Contacts of the helix formed by residues 363 - 384 (chain C) in PDB entry 3V81
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 ASN 363 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C THR* 1.3 82.4 + - - +
364C ASP* 1.3 59.4 + - - +
365C VAL* 3.0 11.2 + - - +
366C LYS* 2.9 27.8 + - - +
367C GLN* 3.0 25.5 + - - +
401C TRP* 3.4 21.6 - - - -
425C LEU* 4.4 8.0 - - + +
508C ALA 3.2 15.4 + - - -
509C GLN 3.0 19.2 + - - +
510C PRO* 4.6 0.2 - - - +
511C ASP* 3.3 26.5 - - - +
512C LYS* 3.9 4.5 - - - -
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Residues in contact with ASP 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C LYS* 3.0 33.7 + - - -
335C GLY* 5.3 2.1 + - - -
337C TRP* 3.9 15.2 - - + -
363C ASN* 1.3 69.5 - - - +
365C VAL* 1.3 60.2 + - - +
367C GLN* 3.7 5.2 - - - +
368C LEU* 2.8 31.4 + - - +
423C VAL* 4.0 20.5 - - + -
424C LYS 5.0 4.2 + - - +
426C TRP* 4.5 9.2 + - - -
511C ASP* 2.9 22.9 + - - +
512C LYS* 2.9 23.1 + - - +
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Residues in contact with VAL 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C ASN* 3.0 7.0 + - - +
364C ASP* 1.3 77.8 - - - +
366C LYS* 1.3 57.1 + - - +
368C LEU* 3.3 4.6 + - + +
369C THR* 2.9 28.4 + - - -
393C ILE* 4.2 10.5 - - + -
397C THR* 4.7 3.6 - - + -
398C TRP* 3.8 20.3 - - + -
401C TRP* 3.3 38.1 - - + +
423C VAL* 3.7 21.5 - - + -
424C LYS 4.5 3.6 - - - +
425C LEU* 3.9 28.7 - - + -
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Residues in contact with LYS 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C HIS 4.3 14.1 + - - -
362C THR* 3.6 19.4 - - - +
363C ASN* 2.9 28.3 + - - +
365C VAL* 1.3 74.0 - - - +
367C GLN* 1.3 61.6 + - - +
369C THR* 3.0 9.5 + - - -
370C GLU* 2.9 42.1 + - - +
401C TRP* 3.9 19.5 - - + +
405C TYR* 3.0 34.5 + - + -
508C ALA* 3.9 20.8 + - - +
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Residues in contact with GLN 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C GLY* 3.4 32.6 + - - -
337C TRP* 3.5 17.0 + - + +
354C TYR* 3.8 5.9 - - + -
356C ARG 3.8 15.8 + - - +
357C MET* 4.2 9.9 - - - +
358C ARG 5.7 1.3 - - - +
362C THR* 3.2 21.1 - - + +
363C ASN 3.0 12.7 + - - +
364C ASP* 3.9 4.9 - - - +
366C LYS* 1.3 80.2 - - - +
368C LEU* 1.3 58.4 + - - +
370C GLU* 3.4 17.2 + - - +
371C ALA* 3.0 26.7 + - - +
512C LYS* 2.8 34.9 + - - +
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Residues in contact with LEU 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C ILE* 4.0 28.7 - - + -
337C TRP* 3.6 31.3 - - + -
364C ASP 2.8 22.6 + - - +
365C VAL* 3.7 4.9 - - - +
366C LYS 3.2 0.2 - - - -
367C GLN* 1.3 69.5 - - - +
369C THR* 1.3 66.7 + - - +
371C ALA* 3.2 4.9 + - + +
372C VAL* 2.9 25.9 + - + +
391C LEU* 4.3 16.8 - - + -
392C PRO* 4.6 7.6 - - + -
393C ILE* 4.0 35.4 - - + -
398C TRP* 6.1 1.3 - - + -
411C ILE* 5.5 5.4 - - + -
423C VAL* 4.5 8.5 - - + -
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Residues in contact with THR 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C VAL* 2.9 12.8 + - - +
366C LYS* 3.0 10.9 + - - -
368C LEU* 1.3 75.5 - - - +
370C GLU* 1.3 64.4 + - + +
372C VAL* 3.3 9.6 + - + +
373C GLN* 3.0 42.5 + - - +
398C TRP* 3.0 34.3 - - + -
401C TRP* 5.2 1.9 + - - -
409C THR* 3.7 19.6 + - - +
410C TRP 4.6 5.4 - - - +
411C ILE* 5.1 4.5 - - + +
397D THR* 5.2 0.9 - - - +
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Residues in contact with GLU 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C TYR* 3.0 29.4 + - - +
