Contacts of the helix formed by residues 359 - 380 (chain B) in PDB entry 3VS5
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 PRO 359 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B LYS 3.4 8.5 - - - +
358B GLN* 1.3 92.5 - - + +
360B LEU* 1.3 65.3 + - - +
361B PRO* 4.0 14.1 - - + -
362B LYS* 3.3 25.2 + - + +
363B LEU* 3.4 12.0 + - - +
458B TYR* 4.7 1.1 - - - +
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Residues in contact with LEU 360 (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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359B PRO* 1.3 69.3 - - - +
361B PRO* 1.3 73.5 - - + +
363B LEU* 3.1 18.3 + - + +
364B ILE* 3.0 32.5 + - + +
456B VAL* 3.9 28.0 - - + -
458B TYR* 4.9 1.8 + - - -
486B ASN* 3.5 14.6 - - + +
488B PRO* 3.5 34.3 - - + -
491B LEU* 5.2 0.4 - - + -
520B TYR* 3.9 11.7 - - - +
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Residues in contact with PRO 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLN* 5.0 11.9 - - + +
359B PRO* 3.6 14.6 - - + -
360B LEU* 1.3 93.1 - - + +
362B LYS* 1.3 55.2 + - - +
364B ILE* 3.8 4.1 - - + +
365B ASP* 3.1 23.4 + - - +
520B TYR* 3.6 40.7 - - + +
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Residues in contact with LYS 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B GLN* 3.4 25.1 - - + +
359B PRO* 3.3 21.5 + - + +
360B LEU 3.1 0.8 - - - -
361B PRO* 1.3 76.4 - - - +
363B LEU* 1.3 65.8 + - - +
365B ASP* 3.0 32.8 + - + +
366B PHE* 2.9 49.0 + - + -
369B GLN* 4.4 0.6 - - - +
397B SER 5.6 0.4 + - - -
398B LEU* 4.1 33.0 + - - +
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Residues in contact with LEU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU* 4.0 21.8 - - + -
358B GLN* 4.1 14.6 - - + +
359B PRO 3.4 8.9 + - - +
360B LEU* 3.1 26.6 + - + +
362B LYS* 1.3 75.7 - - - +
364B ILE* 1.3 62.8 + - + +
366B PHE* 3.2 15.2 + - + +
367B SER* 3.1 23.0 + - - -
455B ILE* 3.6 36.6 - - + +
456B VAL* 4.3 9.2 - - + +
458B TYR* 3.8 35.9 - - + +
486B ASN* 5.2 2.0 - - - +
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Residues in contact with ILE 364 (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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360B LEU* 3.0 29.8 + - + +
361B PRO* 3.8 5.6 - - + +
363B LEU* 1.3 72.8 - - + +
365B ASP* 1.3 59.8 + - - +
367B SER* 3.2 10.0 + - - -
368B ALA* 2.9 25.6 + - - +
488B PRO* 4.9 2.2 - - + -
491B LEU* 4.3 22.4 - - + -
516B LEU* 4.0 27.8 - - + +
519B PHE* 3.6 38.4 - - + -
520B TYR* 3.2 31.2 - - + +
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Residues in contact with ASP 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LYS* 4.0 14.8 + - - +
161B ARG* 2.9 44.6 + - - +
361B PRO 3.1 15.8 + - - +
362B LYS* 3.0 39.3 + - + +
364B ILE* 1.3 76.8 - - - +
366B PHE* 1.3 62.1 + - - +
368B ALA* 3.1 7.6 + - - +
369B GLN* 3.0 30.0 + - - +
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Residues in contact with PHE 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 4.3 15.9 - - + -
349B PHE* 4.1 28.0 - + - -
350B LEU* 4.5 7.2 - - + -
358B GLN* 4.6 8.1 - - + -
362B LYS* 2.9 44.7 + - + -
363B LEU* 3.3 28.7 - - + +
365B ASP* 1.3 75.9 - - - +
367B SER* 1.3 62.9 + - - +
369B GLN* 3.1 15.0 + - - +
370B ILE* 3.0 29.8 + - + +
394B VAL* 5.6 2.2 - - + -
398B LEU* 3.7 25.4 - - + -
400B CYS* 3.7 24.6 - - - -
455B ILE* 4.9 9.9 - - + -
