Contacts of the helix formed by residues 390 - 416 (chain C) in PDB entry 3SV1
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 SER 390 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C PRO* 1.3 79.2 - - - +
391C LYS* 1.3 54.3 + - - +
392C ASN* 3.1 26.4 + - - +
393C ILE* 2.9 22.3 + - - +
394C ARG* 2.6 30.3 + - - +
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Residues in contact with LYS 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C PRO 3.7 1.0 + - - -
390C SER* 1.3 74.4 + - - +
392C ASN* 1.3 57.8 + - - +
394C ARG* 2.7 28.7 + - + -
395C MET* 2.9 21.3 + - - +
460C TYR* 5.4 5.7 + - + +
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Residues in contact with ASN 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C SER* 3.1 18.2 + - - +
391C LYS* 1.3 79.1 - - - +
393C ILE* 1.3 60.0 + - + +
395C MET* 3.3 30.0 - - - +
396C MET* 4.1 2.3 - - - +
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Residues in contact with ILE 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C GLU* 5.3 4.7 - - - +
389C PRO* 3.7 26.5 - - + -
390C SER* 2.9 27.6 + - - +
392C ASN* 1.3 79.5 - - + +
394C ARG* 1.3 66.8 + - - +
395C MET 3.6 0.4 - - - -
396C MET* 3.5 31.2 - - + +
397C GLN* 3.1 20.3 - - + +
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Residues in contact with ARG 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C SER* 4.9 3.4 + - - -
386C GLU 5.2 0.8 + - - -
387C ARG 4.7 9.9 + - - -
388C ASN* 4.7 4.4 - - - +
389C PRO* 3.9 31.5 + - + +
390C SER 2.6 14.4 + - - +
391C LYS* 2.7 13.8 + - - +
393C ILE* 1.3 77.0 - - - +
395C MET* 1.3 55.6 + - - +
397C GLN* 2.6 59.6 + - - +
398C ALA* 3.4 2.6 + - - +
459C SER* 2.9 45.3 + - - -
460C TYR* 3.6 32.9 - - + -
471C MET* 4.1 18.2 - - - +
500C MET* 5.0 1.8 - - - +
756F GLY* 5.3 3.0 - - - -
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Residues in contact with MET 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C LYS 2.9 19.7 + - - +
392C ASN* 3.3 25.8 - - - +
394C ARG* 1.3 75.4 - - - +
396C MET* 1.3 83.6 + - - +
398C ALA* 2.6 30.0 + - + +
399C GLN* 2.7 43.8 + - + +
460C TYR* 4.0 20.4 + - - +
464C ILE* 6.2 5.2 - - + -
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Residues in contact with MET 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C ASN 4.1 2.0 - - - +
393C ILE* 3.5 38.6 - - + +
394C ARG 3.0 0.4 - - - -
395C MET* 1.3 95.0 - - - +
397C GLN* 1.3 71.5 + - + +
399C GLN* 4.0 8.0 - - - +
400C GLU* 3.2 29.4 + - - +
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Residues in contact with GLN 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C LEU* 3.8 30.2 - - + +
384C LEU 4.8 1.6 + - - -
385C SER* 3.3 34.8 + - - +
386C GLU* 4.5 4.6 + - - -
389C PRO* 4.3 3.8 - - - +
393C ILE* 3.1 16.9 - - + +
394C ARG* 2.6 54.7 + - - +
396C MET* 1.3 83.6 - - + +
398C ALA* 1.3 52.3 + - - +
400C GLU* 3.6 3.5 - - - +
401C ALA* 2.6 36.0 + - - +
471C MET* 4.5 10.8 - - - +
502C CYS* 5.3 0.9 - - - -
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Residues in contact with ALA 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C ARG 3.4 2.2 + - - +
395C MET* 2.6 22.0 + - - +
397C GLN* 1.3 72.3 - - - +
399C GLN* 1.3 59.2 + - + +
401C ALA* 2.6 27.9 + - - +
402C VAL* 2.7 18.7 + - - +
460C TYR* 4.4 20.0 - - + -
462C ALA* 4.6 6.5 - - + -
464C ILE* 4.8 4.7 - - + -
