Contacts of the helix formed by residues 459 - 473 (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 459 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457D GLN 3.8 0.4 + - - -
458D GLU* 1.3 74.8 - - - +
460D GLU* 1.3 67.4 + - - +
462D HIS* 3.2 19.6 + - - +
463D THR* 3.3 13.6 + - - -
534D ILE* 3.9 13.5 - - - +
535D SER 2.2 32.9 + - - -
536D MET* 2.4 30.6 + - - +
537D ALA* 3.4 1.4 + - - -
538D THR* 5.6 0.9 - - - -
542D ASP* 4.3 18.0 - - - +
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Residues in contact with GLU 460 (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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458D GLU* 3.3 15.8 - - - +
459D SER* 1.3 83.2 - - - +
461D ARG* 1.3 60.5 + - + +
462D HIS 3.2 1.8 - - - -
463D THR* 3.4 20.9 + - - +
464D ASP* 2.8 35.7 + - - +
479D ARG* 2.5 42.2 + - - +
486D ARG* 4.7 6.9 + - - -
542D ASP* 5.2 2.6 - - - +
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Residues in contact with ARG 461 (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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293D ARG 5.5 2.6 + - - -
295D GLY* 5.7 3.4 - - - +
457D GLN* 3.6 38.3 + - + +
458D GLU* 3.3 27.2 + - + +
460D GLU* 1.3 77.4 - - - +
462D HIS* 1.3 60.5 + - - +
464D ASP* 3.6 12.4 + - - +
465D VAL* 3.4 24.1 + - - +
510D GLU* 2.9 69.2 + - - +
511D ILE* 5.4 0.5 - - - +
513D ASP* 3.9 11.9 + - - +
514D VAL* 3.6 18.7 - - + +
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Residues in contact with HIS 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457D GLN* 3.7 18.4 - - + +
458D GLU 3.2 21.9 + - - -
459D SER* 3.2 10.1 + - - +
460D GLU 3.2 0.2 - - - -
461D ARG* 1.3 74.5 - - - +
463D THR* 1.3 66.3 + - - +
464D ASP 3.0 1.3 - - - -
465D VAL* 2.8 14.9 + - - +
466D ILE* 3.0 20.6 - - + +
514D VAL* 4.2 12.1 - - + -
518D PHE* 4.5 1.3 - + - -
532D TYR* 2.8 37.5 + + - -
534D ILE* 4.3 7.7 - - + +
542D ASP 5.1 1.2 + - - +
545D ALA* 4.9 7.6 - - + -
546D VAL* 3.5 30.0 - - + +
549D LEU* 4.1 24.7 - - + -
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Residues in contact with THR 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459D SER 3.3 8.0 + - - -
460D GLU* 3.3 29.7 + - - +
462D HIS* 1.3 76.4 - - - +
464D ASP* 1.3 58.0 + - - +
466D ILE* 3.9 1.2 - - - +
467D ASP* 2.9 29.9 + - - +
478D TYR* 3.8 31.2 - - + -
479D ARG* 4.2 23.1 - - - -
486D ARG* 4.0 24.2 + - - +
542D ASP* 4.8 5.2 + - - -
545D ALA* 5.8 0.6 - - - +
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Residues in contact with ASP 464 (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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460D GLU* 2.8 24.4 + - - +
461D ARG* 3.6 21.7 - - - +
462D HIS 3.0 0.2 + - - -
463D THR* 1.3 76.6 - - - +
465D VAL* 1.3 61.8 + - - +
467D ASP* 3.5 5.3 + - - +
468D ALA* 3.1 22.3 + - - +
479D ARG* 2.5 33.1 + - - +
510D GLU* 4.4 7.6 - - + +
511D ILE* 3.7 19.1 - - + +
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Residues in contact with VAL 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461D ARG 3.4 15.9 - - - +
462D HIS* 2.8 13.6 + - - +
464D ASP* 1.3 72.8 - - - +
466D ILE* 1.3 62.5 + - - +
468D ALA* 3.0 14.6 + - - +
469D ILE* 3.0 21.7 + - + +
505D LEU* 5.7 1.8 - - + -
511D ILE* 3.9 31.4 - - + +
514D VAL* 3.8 26.7 - - + -
515D ILE* 4.0 18.4 - - + -
549D LEU* 3.7 28.3 - - + -
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Residues in contact with ILE 466 (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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462D HIS 3.0 31.4 + - - +
463D THR* 4.5 0.9 - - - +
465D VAL* 1.3 75.0 - - - +
467D ASP* 1.3 58.0 + - - +
