Contacts of the helix formed by residues 371 - 390 (chain B) in PDB entry 2NVX
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 GLU 371 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B LEU* 3.3 48.5 - - + +
290B GLY* 5.6 0.2 - - - -
291B ILE* 5.3 2.0 - - + -
327B ARG* 4.4 13.8 + - - +
357B GLN* 4.4 13.8 + - - +
368B GLU* 3.3 18.0 - - - +
369B GLY* 3.9 5.0 - - - -
370B PHE* 1.3 87.3 + - - +
372B SER* 1.3 63.8 + - - +
373B ARG 3.3 2.2 - - - +
374B LYS* 3.6 4.8 + - - +
375B ALA* 3.2 25.5 + - - +
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Residues in contact with SER 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ILE* 5.1 4.9 - - - -
300B HIS* 4.5 4.1 - - - -
371B GLU* 1.3 76.9 + - - +
373B ARG* 1.3 63.4 + - - +
374B LYS 3.1 2.0 - - - -
375B ALA* 4.0 6.5 - - - +
376B PHE* 3.1 47.1 + - - +
566B LEU* 4.2 1.8 - - - +
567B GLU* 4.3 25.6 + - - -
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Residues in contact with ARG 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ILE* 3.9 33.1 + - + +
370B PHE* 3.5 44.5 - - + -
371B GLU 3.3 0.8 - - - +
372B SER* 1.3 78.3 - - - +
374B LYS* 1.3 60.1 + - + +
377B PHE* 3.9 10.7 + - - +
555B ILE* 6.3 0.4 - - - +
565B PRO* 5.4 4.4 - - - +
566B LEU* 3.3 36.0 - - + +
567B GLU* 2.7 34.0 + - + +
585B VAL* 4.6 5.3 - - - +
586B TRP 4.2 7.2 + - - -
587B HIS* 3.3 43.6 + - - +
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Residues in contact with LYS 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU* 4.2 8.1 - - + -
356B LEU 3.1 24.3 + - - +
357B GLN* 3.2 32.3 + - - +
360B PHE* 3.7 39.6 + - + +
361B LEU* 3.9 15.2 - - + +
363B HIS 4.7 2.0 - - - -
364B ILE* 4.3 14.6 - - + -
365B THR* 4.0 25.3 + - - +
367B LEU 5.0 0.4 + - - -
370B PHE 4.4 13.2 + - - +
371B GLU 3.6 7.7 + - - +
373B ARG* 1.3 79.4 - - + +
375B ALA* 1.3 53.2 + - - +
376B PHE 3.1 1.8 - - - -
377B PHE* 2.7 27.7 + - - +
378B LEU* 2.7 18.4 + - - +
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Residues in contact with ALA 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B PHE* 3.3 19.3 - - + -
289B LEU* 3.5 20.5 - - + +
291B ILE* 3.5 31.2 - - + -
300B HIS* 3.6 12.6 + - + +
371B GLU 3.2 9.3 + - - +
372B SER* 3.8 1.8 + - - +
374B LYS* 1.3 77.1 - - - +
376B PHE* 1.3 57.4 + - - +
378B LEU* 4.2 5.2 - - - -
379B GLY* 3.0 21.3 + - - -
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Residues in contact with PHE 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B HIS* 3.5 44.4 - + - -
303B TYR* 3.7 3.4 + + - -
372B SER* 3.1 41.2 + - - +
374B LYS 3.1 0.6 - - - -
375B ALA* 1.3 73.0 - - - +
377B PHE* 1.3 57.8 + - - +
379B GLY* 3.0 2.1 + - - -
380B TYR* 2.7 35.3 + - - +
566B LEU* 3.6 33.0 - - + -
567B GLU 5.1 1.6 - - - -
569B TYR* 3.2 46.2 - + - -
571B PRO* 4.8 8.1 - - + -
586B TRP* 3.5 27.1 - + + -
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Residues in contact with PHE 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B ASN 5.4 1.6 - - - -
223B VAL* 5.5 5.4 - - + -
240B ILE* 3.7 26.7 - - + -
361B LEU* 3.0 32.8 - - + -
363B HIS* 4.1 3.1 - - - -
364B ILE* 4.4 8.1 - - + -