469C VAL* 4.5 21.1 - - + -
471C MET* 5.8 1.7 - - - -
502C CYS* 5.2 2.5 - - - -
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Residues in contact with GLN 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C MET* 2.7 54.8 + - + +
396C MET* 4.0 6.5 - - - +
398C ALA* 1.3 73.0 - - + +
400C GLU* 1.3 51.7 + - - +
402C VAL* 3.0 11.4 - - - +
403C SER* 2.5 38.5 + - - +
464C ILE* 4.6 18.1 - - + +
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Residues in contact with GLU 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C MET* 3.2 24.2 + - - +
397C GLN* 4.0 4.0 - - - +
398C ALA 3.2 0.6 - - - -
399C GLN* 1.3 76.4 - - - +
401C ALA* 1.3 61.8 + - - +
403C SER* 3.5 16.0 - - - -
404C ARG* 2.7 41.6 + - - +
407C ARG* 3.5 13.7 + - - -
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Residues in contact with ALA 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C THR* 3.5 11.1 - - + +
383C LEU* 5.1 2.9 - - + -
397C GLN 2.6 22.1 + - - +
398C ALA* 2.6 21.3 + - - +
400C GLU* 1.3 70.8 - - - +
402C VAL* 1.3 54.7 + - - +
404C ARG* 3.1 7.0 + - - +
405C VAL* 2.8 31.4 + - - +
469C VAL* 4.6 2.9 - - + -
502C CYS* 3.7 33.0 - - + -
504C VAL* 4.6 0.4 - - - -
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Residues in contact with VAL 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C ALA 2.7 16.3 + - - +
399C GLN* 3.0 19.1 - - - +
401C ALA* 1.3 70.7 - - - +
403C SER* 1.3 63.8 + - - +
405C VAL* 3.0 0.7 + - - +
406C LYS* 2.3 54.7 + - + +
464C ILE* 5.0 5.6 - - + -
467C ILE* 3.9 15.9 - - + -
469C VAL* 3.2 35.0 - - + -
504C VAL* 4.0 21.8 - - + -
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Residues in contact with SER 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C GLN* 2.5 23.5 + - - +
400C GLU* 3.5 18.9 - - - -
402C VAL* 1.3 82.8 - - - +
404C ARG* 1.3 58.1 + - - +
406C LYS* 4.2 7.2 - - - -
407C ARG* 2.8 56.2 + - - +
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Residues in contact with ARG 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C SER 3.5 19.8 + - - -
381C THR* 3.0 36.4 + - - +
382C GLN 5.5 0.2 - - - +
400C GLU* 2.7 23.5 + - - +
401C ALA* 3.2 7.9 - - - +
403C SER* 1.3 81.8 - - - +
405C VAL* 1.3 63.3 + - - +
407C ARG* 3.8 5.0 - - - +
408C MET* 3.1 52.5 + - - +
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Residues in contact with VAL 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C LEU* 3.8 17.3 - - + +
379C GLY* 3.4 32.8 - - - +
380C SER 3.1 30.1 - - - +
381C THR* 3.6 4.3 - - + -
401C ALA 2.8 18.5 + - - +
402C VAL 3.6 4.5 - - - +
404C ARG* 1.3 78.1 - - - +
406C LYS* 1.3 62.0 + - + +
408C MET* 3.2 7.1 + - + +
409C GLN* 3.1 20.4 + - - +
504C VAL* 3.2 31.2 - - + -
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Residues in contact with LYS 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C LEU* 5.1 13.5 - - + -
402C VAL* 2.3 49.7 + - + +
403C SER* 4.0 6.1 - - - +
405C VAL* 1.3 67.5 - - + +
407C ARG* 1.3 60.6 + - + +
409C GLN* 2.9 25.8 + - - +
410C LYS* 3.1 16.4 + - + +
467C ILE* 5.7 9.2 - - + -
504C VAL* 5.8 2.7 - - + -
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Residues in contact with ARG 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C GLU* 3.5 23.2 + - - -
403C SER* 2.8 39.1 + - - +
404C ARG* 3.8 4.6 - - - +
406C LYS* 1.3 73.2 - - + +