469D ILE* 3.2 11.5 + - + +
470D THR* 2.9 29.3 + - + +
478D TYR* 3.5 39.7 - - + -
489D TRP* 3.9 20.2 - - + -
490D LEU* 5.1 0.7 - - + -
500D LEU* 6.2 0.2 - - + -
545D ALA* 4.1 20.9 - - + -
548D LEU* 5.0 11.0 - - + -
549D LEU* 3.5 37.7 - - + -
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Residues in contact with ASP 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463D THR 2.9 19.2 + - - +
464D ASP* 3.9 5.6 - - - +
466D ILE* 1.3 76.7 - - - +
468D ALA* 1.3 56.9 + - - +
470D THR* 3.1 5.2 + - - -
471D THR* 3.0 42.5 + - - -
477D SER* 2.5 29.8 + - - -
478D TYR* 3.1 9.3 + - - +
479D ARG* 2.8 35.3 + - + +
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Residues in contact with ALA 468 (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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464D ASP 3.1 12.9 + - - +
465D VAL* 3.0 10.2 + - - +
467D ASP* 1.3 77.9 + - - +
469D ILE* 1.3 60.6 + - - +
471D THR* 4.1 4.4 - - - -
472D HIS* 3.2 25.3 + - - +
505D LEU* 3.6 15.2 - - + +
506D PRO* 4.6 8.9 - - + +
511D ILE* 3.8 20.9 - - + -
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Residues in contact with ILE 469 (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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465D VAL* 3.0 28.8 + - + +
466D ILE* 3.2 15.4 + - + +
468D ALA* 1.3 74.6 - - - +
470D THR* 1.3 68.2 + - + +
472D HIS* 3.2 2.3 + - - +
473D LEU* 3.1 36.5 + - + +
475D ILE* 6.0 0.2 - - + -
489D TRP* 5.3 0.9 - - + -
500D LEU* 3.7 49.1 - - + +
501D LEU* 4.2 18.8 - - + -
502D PRO* 4.5 2.7 - - + -
505D LEU* 3.6 24.5 - - + -
549D LEU* 4.5 10.8 - - + -
552D GLU* 6.4 0.9 - - + -
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Residues in contact with THR 470 (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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466D ILE* 2.9 18.1 + - + +
467D ASP* 3.1 10.0 + - - -
469D ILE* 1.3 75.0 - - - +
471D THR* 1.3 62.4 + - - +
473D LEU 3.5 0.3 + - - -
474D GLY 3.3 2.6 + - - -
475D ILE* 2.9 41.4 + - + +
476D GLY 2.9 23.8 + - - +
477D SER* 3.9 0.2 - - - -
478D TYR* 3.2 28.0 + - + -
481D TRP* 4.2 9.0 - - + -
489D TRP* 4.0 31.6 - - + -
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Residues in contact with THR 471 (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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467D ASP* 3.0 30.2 + - - -
468D ALA* 4.1 4.5 - - - -
470D THR* 1.3 75.6 + - - +
472D HIS* 1.3 65.0 + - - +
474D GLY* 3.2 12.8 + - - -
476D GLY 3.5 12.3 + - - +
477D SER* 4.4 5.5 - - - -
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Residues in contact with HIS 472 (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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497B LYS* 3.7 31.7 - - + +
468D ALA 3.2 20.6 + - - +
469D ILE 3.2 3.1 + - - +
471D THR* 1.3 80.0 - - - +
473D LEU* 1.3 74.5 + - + +
474D GLY 3.2 0.7 + - - -
502D PRO* 3.9 9.2 - - + -
504D ASP* 3.5 23.9 + - - -
505D LEU* 3.4 24.5 - - + -
506D PRO* 3.7 25.2 - - + +
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Residues in contact with LEU 473 (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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497B LYS* 3.7 20.0 - - + +
498B ARG* 3.7 34.5 - - + -
469D ILE* 3.1 17.9 + - + +
470D THR 3.5 0.2 + - - -
472D HIS* 1.3 85.2 - - + +
474D GLY* 1.3 60.9 + - - +
475D ILE* 3.5 19.5 + - + +
500D LEU* 3.9 27.8 - - + +
502D PRO* 3.4 28.0 - - + -
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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
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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