356C ARG 4.3 1.4 - - - +
358C ARG* 3.7 43.1 + - - +
362C THR* 5.2 1.4 + - - -
366C LYS* 2.9 25.7 + - - +
367C GLN* 3.6 22.3 - - - +
368C LEU 3.2 0.2 - - - -
369C THR* 1.3 78.3 - - + +
371C ALA* 1.3 56.3 + - - +
373C GLN* 3.3 15.0 + - - +
374C LYS* 3.0 26.3 + - - +
394D GLN* 5.7 6.3 - - + +
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Residues in contact with ALA 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C ILE* 4.3 14.6 - - + -
337C TRP* 4.5 11.2 - - + -
354C TYR* 3.8 33.5 - - + -
367C GLN 3.0 14.7 + - - +
368C LEU* 3.6 11.2 - - + +
370C GLU* 1.3 71.7 - - - +
372C VAL* 1.3 60.1 + - - +
374C LYS* 3.3 2.0 + - - +
375C ILE* 2.9 38.4 + - + +
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Residues in contact with VAL 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C ILE* 4.0 6.7 - - + -
368C LEU* 2.9 19.1 + - + +
369C THR* 3.6 11.2 - - + +
371C ALA* 1.3 76.2 - - - +
373C GLN* 1.3 56.3 + - + +
375C ILE* 3.6 0.6 + - - -
376C THR* 2.5 43.5 + - - +
389C PHE* 3.6 16.9 - - + -
391C LEU* 3.7 32.8 - - + -
410C TRP 5.3 1.6 - - - +
411C ILE* 3.5 34.5 - - + -
412C PRO* 4.0 9.9 - - + -
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Residues in contact with GLN 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C THR* 3.0 36.2 + - - +
370C GLU* 3.7 15.8 - - - +
371C ALA 3.2 0.2 - - - -
372C VAL* 1.3 76.2 - - + +
374C LYS* 1.3 67.3 + - - +
375C ILE 3.1 1.3 + - - -
376C THR* 3.6 5.7 - - - +
377C THR* 2.9 27.4 + - - +
409C THR* 5.0 0.3 + - - -
410C TRP 4.1 8.4 - - - +
394D GLN* 5.4 3.6 - - - +
396D GLU* 4.5 12.4 - - + +
397D THR* 2.7 52.2 + - - +
400D THR* 4.7 10.0 + - - +
401D TRP* 5.1 9.2 - - - +
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Residues in contact with LYS 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C TYR* 3.3 26.7 + - + +
353C LYS 3.8 15.5 + - - +
354C TYR* 3.6 37.9 - - + +
370C GLU 3.0 14.2 + - - +
371C ALA 3.7 7.0 - - - +
373C GLN* 1.3 77.2 - - - +
375C ILE* 1.3 62.2 + - + +
377C THR* 3.4 5.9 + - - +
378C GLU* 3.1 39.7 + - + +
710E G 5.3 0.8 + - - -
711E C 3.4 27.2 + - - +
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Residues in contact with ILE 375 (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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327C ALA* 4.0 15.7 - - + -
329C ILE* 3.4 31.4 - - + -
339C TYR* 3.6 42.2 - - + -
341C ILE* 4.1 17.3 - - + -
354C TYR* 6.0 0.4 - - + -
371C ALA* 2.9 29.4 + - + +
374C LYS* 1.3 74.1 - - + +
376C THR* 1.3 54.9 + - - +
378C GLU* 3.3 7.3 + - - +
379C SER* 2.8 38.0 + - - +
389C PHE* 3.7 24.2 - - + -
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Residues in contact with THR 376 (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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372C VAL* 2.5 28.0 + - - +
373C GLN* 3.3 8.4 + - - +
375C ILE* 1.3 75.2 - - - +
377C THR* 1.3 63.9 + - - +
379C SER* 3.2 7.4 + - - -
380C ILE* 3.0 26.4 + - + +
386C THR* 3.9 25.8 - - + +
387C PRO* 4.5 2.0 - - - -
389C PHE* 3.7 18.1 - - - -
412C PRO* 4.2 4.2 - - - +
400D THR* 3.9 24.7 - - + -
401D TRP* 4.0 11.7 + - + -
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Residues in contact with THR 377 (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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373C GLN* 2.9 19.8 + - - +
374C LYS* 3.8 4.5 - - - +
