Contacts of the helix formed by residues 408 - 426 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D PHE* 3.5 1.9 - - - +
407D THR* 1.3 82.9 + - - +
409D ILE* 1.3 63.7 + - - +
410D GLU* 3.2 20.5 + - - +
411D GLU* 2.6 41.3 + - - +
412D PHE* 3.6 11.8 + - - +
448D LEU* 3.4 18.0 - - - +
527D ASP* 5.0 4.3 - - - -
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Residues in contact with ILE 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408D SER* 1.3 76.8 - - - +
410D GLU* 1.3 71.7 + - + +
412D PHE* 3.3 6.3 + - + +
413D LEU* 3.0 35.5 + - + +
443D VAL* 3.7 34.5 - - + +
444D PHE* 5.9 2.5 - - + -
447D GLY* 4.7 16.4 - - - -
448D LEU* 4.7 11.7 - - + +
452D LYS* 6.1 0.7 - - - +
527D ASP* 3.3 31.9 - - + +
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Residues in contact with GLU 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408D SER* 3.4 19.0 - - - +
409D ILE* 1.3 93.3 + - + +
411D GLU* 1.3 63.2 + - - +
413D LEU* 3.8 10.9 - - + +
414D GLU* 3.2 28.6 + - - +
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Residues in contact with GLU 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381D LYS* 2.7 29.0 + - - +
402D ALA 5.1 0.7 - - - +
403D GLU* 4.6 2.6 - - - +
405D SER 3.4 8.7 - - - +
406D PHE* 3.6 15.1 - - + -
407D THR* 3.0 36.4 + - - +
408D SER* 2.6 21.8 + - - +
410D GLU* 1.3 72.8 - - - +
412D PHE* 1.3 59.4 + - - +
414D GLU* 3.7 10.4 + - - +
415D PRO* 3.3 17.5 - - - +
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Residues in contact with PHE 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D TYR* 3.9 39.0 - + + -
323D ILE* 4.8 6.1 - - + -
378D VAL* 3.6 23.7 - - + +
382D LEU* 4.3 10.1 - - + -
406D PHE* 3.6 31.4 - + + -
408D SER 3.6 11.9 + - - +
409D ILE* 3.3 9.1 + - + +
410D GLU 3.2 0.6 - - - -
411D GLU* 1.3 80.4 - - - +
413D LEU* 1.3 60.8 + - - +
415D PRO* 3.4 10.2 - - - +
416D LEU* 3.6 23.8 - - + +
439D LEU* 5.3 0.7 - - + -
443D VAL* 3.6 34.8 - - + -
448D LEU* 3.7 20.6 - - + -
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Residues in contact with LEU 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409D ILE* 3.0 33.3 + - + +
410D GLU* 3.2 11.1 + - + +
412D PHE* 1.3 77.7 - - - +
414D GLU* 1.3 59.6 + - - +
415D PRO 3.4 0.2 - - - -
416D LEU* 3.1 5.7 + - + +
417D GLU* 2.8 47.1 + - - +
440D LEU* 3.8 22.9 - - + -
443D VAL* 3.6 27.1 - - + -
444D PHE* 3.5 45.1 - - + -
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Residues in contact with GLU 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410D GLU* 3.2 17.8 + - - +
411D GLU* 3.9 8.6 - - - +
413D LEU* 1.3 74.6 - - - +
415D PRO* 1.3 69.1 - - + +
417D GLU* 3.9 5.3 - - - +
418D LEU* 3.0 23.4 + - - +
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Residues in contact with PRO 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D ARG* 6.0 4.7 - - - +
374D ILE* 4.9 9.0 - - + +
375D LEU* 5.9 0.4 - - + -
377D HIS* 5.9 4.7 - - + -
378D VAL* 3.6 32.3 - - + -
406D PHE* 4.9 6.7 - - + -
411D GLU 3.3 18.6 - - - +
412D PHE 3.4 11.2 - - - +
414D GLU* 1.3 91.6 - - + +
416D LEU* 1.3 61.6 + - + +
418D LEU* 3.3 12.9 + - + +
419D CYS* 3.1 27.8 + - - -
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Residues in contact with LEU 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323D ILE* 4.0 7.6 - - + -
375D LEU* 3.9 25.1 - - + -
378D VAL* 5.0 4.9 - - + -
412D PHE* 3.6 40.4 - - + +
413D LEU* 3.1 8.4 + - - +
415D PRO* 1.3 76.9 - - + +
417D GLU* 1.3 61.0 + - - +
419D CYS* 3.1 10.1 + - - +
420D TYR* 3.0 20.8 + - - +
436D LEU* 4.3 11.1 - - + +
439D LEU* 3.8 31.0 - - + -
440D LEU* 3.7 21.8 - - + -
443D VAL* 4.1 14.6 - - + -
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Residues in contact with GLU 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D TYR* 2.5 40.8 + - + +
413D LEU* 2.8 46.1 + - + +
414D GLU* 4.2 3.9 - - - +
416D LEU* 1.3 73.0 - - - +
418D LEU* 1.3 61.9 + - - +