373B ARG 3.9 11.7 + - - +
374B LYS* 2.7 15.3 + - - +
376B PHE* 1.3 75.9 - - - +
378B LEU* 1.3 56.1 + - - +
380B TYR* 3.0 20.3 + + - +
381B MET* 2.9 46.2 + - + +
581B PHE* 3.9 24.5 - + - -
584B GLY 3.9 21.8 - - - -
586B TRP* 3.8 24.6 - + + -
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Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LEU* 5.2 1.3 - - + -
256B VAL* 4.7 9.6 - - + -
271B ALA* 5.4 4.7 - - + -
282B ILE* 4.7 7.2 - - + +
285B ILE* 3.4 33.4 - - + -
286B PHE* 3.5 35.4 - - + +
289B LEU* 5.0 3.1 - - + -
360B PHE* 4.1 26.0 - - + -
361B LEU* 5.2 0.4 - - - +
374B LYS 2.7 17.4 + - - +
375B ALA* 3.7 4.7 - - - +
377B PHE* 1.3 72.0 - - - +
379B GLY* 1.3 60.1 + - - +
381B MET* 3.4 19.3 + - + +
382B ILE* 2.9 41.9 + - + +
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Residues in contact with GLY 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B PHE* 3.9 2.9 - - - -
300B HIS 3.5 19.7 - - - -
301B ILE* 3.5 28.2 - - - -
375B ALA 3.0 15.4 + - - -
376B PHE 3.4 4.0 - - - -
378B LEU* 1.3 76.5 - - - +
380B TYR* 1.3 56.2 + - - +
382B ILE* 3.4 1.6 + - - -
383B ASN* 2.9 24.3 + - - +
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Residues in contact with TYR 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B VAL* 3.6 34.7 - - + +
303B TYR* 3.4 15.9 + + - +
376B PHE 2.7 12.6 + - - +
377B PHE* 3.0 28.9 + + - +
379B GLY* 1.3 74.9 - - - +
381B MET* 1.3 64.2 + - + +
383B ASN* 3.3 7.6 + - + +
384B ARG* 3.0 48.7 + - - +
579B ARG* 3.7 23.8 - - - -
581B PHE* 3.5 25.5 - + - -
586B TRP* 4.2 7.9 - + + -
623B GLU* 2.7 29.6 + - - -
625B LYS* 4.8 4.7 + - - -
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Residues in contact with MET 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B VAL* 4.0 23.3 - - + -
238B ALA* 4.6 10.9 - - + +
239B GLU 5.9 0.2 - - - -
240B ILE* 4.1 15.9 - - + -
254B LEU* 3.6 33.9 - - + -
256B VAL* 4.0 19.1 - - + -
361B LEU* 4.0 10.8 - - + -
377B PHE* 2.9 41.4 + - + +
378B LEU* 3.5 27.8 - - + +
380B TYR* 1.3 74.6 - - + +
382B ILE* 1.3 67.5 + - - +
384B ARG* 2.7 14.6 + - - +
385B LEU* 2.8 15.9 + - - +
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Residues in contact with ILE 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B VAL* 3.6 18.8 - - + -
269B ILE* 3.8 32.3 - - + -
282B ILE* 3.6 28.5 - - + -
286B PHE* 4.5 2.9 - - + -
301B ILE* 3.8 37.5 - - + -
314B LEU* 4.7 2.2 - - + -
378B LEU* 2.9 27.3 + - + +
379B GLY* 4.0 0.2 - - - -
381B MET* 1.3 74.2 - - - +
383B ASN* 1.3 62.2 + - - +
385B LEU* 3.7 6.0 - - + +
386B LEU* 3.1 34.2 + - + +
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Residues in contact with ASN 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ILE* 3.3 16.8 - - - +
303B TYR* 3.2 31.7 + - + -
310B MET* 3.9 20.0 - - - +
379B GLY 2.9 15.9 + - - +
380B TYR* 3.5 12.5 + - + +
381B MET 3.1 0.6 - - - -
382B ILE* 1.3 75.0 - - - +
384B ARG* 1.3 66.9 + - - +
386B LEU* 4.1 0.9 - - - +
387B LEU* 3.1 46.5 + - - +
579B ARG* 5.2 7.9 - - - +
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Residues in contact with ARG 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B VAL* 4.1 29.9 - - + +