376C THR* 1.3 72.7 - - - +
378C GLU* 1.3 64.8 + - - +
380C ILE* 3.2 9.0 + - - +
381C VAL* 3.2 28.1 + - + +
25D PRO* 5.5 6.1 - - + +
400D THR* 3.6 22.1 + - - +
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Residues in contact with GLU 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C TYR* 3.0 27.1 + - - -
341C ILE* 4.2 5.8 - - + +
350C LYS* 3.4 34.7 + - - +
374C LYS* 3.1 33.8 + - - +
375C ILE* 3.5 8.8 - - - +
377C THR* 1.3 75.3 - - - +
379C SER* 1.3 65.3 + - - +
381C VAL* 3.1 8.7 + - + +
382C ILE* 3.0 37.5 + - + +
383C TRP* 5.7 1.1 - - + -
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Residues in contact with SER 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C LEU* 5.0 0.4 - - - -
341C ILE* 4.7 1.7 - - - +
375C ILE* 2.8 21.0 + - - +
376C THR 3.5 2.9 - - - -
378C GLU* 1.3 73.8 - - - +
380C ILE* 1.3 59.2 + - - +
383C TRP* 2.8 56.1 + - - -
384C GLY 3.4 0.5 + - - -
385C LYS 3.4 12.5 - - - +
387C PRO* 3.1 43.5 - - - +
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Residues in contact with ILE 380 (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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376C THR* 3.0 26.5 + - + +
377C THR* 3.7 8.3 - - - +
378C GLU 3.2 0.6 - - - -
379C SER* 1.3 73.5 - - - +
381C VAL* 1.3 68.9 + - - +
384C GLY* 2.8 26.3 + - - +
385C LYS 3.7 17.5 - - - +
386C THR* 3.9 17.5 - - - +
25D PRO* 4.2 16.8 - - + +
26D LEU* 3.8 28.6 - - - +
27D THR* 4.3 17.7 - - + +
135D ILE* 5.4 0.9 - - - +
400D THR* 4.7 14.6 - - + +
401D TRP* 6.1 1.3 - - + -
404D GLU* 6.0 0.7 - - - +
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Residues in contact with VAL 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C THR* 3.2 15.3 + - + +
378C GLU* 3.1 10.4 + - + +
380C ILE* 1.3 77.6 - - - +
382C ILE* 1.3 70.1 + - + +
25D PRO* 3.6 32.8 - - + -
135D ILE* 4.0 0.9 - - - -
136D ASN* 2.9 35.8 + - - +
137D ASN* 5.3 7.4 - - - +
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Residues in contact with ILE 382 (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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96C HIS* 3.9 26.5 - - + +
98C ALA 4.3 0.4 - - - -
99C GLY* 3.6 22.5 - - - +
350C LYS* 4.2 21.1 - - + +
378C GLU* 3.0 34.3 + - + +
381C VAL* 1.3 87.0 - - + +
383C TRP* 1.3 93.2 + - + +
135D ILE* 3.4 7.1 - - - +
136D ASN* 3.2 30.3 + - - +
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Residues in contact with TRP 383 (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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98C ALA* 2.9 35.3 + - + -
99C GLY* 4.0 3.1 - - - -
319C TYR* 3.4 51.5 + + + +
325C LEU* 3.2 31.4 - - + -
341C ILE* 3.9 29.6 - - + -
349C LEU* 4.1 21.0 - - + +
350C LYS* 4.0 20.0 - - + -
378C GLU* 5.2 0.7 - - - -
379C SER* 2.8 46.0 + - - +
382C ILE* 1.3 95.5 - - + +
384C GLY* 1.3 63.8 + - - +
385C LYS* 3.1 8.7 + - + +
28D GLU* 4.5 5.9 - - - +
135D ILE* 4.0 13.6 - - - +
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Residues in contact with GLY 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C SER 3.4 0.2 + - - -
380C ILE* 2.8 23.6 + - - -
382C ILE 3.6 1.0 - - - -
383C TRP* 1.3 78.4 - - - +
385C LYS* 1.3 58.2 + - - +
26D LEU 4.2 4.5 - - - -
27D THR* 3.4 11.0 - - - -
28D GLU* 2.9 29.6 + - - +
29D GLU 4.8 0.2 + - - -
135D ILE* 4.0 20.7 - - - +
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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