
219A PHE* 3.8 22.9 - + - -
372A ILE 3.3 10.4 + - - +
373A ARG* 3.2 27.0 + - - +
375A VAL* 1.3 78.5 - - - +
377A ASN* 1.3 78.5 + - - +
379A CYS* 3.2 8.5 - - - -
380A ARG* 3.1 40.5 + - + +
253R PHE* 3.8 30.7 - + - -
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Residues in contact with ASN 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ARG* 2.8 43.7 + - - +
374A ARG* 4.5 4.1 - - - +
376A PHE* 1.3 87.3 - - - +
378A ASP* 1.3 67.2 + - - +
380A ARG* 4.2 10.4 - - - +
381A ASP* 3.9 14.7 + - - +
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Residues in contact with ASP 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ILE* 4.1 16.6 - - + +
360A TYR* 3.7 28.6 - - + +
362A HIS* 2.4 37.2 + - - -
374A ARG* 3.2 20.0 + - - +
376A PHE 3.2 0.8 - - - -
377A ASN* 1.3 85.1 - - - +
379A CYS* 1.3 64.8 + - - +
380A ARG 3.3 1.1 - - - -
381A ASP* 3.6 8.8 + - - +
382A ILE* 3.3 25.5 + - - +
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Residues in contact with CYS 379 (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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43A LEU* 5.6 2.2 - - + -
219A PHE* 3.5 35.9 - - + -
242A THR* 4.4 18.2 - - + -
243A ALA* 4.9 6.5 - - + -
288A ILE* 4.8 0.8 - - + +
375A VAL* 3.2 18.5 + - + +
376A PHE* 3.2 16.2 - - - -
378A ASP* 1.3 76.0 - - - +
380A ARG* 1.3 66.4 + - - +
381A ASP 3.2 0.4 - - - -
382A ILE* 3.0 13.2 + - + +
383A ILE* 3.0 39.1 + - - +
253R PHE* 5.2 2.0 - - - -
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Residues in contact with ARG 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A PHE* 3.1 33.9 + - + +
377A ASN* 4.2 11.2 - - - +
378A ASP 3.3 0.2 - - - -
379A CYS* 1.3 85.0 - - - +
381A ASP* 1.3 57.1 + - - +
383A ILE* 3.3 4.1 + - - +
384A GLN* 3.0 41.1 + - - +
249R VAL 3.3 24.4 + - - -
250R VAL 4.1 10.1 + - - -
252R VAL* 3.4 34.4 - - + +
253R PHE* 5.0 14.3 - - + -
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Residues in contact with ASP 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A TYR* 5.5 0.2 - - - -
360A TYR* 2.3 38.4 + - + +
377A ASN 3.9 9.9 + - - +
378A ASP* 3.6 11.2 + - - +
379A CYS 3.2 0.6 - - - -
380A ARG* 1.3 79.8 - - - +
382A ILE* 1.3 57.3 + - - +
384A GLN* 3.9 2.6 - - - +
385A ARG* 3.0 39.1 + - - +
326R LYS* 2.5 44.4 + - - +
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Residues in contact with ILE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A THR* 4.3 21.8 - - + +
243A ALA* 3.8 20.4 - - + -
286A SER* 3.6 29.4 - - - +
288A ILE* 4.7 3.4 - - + -
360A TYR* 3.8 22.7 - - + +
378A ASP 3.3 18.4 + - - +
379A CYS* 3.0 16.6 + - + +
381A ASP* 1.3 77.0 - - - +
383A ILE* 1.3 51.7 + - + +
385A ARG* 3.3 5.8 + - - +
386A MET* 2.7 37.0 + - + +
389A ARG* 5.5 0.9 + - - -
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Residues in contact with ILE 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A HIS* 3.8 21.3 - - + +
242A THR* 4.7 14.8 - - + +
379A CYS* 3.0 21.4 + - - +
380A ARG 4.0 0.2 - - - +
381A ASP 3.3 0.2 - - - -
382A ILE* 1.3 75.7 - - + +
384A GLN* 1.3 65.3 + - - +
386A MET* 3.7 13.6 - - + +
387A HIS* 3.0 57.6 + - + +
252R VAL* 3.9 19.7 - - + +
253R PHE* 3.7 33.4 - - + -
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Residues in contact with GLN 384 (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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380A ARG* 3.0 35.4 + - - +
381A ASP* 3.9 5.6 - - - +
383A ILE* 1.3 76.4 - - - +
385A ARG* 1.3 56.7 + - - +
387A HIS* 3.2 6.8 + - - +
388A LEU* 3.0 35.1 + - + +
248R ILE* 3.2 35.0 + - + +
249R VAL* 4.5 4.0 + - - +
