Contacts of the helix formed by residues 408 - 426 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406E PHE* 3.5 1.7 + - - +
407E THR* 1.3 84.6 + - - +
409E ILE* 1.3 63.3 + - - +
410E GLU* 3.3 17.3 + - - +
411E GLU* 3.1 24.9 + - - +
412E PHE* 3.4 15.1 + - - +
448E LEU* 3.5 13.9 - - - +
527E ASP* 4.7 5.8 - - - -
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Residues in contact with ILE 409 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408E SER* 1.3 74.2 - - - +
410E GLU* 1.3 77.6 + - + +
412E PHE* 3.3 6.6 + - - +
413E LEU* 2.9 50.2 + - + +
443E VAL* 4.9 12.6 - - + +
444E PHE* 5.0 12.8 - - + -
447E GLY* 4.2 10.1 - - - -
448E LEU* 4.1 31.2 - - + +
527E ASP* 4.2 17.3 + - + +
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Residues in contact with GLU 410 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408E SER* 3.3 19.5 + - - +
409E ILE* 1.3 94.1 + - + +
411E GLU* 1.3 60.2 + - - +
413E LEU* 3.3 9.8 + - + +
414E GLU* 3.2 34.3 + - - +
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Residues in contact with GLU 411 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381E LYS* 3.9 13.2 + - - -
402E ALA 5.1 0.5 - - - +
403E GLU* 4.5 3.6 - - - +
405E SER 3.4 19.0 - - - +
406E PHE* 3.5 16.2 - - + -
407E THR* 3.1 33.9 + - - +
408E SER* 3.1 16.4 + - - +
409E ILE 3.3 0.2 - - - -
410E GLU* 1.3 76.7 - - - +
412E PHE* 1.3 59.8 + - - +
414E GLU* 3.9 15.5 + - - +
415E PRO* 3.4 16.6 - - - +
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Residues in contact with PHE 412 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319E TYR* 4.0 42.2 - + + -
323E ILE* 4.9 4.0 - - + -
378E VAL* 3.7 23.6 - - + -
382E LEU* 4.3 7.2 - - + -
406E PHE* 3.7 36.0 - + + -
408E SER 3.4 10.8 + - - +
409E ILE* 3.3 7.8 + - - +
410E GLU 3.2 0.4 - - - -
411E GLU* 1.3 77.7 - - - +
413E LEU* 1.3 62.3 + - - +
415E PRO* 3.3 9.5 - - - +
416E LEU* 3.5 24.2 - - + +
439E LEU* 5.4 0.9 - - + -
443E VAL* 3.6 33.9 - - + -
447E GLY 6.0 0.4 - - - -
448E LEU* 3.8 19.1 - - + -
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Residues in contact with LEU 413 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409E ILE* 2.9 36.0 + - + +
410E GLU* 3.3 9.8 + - + +
412E PHE* 1.3 77.0 - - - +
414E GLU* 1.3 60.7 + - - +
415E PRO 3.4 0.2 - - - -
416E LEU* 3.0 6.8 + - + -
417E GLU* 2.8 45.8 + - + +
440E LEU* 3.7 23.1 - - + -
443E VAL* 3.7 24.2 - - + -
444E PHE* 3.4 47.3 - - + -
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Residues in contact with GLU 414 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410E GLU* 3.2 24.5 + - - +
411E GLU* 4.0 16.2 - - - +
413E LEU* 1.3 73.9 - - - +
415E PRO* 1.3 69.4 - - + +
417E GLU* 3.6 7.3 + - - +
418E LEU* 3.1 23.7 + - - +
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Residues in contact with PRO 415 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342E ARG* 6.2 2.9 - - - +
374E ILE* 4.0 14.8 - - + +
375E LEU* 6.1 0.2 - - - -
377E HIS* 6.1 4.3 - - + -
378E VAL* 3.6 33.0 - - + -
406E PHE* 4.8 7.9 - - + -
411E GLU 3.4 13.5 - - - +
412E PHE 3.3 16.2 - - - +
414E GLU* 1.3 92.2 - - + +
416E LEU* 1.3 61.0 + - - +
418E LEU* 3.3 11.1 + - + +
419E CYS* 3.1 27.3 + - - -
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Residues in contact with LEU 416 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323E ILE* 4.0 14.8 - - + -
375E LEU* 4.1 15.3 - - + -
378E VAL* 4.7 9.0 - - + -
412E PHE* 3.5 29.4 - - + +
413E LEU* 3.0 8.4 + - + +
415E PRO* 1.3 77.4 - - + +
417E GLU* 1.3 58.2 + - - +
419E CYS* 3.2 8.3 + - - +
420E TYR* 3.1 25.1 + - - +
436E LEU* 4.2 11.2 - - + +
439E LEU* 3.9 27.6 - - + -
440E LEU* 3.7 22.7 - - + -
443E VAL* 3.9 27.4 - - + -
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Residues in contact with GLU 417 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278E TYR* 2.6 39.2 + - - +
413E LEU* 2.8 42.3 + - + +
414E GLU* 4.2 6.0 + - - +
416E LEU* 1.3 71.0 - - - +
418E LEU* 1.3 64.2 + - - +
420E TYR* 3.8 7.6 - - - +
421E LYS* 3.1 32.4 + - + +
