Contacts of the helix formed by residues 408 - 426 (chain H) in PDB entry 6V3O
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 408 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406H PHE* 3.6 1.2 - - - +
407H THR* 1.3 79.9 + - - +
409H ILE* 1.3 66.3 + - - +
410H GLU* 3.3 17.6 + - - +
411H GLU* 3.2 25.7 + - - +
412H PHE* 3.3 15.9 + - - +
448H LEU* 3.5 12.5 - - - +
527H ASP* 5.5 1.1 - - - -
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Residues in contact with ILE 409 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408H SER* 1.3 73.5 - - - +
410H GLU* 1.3 65.8 + - - +
412H PHE* 3.2 7.6 + - + +
413H LEU* 2.8 36.4 + - + +
443H VAL* 3.3 38.4 - - + +
444H PHE* 6.0 0.4 - - - -
447H GLY* 4.2 6.5 - - - -
448H LEU* 3.5 37.2 - - + +
527H ASP* 4.1 26.9 - - + +
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Residues in contact with GLU 410 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408H SER* 3.3 20.0 + - - +
409H ILE* 1.3 84.8 + - - +
411H GLU* 1.3 61.7 + - - +
413H LEU* 3.2 11.2 + - + +
414H GLU* 3.1 28.7 + - - +
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Residues in contact with GLU 411 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381H LYS* 3.0 25.1 + - - +
402H ALA 4.9 0.5 - - - +
403H GLU* 4.3 3.5 - - - +
405H SER 3.2 13.4 - - - +
406H PHE* 3.5 14.1 - - + -
407H THR* 3.0 29.5 + - - -
408H SER* 3.2 20.3 + - - +
409H ILE 3.3 0.2 - - - -
410H GLU* 1.3 76.9 - - - +
412H PHE* 1.3 59.9 + - - +
414H GLU* 3.8 17.5 + - - +
415H PRO* 3.4 16.1 - - - +
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Residues in contact with PHE 412 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319H TYR* 3.9 39.9 - + + -
323H ILE* 4.9 4.5 - - + -
378H VAL* 3.6 23.8 - - + -
382H LEU* 4.3 10.1 - - + -
406H PHE* 3.6 36.3 - + + -
408H SER 3.3 11.1 + - - +
409H ILE* 3.2 11.4 + - + +
410H GLU 3.2 0.4 - - - -
411H GLU* 1.3 78.9 - - - +
413H LEU* 1.3 60.1 + - - +
415H PRO* 3.2 11.1 - - - +
416H LEU* 3.7 19.0 - - + +
439H LEU* 5.4 0.7 - - + -
443H VAL* 3.7 38.8 - - + -
447H GLY 5.8 0.2 - - - -
448H LEU* 4.2 16.4 - - + -
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Residues in contact with LEU 413 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409H ILE* 2.8 31.7 + - + +
410H GLU* 3.2 11.4 + - + +
412H PHE* 1.3 78.6 - - - +
414H GLU* 1.3 65.6 + - - +
416H LEU* 3.1 7.2 + - + +
417H GLU* 2.9 40.4 + - - +
440H LEU* 3.7 24.2 - - + -
443H VAL* 3.7 24.9 - - + -
444H PHE* 3.5 46.2 - - + -
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Residues in contact with GLU 414 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410H GLU* 3.1 18.0 + - - +
411H GLU* 3.9 16.7 - - - +
413H LEU* 1.3 74.2 - - - +
415H PRO* 1.3 70.7 - - + +
417H GLU* 3.6 5.6 + - - +
418H LEU* 3.1 22.2 + - - +
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Residues in contact with PRO 415 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342H ARG* 5.3 11.9 - - - +
374H ILE* 4.1 14.8 - - + +
375H LEU* 6.0 0.2 - - - -
377H HIS* 6.0 3.6 - - + -
378H VAL* 3.6 31.6 - - + -
406H PHE* 4.9 8.3 - - + -
411H GLU 3.4 9.0 - - - +
412H PHE 3.2 16.4 - - - +
414H GLU* 1.3 95.2 - - + +
416H LEU* 1.3 61.3 + - - +
418H LEU* 3.2 11.9 + - + +
419H CYS* 3.1 25.9 + - - -
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Residues in contact with LEU 416 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323H ILE* 3.9 8.5 - - + -
375H LEU* 3.8 25.1 - - + -
378H VAL* 4.5 11.0 - - + -
412H PHE* 3.7 26.5 - - + +
413H LEU* 3.1 6.8 + - + +
415H PRO* 1.3 75.8 - - - +
417H GLU* 1.3 59.0 + - - +
419H CYS* 3.2 8.8 + - - +
420H TYR* 3.0 26.0 + - - +
436H LEU* 4.3 13.7 - - + +
439H LEU* 3.7 32.1 - - + -
440H LEU* 3.8 21.2 - - + +
443H VAL* 4.2 21.8 - - + -
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Residues in contact with GLU 417 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278H TYR* 2.4 40.0 + - + +
413H LEU* 2.9 39.9 + - + +
414H GLU* 4.1 4.5 - - - +
416H LEU* 1.3 73.8 - - - +
418H LEU* 1.3 65.9 + - - +
420H TYR* 3.2 8.1 + - - +