252R VAL* 3.4 22.5 - - + +
322R VAL* 4.0 12.9 - - - +
326R LYS* 3.3 32.8 + - - +
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Residues in contact with ARG 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A TYR* 5.2 17.2 - - - +
360A TYR* 3.9 8.2 + - - -
381A ASP* 3.0 47.1 + - - +
382A ILE* 3.5 5.8 - - - +
384A GLN* 1.3 74.0 - - - +
386A MET* 1.3 62.8 + - - +
388A LEU* 3.9 10.6 - - + +
389A ARG* 3.4 53.6 + - - +
394A LEU* 3.8 24.4 - - + +
326R LYS* 2.6 46.5 + - + +
329R GLU* 4.7 5.3 - - - +
330R THR* 2.8 24.8 + - - +
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Residues in contact with MET 386 (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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382A ILE* 2.7 25.0 + - + +
383A ILE* 3.7 16.6 - - + +
384A GLN 3.2 0.6 - - - -
385A ARG* 1.3 74.4 - - - +
387A HIS* 1.3 89.9 + - + +
389A ARG* 3.9 11.2 + - - +
390A GLN* 3.6 31.2 + - - +
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Residues in contact with HIS 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ILE* 3.0 27.2 + - + +
384A GLN* 3.2 5.1 + - - +
386A MET* 1.3 105.2 - - + +
388A LEU* 1.3 64.6 + - - +
389A ARG 3.3 0.4 - - - -
390A GLN* 3.5 24.3 + - - +
391A TYR* 3.2 24.1 - - - -
247R LEU* 3.6 39.8 - - + +
248R ILE* 4.7 11.0 - - + -
252R VAL 3.3 25.7 + - - -
253R PHE* 4.8 3.8 - - - -
254R THR* 5.0 9.0 + - - -
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Residues in contact with LEU 388 (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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384A GLN* 3.0 23.9 + - + +
385A ARG* 4.2 9.0 - - + +
386A MET 3.5 0.2 - - - -
387A HIS* 1.3 74.3 - - - +
389A ARG* 1.3 62.8 + - - +
391A TYR* 3.5 3.9 + - - -
392A GLU 3.3 2.4 + - - -
393A LEU* 2.8 50.7 + - + +
394A LEU* 3.8 41.7 - - + +
248R ILE* 3.7 33.0 - - + -
319R ILE* 5.2 1.3 - - + -
322R VAL* 5.5 4.5 - - + -
323R LEU* 4.4 14.1 - - + -
326R LYS* 4.4 15.9 - - + -
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Residues in contact with ARG 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ARG* 3.5 53.4 + - - +
357A HIS* 4.1 2.2 - - - +
358A TYR* 5.6 2.6 - - - +
382A ILE 5.5 0.4 + - - -
385A ARG* 3.4 49.1 + - - +
386A MET* 4.1 10.9 - - - +
387A HIS 3.3 0.6 - - - -
388A LEU* 1.3 76.3 - - - +
390A GLN* 1.3 58.9 + - - +
392A GLU* 2.9 27.9 + - - +
394A LEU* 3.4 24.3 + - - +
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Residues in contact with GLN 390 (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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386A MET* 3.6 27.9 + - + +
387A HIS* 3.5 24.8 + - - +
388A LEU 3.3 0.6 - - - -
389A ARG* 1.3 77.6 - - + +
391A TYR* 1.3 60.9 + - + +
392A GLU* 3.1 13.7 - - - +
178R CYS* 4.3 17.7 - - - -
180R ARG* 3.3 54.9 + - - +
247R LEU* 5.1 2.9 - - - +
395R ASN* 3.5 6.2 + - - +
397R GLU* 6.2 1.3 - - + -
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Residues in contact with TYR 391 (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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387A HIS* 3.2 23.3 - - + -
388A LEU* 3.5 4.3 + - - +
389A ARG 3.2 0.8 - - - -
390A GLN* 1.3 74.8 - - + +
392A GLU* 1.3 73.1 + - - +
393A LEU* 3.1 26.4 + - + +
180R ARG* 3.4 31.0 - - - +
184R HIS* 3.9 19.5 - + - -
243R TYR* 3.3 33.8 - - - -
244R LEU* 3.7 36.2 - - + +
247R LEU* 3.9 17.1 - - + +
248R ILE* 5.0 7.2 - - + -
347R ILE* 3.9 7.3 - - - +
348R LEU* 5.7 0.4 - - + -
351R LEU* 5.8 1.3 - - + -
391R TYR* 4.5 27.5 - + + -
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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