408C MET* 1.3 58.6 + - - +
410C LYS* 3.8 23.6 - - + +
411C ALA* 3.8 16.1 + - - +
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Residues in contact with MET 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C LEU 3.5 10.5 - - - +
379C GLY* 4.6 7.4 - - - -
380C SER 4.7 6.5 - - - +
404C ARG* 3.1 38.2 + - - +
405C VAL* 3.4 10.8 - - + +
406C LYS 3.0 0.4 - - - -
407C ARG* 1.3 75.7 - - - +
409C GLN* 1.3 97.6 + - + +
410C LYS 3.3 0.2 - - - -
411C ALA* 3.4 7.5 + - - +
412C ALA* 2.9 27.8 + - + +
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Residues in contact with GLN 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C LEU* 2.6 48.3 + - + +
405C VAL 3.1 16.3 + - - +
406C LYS* 2.9 10.4 + - - +
408C MET* 1.3 90.9 - - + +
410C LYS* 1.3 71.6 + - - +
412C ALA* 2.7 16.0 + - - +
413C LYS* 2.8 29.3 + - - +
426C THR* 2.9 46.2 + - - -
427C LEU* 3.7 8.7 + - - +
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Residues in contact with LYS 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C LYS* 3.1 14.5 + - + +
407C ARG* 3.8 27.3 - - + +
409C GLN* 1.3 81.3 - - - +
411C ALA* 1.3 60.2 + - - +
412C ALA 2.9 3.1 + - - -
413C LYS* 3.1 22.5 + - - +
414C ILE* 3.2 19.2 + - + +
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Residues in contact with ALA 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407C ARG 3.8 9.0 + - - +
408C MET* 3.4 9.1 + - - +
409C GLN 3.2 0.4 - - - -
410C LYS* 1.3 77.8 - - - +
412C ALA* 1.3 59.3 + - - +
414C ILE* 3.4 16.8 - - + +
415C LYS* 3.3 28.7 + - - +
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Residues in contact with ALA 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C MET* 2.9 18.4 + - + +
409C GLN* 2.7 29.1 + - - +
411C ALA* 1.3 69.7 - - - +
413C LYS* 1.3 60.2 + - - +
414C ILE 3.0 1.3 - - - -
415C LYS* 2.8 29.4 + - - +
416C LYS* 3.4 8.5 + - - +
426C THR* 3.8 19.6 - - + +
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Residues in contact with LYS 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C GLN* 2.8 33.4 + - - +
410C LYS* 3.7 12.0 - - - +
412C ALA* 1.3 75.4 - - - +
414C ILE* 1.3 60.5 + - + +
416C LYS* 2.9 27.4 + - + +
417C LYS* 3.3 5.0 + - - +
425C GLN 6.2 0.7 - - - +
426C THR* 3.6 30.3 - - + +
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Residues in contact with ILE 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C LYS* 3.2 18.3 + - + +
411C ALA* 3.4 18.6 - - + +
413C LYS* 1.3 78.1 - - + +
415C LYS* 1.3 60.9 + - - +
416C LYS 3.0 5.4 - - - -
417C LYS* 3.1 26.0 + - + +
418C ALA* 4.0 1.7 + - - +
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Residues in contact with LYS 415 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C ALA* 3.3 15.9 + - - +
412C ALA* 2.8 15.7 + - - +
414C ILE* 1.3 80.2 - - - +
416C LYS* 1.3 64.4 + - + +
417C LYS 3.2 0.2 - - - -
418C ALA* 3.4 23.2 + - + +
419C ASN* 4.9 0.5 - - - +
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Residues in contact with LYS 416 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C ALA 3.8 12.8 - - - +
413C LYS* 2.9 12.0 + - - +
415C LYS* 1.3 83.0 - - + +
417C LYS* 1.3 62.1 + - - +
418C ALA 3.0 1.6 - - - -
419C ASN* 3.0 51.8 + - + +
425C GLN* 3.4 41.9 + - - +
426C THR* 4.2 14.1 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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