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Residues in contact with SER 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B LEU 3.1 11.9 + - - -
364B ILE* 3.3 13.8 - - - -
366B PHE* 1.3 77.9 - - - +
368B ALA* 1.3 57.7 + - - +
370B ILE* 3.3 5.1 + - - +
371B ALA* 2.8 29.8 + - - +
448B PHE* 3.5 6.1 - - - -
452B LEU* 3.4 27.2 - - - +
455B ILE* 3.2 26.4 - - - +
491B LEU* 6.0 1.3 - - - +
516B LEU* 3.6 10.1 - - - -
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Residues in contact with ALA 368 (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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157B LYS* 5.2 1.1 - - - -
161B ARG* 3.8 7.4 - - - +
364B ILE 2.9 12.7 + - - +
365B ASP* 3.1 13.4 + - - +
367B SER* 1.3 76.4 - - - +
369B GLN* 1.3 57.0 + - - +
371B ALA* 3.2 4.5 + - - +
372B GLU* 2.9 28.6 + - - +
513B GLN* 4.3 4.3 - - - +
516B LEU* 3.9 29.1 - - + +
517B ASP* 3.4 23.4 - - - +
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Residues in contact with GLN 369 (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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161B ARG* 3.4 28.0 - - - +
321B LYS* 3.2 39.1 - - + +
362B LYS* 4.4 1.0 - - - +
365B ASP* 3.0 27.4 + - - +
366B PHE* 3.3 22.5 - - - +
368B ALA* 1.3 76.4 - - - +
370B ILE* 1.3 57.0 + - - +
372B GLU* 3.1 9.4 + - - +
373B GLY 3.0 22.9 + - - -
398B LEU 3.5 20.4 + - - -
399B VAL* 3.5 8.7 - - - +
400B CYS* 3.2 26.5 + - + +
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Residues in contact with ILE 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B LYS* 5.6 0.4 - - - -
346B LEU* 4.0 18.8 - - + -
366B PHE 3.0 16.6 + - - +
367B SER* 3.3 6.0 + - - +
369B GLN* 1.3 71.1 - - - +
371B ALA* 1.3 61.1 + - - +
373B GLY* 3.2 1.6 + - - -
374B MET* 2.8 31.5 + - + +
387B LEU* 4.8 1.6 - - + -
392B ILE* 4.1 32.5 - - + -
400B CYS* 4.3 7.2 - - + -
402B ILE* 3.8 15.1 - - + +
448B PHE* 3.6 18.8 - - + -
451B LEU* 4.1 17.3 - - + -
455B ILE* 4.0 25.1 - - + -
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Residues in contact with ALA 371 (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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367B SER 2.8 17.2 + - - +
368B ALA* 3.2 7.4 + - - +
370B ILE* 1.3 76.7 - - - +
372B GLU* 1.3 57.8 + - - +
374B MET* 3.7 4.4 - - - +
375B ALA* 2.8 30.7 + - - +
448B PHE* 3.8 19.0 - - + -
509B PHE* 4.0 6.0 - - + +
512B ILE* 3.9 13.2 - - + -
513B GLN* 3.8 24.8 - - - +
516B LEU* 4.3 1.6 - - + -
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Residues in contact with GLU 372 (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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155B SER* 5.6 0.8 + - - -
158B ASP* 4.5 10.5 - - - +
161B ARG* 3.8 15.4 + - - -
319B HIS* 3.6 22.2 + - + +
320B ASP* 5.6 1.6 - - - +
321B LYS* 2.9 32.8 + - - +
368B ALA 2.9 12.8 + - - +
369B GLN* 3.1 8.1 + - - +
371B ALA* 1.3 77.8 - - - +
373B GLY* 1.3 56.1 + - - +
375B ALA* 3.4 3.3 + - - +
376B PHE* 3.2 24.9 + - - +
513B GLN* 3.6 32.7 + - + +
517B ASP* 5.4 2.4 - - - +
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Residues in contact with GLY 373 (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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319B HIS* 4.4 2.0 - - - -
321B LYS* 3.9 16.7 - - - +
322B LEU* 3.6 11.3 - - - +
369B GLN 3.0 10.9 + - - -
370B ILE 3.7 2.7 - - - -
372B GLU* 1.3 75.3 - - - +
374B MET* 1.3 61.6 + - - +