421H LYS* 3.0 25.5 + - - +
440H LEU* 4.2 11.2 - - + -
444H PHE* 5.0 2.5 - - - -
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Residues in contact with LEU 418 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336H ASN* 5.0 4.5 - - - +
338H GLU* 3.7 42.0 - - + +
339H LEU* 4.2 31.4 - - + +
342H ARG* 4.6 22.2 - - + +
374H ILE* 4.7 11.7 - - + -
414H GLU 3.1 14.7 + - - +
415H PRO* 3.2 13.7 + - + +
417H GLU* 1.3 76.9 - - - +
419H CYS* 1.3 57.3 + - - +
421H LYS* 3.5 5.4 + - + +
422H SER* 3.0 29.0 + - - -
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Residues in contact with CYS 419 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330H LEU* 5.2 3.1 - - + -
339H LEU* 4.0 7.2 - - - -
371H TYR* 3.9 28.0 - - + -
374H ILE* 4.0 24.7 - - - -
375H LEU* 4.7 14.6 - - + -
415H PRO 3.1 18.2 + - - +
416H LEU* 3.7 8.7 - - - +
417H GLU 3.2 0.2 - - - -
418H LEU* 1.3 73.7 - - - +
420H TYR* 1.3 60.8 + - - +
422H SER* 3.7 6.4 - - - -
423H LEU* 2.9 34.0 + - - +
436H LEU* 4.0 14.1 - - + -
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Residues in contact with TYR 420 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278H TYR* 4.3 23.6 - + + +
416H LEU 3.0 13.8 + - - +
417H GLU* 3.2 11.2 + - - +
419H CYS* 1.3 77.7 - - - +
421H LYS* 1.3 61.2 + - + +
423H LEU* 3.8 2.1 - - - +
424H CYS* 3.0 51.6 + - - -
429H LYS* 3.7 15.6 + - - -
432H ALA* 3.7 27.1 - - + +
433H ASP* 2.6 29.0 + - - -
436H LEU* 3.7 13.4 - - + +
437H LEU* 4.6 14.8 - - + +
440H LEU* 3.9 20.2 - - + -
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Residues in contact with LYS 421 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336H ASN* 3.8 11.0 - - - +
338H GLU* 4.7 12.1 - - - +
417H GLU 3.0 15.4 + - - +
418H LEU* 4.0 5.6 - - + +
420H TYR* 1.3 77.5 - - + +
422H SER* 1.3 55.8 + - - +
424H CYS* 3.2 6.5 + - + -
425H ASP* 2.7 80.3 + - - +
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Residues in contact with SER 422 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335H CYS* 3.6 0.5 - - - -
336H ASN* 3.1 37.3 + - - +
339H LEU* 3.8 10.4 - - - +
371H TYR* 2.6 34.7 + - - -
418H LEU 3.0 19.4 + - - -
419H CYS 3.7 4.5 - - - -
421H LYS* 1.3 75.9 - - - +
423H LEU* 1.3 62.3 + - - +
425H ASP* 3.3 1.6 + - - +
426H CYS* 3.2 29.6 + - - -
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Residues in contact with LEU 423 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330H LEU* 4.4 20.4 - - + -
332H MET* 3.7 27.4 - - + -
334H ARG 5.6 0.2 - - - +
371H TYR* 3.9 20.9 - - + +
419H CYS 2.9 20.7 + - - +
420H TYR 3.8 3.6 - - - +
422H SER* 1.3 76.8 + - - +
424H CYS* 1.3 60.9 + - - +
426H CYS* 3.5 4.6 + - - -
428H ASP* 2.8 54.3 + - + +
431H ILE* 4.8 2.7 - - + -
432H ALA* 3.8 32.5 - - + +
436H LEU* 3.8 15.3 - - + -
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Residues in contact with CYS 424 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420H TYR* 3.0 45.0 + - - +
421H LYS* 3.2 8.0 + - + +
423H LEU* 1.3 74.1 - - - +
425H ASP* 1.3 70.0 + - - +
427H GLY* 3.2 12.6 + - - -
429H LYS* 3.6 47.5 + - + +
432H ALA* 4.5 1.8 - - - -
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Residues in contact with ASP 425 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336H ASN* 2.7 36.5 + - - +
421H LYS* 2.7 54.3 + - - +
422H SER 3.3 2.6 + - - +
424H CYS* 1.3 75.8 - - - +
426H CYS* 1.3 59.7 + - - +
427H GLY 3.2 3.2 + - - -
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Residues in contact with CYS 426 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G LEU* 5.5 0.2 - - - +
226G ARG* 3.0 27.0 + - - +
334H ARG* 4.0 12.6 - - + +
335H CYS* 3.5 41.1 - - - -
336H ASN* 3.9 1.6 - - - -
371H TYR* 4.5 0.2 - - - -
422H SER 3.2 18.9 + - - +
423H LEU* 4.2 0.7 - - - +
424H CYS 3.2 1.0 - - - -
425H ASP* 1.3 78.3 - - - +
427H GLY* 1.3 57.5 + - - +
428H ASP* 3.3 13.3 + - - +
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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
------------------------------------------------------------
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