225B VAL* 3.8 23.6 - - + +
380B TYR* 3.0 33.1 + - - +
381B MET 2.7 14.1 + - - +
383B ASN* 1.3 78.9 - - - +
385B LEU* 1.3 63.8 + - - +
387B LEU* 3.3 20.8 + - - +
388B CYS* 3.3 17.5 + - - +
393B LYS* 5.3 4.4 - - - +
396B ASP* 5.5 1.6 - - - +
579B ARG* 5.0 2.4 - - - +
621B GLU* 2.7 30.1 + - - +
623B GLU* 2.5 44.4 + - - -
625B LYS* 5.7 1.0 - - - +
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Residues in contact with LEU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B VAL* 3.8 16.6 - - + +
236B HIS* 3.8 7.3 - - + -
237B VAL 3.6 15.7 - - - +
238B ALA* 3.4 34.4 - - + +
256B VAL* 3.6 25.1 - - + +
257B LYS 4.2 2.9 - - - +
258B LEU* 3.7 29.2 - - + -
269B ILE* 4.4 15.0 - - + -
381B MET 2.8 18.2 + - - +
382B ILE* 3.7 7.4 - - + +
384B ARG* 1.3 74.2 - - - +
386B LEU* 1.3 55.3 + - - +
388B CYS* 3.5 3.8 + - - +
389B ALA* 3.2 22.0 + - - +
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Residues in contact with LEU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B LEU* 4.1 20.6 - - + -
269B ILE* 3.4 29.4 - - + -
301B ILE* 4.8 0.7 - - + -
310B MET* 3.9 25.1 - - + -
313B MET* 4.4 25.6 - - + +
314B LEU* 3.8 36.1 - - + -
382B ILE* 3.1 21.1 + - + +
383B ASN 4.6 1.1 - - - +
385B LEU* 1.3 72.5 - - + +
387B LEU* 1.3 63.4 + - - +
388B CYS 3.1 2.2 - - - -
389B ALA* 3.5 6.6 - - + +
390B LEU* 3.2 31.0 + - + +
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B MET* 6.2 3.8 - - - -
383B ASN* 3.1 33.8 + - - +
384B ARG* 3.3 36.1 + - - +
386B LEU* 1.3 77.3 - - - +
388B CYS* 1.3 59.1 + - - +
390B LEU* 4.2 2.1 + - - +
391B ASP 3.9 0.9 + - - -
392B ARG* 3.3 48.7 + - + +
393B LYS* 3.2 44.4 + - + -
579B ARG* 6.3 0.2 - - - +
621B GLU* 4.2 7.6 - - - +
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Residues in contact with CYS 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B VAL* 3.7 32.5 - - + -
227B LYS* 3.8 30.5 - - - -
236B HIS* 4.6 6.5 - - - -
384B ARG 3.3 14.0 + - - +
385B LEU 4.0 0.2 - - - +
386B LEU 3.1 0.2 - - - -
387B LEU* 1.3 78.2 - - - +
389B ALA* 1.3 58.5 + - - +
390B LEU 3.4 0.7 - - - -
391B ASP* 3.0 22.4 + - - +
393B LYS* 3.5 20.6 - - + +
394B ASP 4.3 4.5 - - - +
395B GLN* 4.3 11.2 - - - -
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Residues in contact with ALA 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B HIS* 3.2 31.9 + - + +
258B LEU* 3.8 17.0 - - + -
267B ARG* 4.3 17.6 + - - +
313B MET* 5.7 3.9 - - + +
385B LEU 3.2 12.9 + - - +
386B LEU* 3.3 10.7 + - + +
388B CYS* 1.3 75.6 - - - +
390B LEU* 1.3 62.6 + - + +
391B ASP* 3.2 9.8 + - - +
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Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B GLN* 3.9 34.1 - - + +
310B MET* 4.0 13.7 - - + +
313B MET* 3.9 37.0 - - + -
386B LEU* 3.2 18.8 + - + +
387B LEU 4.2 2.0 + - - +
389B ALA* 1.3 81.2 - - + +
391B ASP* 1.3 72.1 + - - +
392B ARG* 3.2 51.4 - - + +
50I THR* 5.3 1.6 + - - -
90I GLN* 4.9 6.6 + - - -
92I ARG* 5.0 5.6 + - - -
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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