376B PHE* 3.6 5.5 + - - +
377B ILE* 3.3 26.0 + - - +
402B ILE* 3.6 16.8 - - - -
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Residues in contact with MET 374 (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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370B ILE* 2.8 23.3 + - + +
371B ALA 3.8 1.1 - - - +
373B GLY* 1.3 75.4 - - - +
375B ALA* 1.3 61.0 + - - +
377B ILE* 3.4 21.0 + - + +
378B GLU* 2.9 28.8 + - - +
384B HIS* 4.3 7.0 - - + -
387B LEU* 3.6 32.1 - - + -
402B ILE* 3.8 17.7 - - + -
441B ILE* 4.1 6.5 - - + -
444B ASP* 4.0 21.5 - - + +
509B PHE* 3.4 51.9 - - + -
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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
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371B ALA 2.8 18.2 + - - +
372B GLU 3.6 3.1 - - - +
373B GLY 3.3 0.2 - - - -
374B MET* 1.3 76.0 - - - +
376B PHE* 1.3 57.8 + - - +
378B GLU* 3.6 7.1 - - - +
379B GLN* 3.0 28.8 + - - +
509B PHE* 3.7 23.8 - - - +
510B GLU* 4.0 7.9 - - + +
513B GLN* 3.5 21.5 - - - +
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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
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316B THR 4.8 0.2 - - - -
317B LEU* 3.7 30.3 - - + -
318B GLN 3.5 21.3 - - - -
319B HIS* 3.5 48.5 - + + +
322B LEU* 4.3 12.6 - - + -
372B GLU 3.2 10.1 + - - +
373B GLY 3.6 7.4 - - - +
375B ALA* 1.3 74.9 - - - +
377B ILE* 1.3 63.0 + - + +
379B GLN* 3.3 6.8 + - + +
380B ARG* 2.9 60.8 + - + +
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Residues in contact with ILE 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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317B LEU* 5.3 3.1 - - + -
322B LEU* 4.1 24.2 - - + -
373B GLY 3.3 14.4 + - - +
374B MET* 3.4 28.9 + - + +
376B PHE* 1.3 80.3 - - + +
378B GLU* 1.3 61.2 + - - +
380B ARG* 3.3 5.4 + - - -
381B ASN 3.1 3.8 + - - -
382B TYR* 2.9 66.6 + - + +
383B ILE* 4.1 4.5 - - - +
384B HIS* 4.4 9.0 - - + +
402B ILE* 4.8 0.9 - - + -
405B PHE* 4.1 26.2 - - + -
441B ILE* 4.2 9.2 - - + -
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Residues in contact with GLU 378 (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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374B MET 2.9 17.7 + - - +
375B ALA 3.6 6.3 - - - +
377B ILE* 1.3 75.3 - - - +
379B GLN* 1.3 67.9 + - - +
381B ASN* 3.1 19.5 + - - +
382B TYR 4.8 0.9 - - - -
441B ILE* 3.9 34.8 - - + +
442B LYS* 5.4 2.1 - - - -
508B THR* 3.2 19.7 - - - +
509B PHE* 3.1 26.5 + - + +
510B GLU* 3.2 29.8 + - - +
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Residues in contact with GLN 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ALA 3.0 18.1 + - - +
376B PHE* 3.7 7.6 - - + +
378B GLU* 1.3 80.3 - - - +
380B ARG* 1.3 61.2 + - + +
381B ASN* 3.1 13.6 + - - +
510B GLU* 4.7 11.8 - - - +
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Residues in contact with ARG 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B THR* 2.5 45.2 + - - -
317B LEU* 3.3 35.8 - - + +
376B PHE* 2.9 44.8 + - + +
377B ILE 3.9 2.7 - - - +
378B GLU 3.2 0.4 - - - -
379B GLN* 1.3 78.1 - - + +
381B ASN* 1.3 70.9 + - - +
382B TYR* 3.1 5.3 + - - +
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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
------------------------------------------------------------
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