420D TYR* 3.7 8.6 - - - +
421D LYS* 3.0 24.9 + - - +
440D LEU* 4.3 10.3 - - + -
444D PHE* 4.6 4.2 - - - -
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Residues in contact with LEU 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D ASN* 5.0 4.3 - - - +
338D GLU* 3.5 38.4 - - + +
339D LEU* 4.1 29.2 - - + +
342D ARG* 4.1 32.1 - - + +
374D ILE* 5.2 7.4 - - + -
414D GLU 3.0 14.9 + - - +
415D PRO* 3.3 17.0 - - + +
417D GLU* 1.3 78.9 - - - +
419D CYS* 1.3 56.2 + - - +
421D LYS* 3.9 4.1 - - + +
422D SER* 3.0 26.5 + - - -
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Residues in contact with CYS 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D LEU* 5.2 2.0 - - + -
339D LEU* 4.0 9.9 - - - -
371D TYR* 3.9 15.9 - - + -
374D ILE* 3.4 29.8 - - - -
375D LEU* 4.4 16.8 - - - -
415D PRO 3.1 19.1 - - - -
416D LEU* 3.1 9.6 + - - +
418D LEU* 1.3 72.8 - - - +
420D TYR* 1.3 61.9 + - - +
422D SER* 3.1 0.3 + - - -
423D LEU* 2.8 35.5 + - + +
436D LEU* 4.1 16.4 - - + -
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Residues in contact with TYR 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D TYR* 4.3 21.8 - + - +
416D LEU 3.0 12.7 + - - +
417D GLU* 3.7 12.3 - - - +
418D LEU 3.3 0.4 - - - -
419D CYS* 1.3 76.5 - - - +
421D LYS* 1.3 64.3 + - - +
423D LEU* 3.5 1.6 + - - +
424D CYS* 3.1 48.6 + - - -
429D LYS* 3.7 16.0 + - - -
432D ALA* 3.7 24.5 - - + -
433D ASP* 2.6 29.0 + - - -
436D LEU* 3.6 14.7 - - + +
437D LEU* 4.5 15.8 - - + +
440D LEU* 3.8 22.4 - - + -
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Residues in contact with LYS 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D ASN* 3.9 9.6 - - - +
338D GLU* 5.0 9.7 + - - +
417D GLU 3.0 16.7 + - - +
418D LEU* 4.0 5.4 - - + +
420D TYR* 1.3 82.0 - - + +
422D SER* 1.3 57.6 + - - +
424D CYS* 3.5 4.0 + - + +
425D ASP* 2.9 65.0 + - - +
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Residues in contact with SER 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335D CYS* 3.4 1.7 - - - -
336D ASN* 2.9 43.6 + - - +
339D LEU* 3.4 21.5 - - - +
371D TYR* 3.0 14.3 + - - -
418D LEU 3.0 18.3 + - - -
419D CYS 3.7 1.1 - - - -
421D LYS* 1.3 75.2 - - - +
423D LEU* 1.3 65.0 + - - +
425D ASP* 3.7 0.9 - - - +
426D CYS* 3.1 26.3 + - - -
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Residues in contact with LEU 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D LEU* 4.3 22.9 - - + -
332D MET* 4.4 14.8 - - + -
371D TYR* 3.5 30.7 - - + +
419D CYS 2.8 22.9 + - - +
422D SER* 1.3 73.7 - - - +
424D CYS* 1.3 59.3 + - - +
426D CYS* 3.2 7.4 + - - -
428D ASP* 2.8 48.8 + - + +
431D ILE* 4.3 7.4 - - + -
432D ALA* 3.8 38.8 - - + +
436D LEU* 3.9 13.9 - - + -
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Residues in contact with CYS 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420D TYR* 3.1 49.1 + - - +
421D LYS* 4.0 4.7 - - + +
423D LEU* 1.3 72.1 - - - +
425D ASP* 1.3 69.0 + - - +
427D GLY* 2.9 15.2 + - - -
429D LYS* 3.6 44.9 + - + +
432D ALA* 4.1 2.7 - - - -
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Residues in contact with ASP 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D ASN* 2.8 39.2 + - - +
421D LYS* 2.9 50.4 + - - +
422D SER 3.7 2.2 - - - +
423D LEU 3.4 0.2 - - - -
424D CYS* 1.3 77.3 - - - +
426D CYS* 1.3 58.7 + - - +
427D GLY 3.4 3.3 + - - -
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Residues in contact with CYS 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LEU* 5.3 1.2 - - - +
226C ARG* 3.0 23.2 + - - -
334D ARG* 3.8 15.6 - - + +
335D CYS* 3.5 42.8 - - - -
336D ASN* 4.0 2.2 - - - -
371D TYR* 5.0 0.2 - - - +
422D SER 3.1 20.2 + - - +
423D LEU* 3.8 4.9 - - - +
424D CYS 3.1 1.2 - - - -
425D ASP* 1.3 76.8 - - - +
427D GLY* 1.3 57.7 + - - +
428D ASP* 3.3 10.8 - - - +
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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