440E LEU* 4.1 13.5 - - + -
444E PHE* 4.6 4.2 - - - -
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Residues in contact with LEU 418 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336E ASN* 4.7 4.9 - - - +
338E GLU* 3.7 40.8 - - + +
339E LEU* 4.0 33.0 - - + +
342E ARG* 4.5 24.7 - - + +
374E ILE* 5.2 5.8 - - + -
414E GLU 3.1 15.2 + - - +
415E PRO* 3.4 14.1 - - + +
416E LEU 3.2 0.2 - - - -
417E GLU* 1.3 77.5 - - - +
419E CYS* 1.3 62.8 + - - +
421E LYS* 3.4 4.5 + - + +
422E SER* 3.1 21.1 + - - -
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Residues in contact with CYS 419 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330E LEU* 5.2 3.4 - - + -
339E LEU* 4.0 15.3 - - - -
371E TYR* 3.8 25.8 - - + -
374E ILE* 4.1 24.0 - - - -
375E LEU* 4.7 15.9 - - + -
415E PRO 3.1 17.9 + - - -
416E LEU* 3.2 8.9 + - - +
418E LEU* 1.3 74.5 - - - +
420E TYR* 1.3 65.5 + - - +
423E LEU* 3.0 29.1 + - - +
436E LEU* 4.1 13.7 - - + -
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Residues in contact with TYR 420 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278E TYR* 4.2 17.4 - + + -
416E LEU 3.1 12.8 + - - +
417E GLU* 3.8 9.4 - - - +
418E LEU 3.3 0.2 - - - -
419E CYS* 1.3 78.1 - - - +
421E LYS* 1.3 80.1 + - + +
423E LEU* 3.4 3.9 + - - +
424E CYS* 3.0 50.3 + - - -
429E LYS* 3.6 15.8 + - - -
432E ALA* 3.6 28.0 - - + -
433E ASP* 2.7 28.4 + - - -
436E LEU* 3.7 12.0 - - + +
437E LEU* 4.5 13.8 - - + +
440E LEU* 3.9 22.2 - - + -
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Residues in contact with LYS 421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278E TYR* 3.2 27.7 + - - -
336E ASN* 4.0 7.4 - - - +
417E GLU* 3.1 23.2 + - + +
418E LEU* 4.1 5.2 - - + +
420E TYR* 1.3 99.2 - - + +
422E SER* 1.3 59.0 + - - +
424E CYS* 3.4 8.2 + - + +
425E ASP* 2.8 39.0 + - - +
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Residues in contact with SER 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335E CYS* 3.4 3.5 - - - +
336E ASN* 2.9 49.2 + - - +
339E LEU* 3.6 14.0 - - - +
371E TYR* 2.9 16.7 + - - -
418E LEU 3.1 17.2 + - - -
419E CYS 4.0 0.4 - - - -
421E LYS* 1.3 74.8 - - - +
423E LEU* 1.3 65.1 + - - +
425E ASP* 3.2 0.9 + - - +
426E CYS* 3.0 27.0 + - - -
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Residues in contact with LEU 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330E LEU* 4.4 15.3 - - + -
332E MET* 3.9 21.8 - - + -
371E TYR* 3.6 26.0 - - + +
419E CYS 3.0 21.8 + - - +
420E TYR 3.6 4.3 - - - +
422E SER* 1.3 76.2 + - - +
424E CYS* 1.3 54.7 + - - +
426E CYS* 3.5 4.7 + - - -
428E ASP* 2.7 56.9 + - + +
431E ILE* 4.3 9.6 - - + -
432E ALA* 3.7 34.1 - - + +
436E LEU* 3.8 13.7 - - + -
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Residues in contact with CYS 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420E TYR* 3.0 44.9 + - - +
421E LYS* 3.7 10.3 - - + +
422E SER 3.2 0.2 - - - -
423E LEU* 1.3 74.8 - - - +
425E ASP* 1.3 67.5 + - - +
427E GLY* 2.9 15.8 + - - -
429E LYS* 3.7 47.7 + - + +
432E ALA* 4.4 1.6 - - - -
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Residues in contact with ASP 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336E ASN* 2.8 36.7 + - - +
421E LYS* 2.8 32.8 + - - +
422E SER 3.2 2.6 + - - +
424E CYS* 1.3 75.7 - - - +
426E CYS* 1.3 58.5 + - - +
427E GLY 3.3 2.7 + - - -
929F PHE* 4.4 11.3 - - - -
931F ASP* 5.6 1.7 - - - +
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Residues in contact with CYS 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334E ARG* 4.1 22.7 - - + +
335E CYS* 3.6 41.3 - - - -
336E ASN* 4.1 2.0 - - - -
371E TYR* 4.8 0.9 - - - +
422E SER 3.0 19.6 + - - +
423E LEU* 4.2 3.8 - - - +
424E CYS 3.1 0.4 - - - -
425E ASP* 1.3 76.3 - - - +
427E GLY* 1.3 57.3 + - - +
428E ASP* 3.3 10.2 + - - +
226F ARG* 3.0 24.1 + - - -
928F GLU* 5.3 0.7 - - - +
929F PHE* 4.0 19.4 - - + -
931F ASP* 5.1 9.0 - - - -
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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