Contacts of the helix formed by residues 468 - 478 (chain D) in PDB entry 6VVT
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 468 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461D VAL* 3.6 14.1 - - - +
466D ALA* 4.1 0.3 - - - +
467D GLN* 1.3 81.2 - - + +
469D ILE* 1.3 68.8 + - + +
470D LYS* 2.8 37.1 + - - +
471D SER* 2.6 28.7 + - - -
472D ALA 3.0 16.8 + - - -
393F LEU* 6.0 0.9 - - + -
463F ASP* 2.9 34.3 + - - +
464F TYR* 5.0 17.5 - - + +
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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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1094C TYR* 5.1 0.4 - - + -
1098C VAL* 4.4 20.6 - - + -
457D MET* 3.6 21.9 - - + +
461D VAL* 4.3 6.5 - - - +
468D ASN* 1.3 74.2 - - + +
470D LYS* 1.3 65.9 + - + +
472D ALA* 2.8 24.9 + - - +
473D LYS 2.9 10.4 + - - -
386F VAL* 4.1 29.2 - - + +
389F VAL* 4.1 24.5 - - + -
390F SER* 4.4 14.4 - - - +
393F LEU* 3.4 30.3 - - + +
464F TYR* 5.3 2.9 - - + +
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Residues in contact with LYS 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D ASN* 2.8 19.3 + - - +
469D ILE* 1.3 80.2 - - + +
471D SER* 1.3 59.4 + - - +
473D LYS* 3.2 18.9 + - - +
474D ARG* 3.4 13.3 + - - +
386F VAL* 6.2 1.8 - - - -
390F SER* 5.6 7.0 - - - -
463F ASP* 4.7 15.0 - - + +
464F TYR* 6.0 4.9 - - + -
465F LEU* 5.9 2.5 - - + -
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Residues in contact with SER 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466D ALA* 3.8 14.4 - - - -
467D GLN* 4.1 5.7 + - - +
468D ASN* 2.6 40.3 + - - -
470D LYS* 1.3 76.1 - - - +
472D ALA* 1.3 60.1 + - - +
474D ARG* 4.0 3.5 + - - +
475D MET* 3.3 30.2 + - - +
463F ASP* 4.5 5.7 - - - +
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Residues in contact with ALA 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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457D MET* 3.5 18.2 - - + +
460D LEU* 3.2 31.6 - - + +
461D VAL* 3.3 21.8 - - + -
466D ALA* 3.7 0.4 - - - +
468D ASN 3.0 3.8 + - - -
469D ILE* 2.8 11.3 + - - +
471D SER* 1.3 76.6 - - - +
473D LYS* 1.3 62.8 + - - +
475D MET* 3.4 2.5 + - - +
476D VAL* 3.2 27.5 + - - +
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Residues in contact with LYS 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453D LYS* 3.5 24.4 - - - +
457D MET* 3.9 18.3 - - + +
469D ILE 2.9 10.5 + - - +
470D LYS* 3.2 12.7 + - - +
472D ALA* 1.3 73.4 - - - +
474D ARG* 1.3 62.1 + - - +
476D VAL* 3.0 5.4 + - - +
477D GLU* 2.9 55.7 + - - +
384F VAL* 5.9 0.4 - - - +
386F VAL* 3.9 37.6 - - + +
387F ASP* 5.1 3.4 + - - -
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Residues in contact with ARG 474 (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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470D LYS 3.4 10.1 + - - +
471D SER* 4.5 3.8 - - - +
473D LYS* 1.3 78.6 - - - +
475D MET* 1.3 60.4 + - - +
477D GLU* 4.2 15.0 - - + +
478D ARG* 2.9 63.0 + - + +
480D ARG* 3.1 44.0 - - - +
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Residues in contact with MET 475 (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 LEU* 4.0 20.2 - - + -
465D HIS* 4.1 15.7 - - - +
466D ALA* 3.4 32.1 - - + -
471D SER* 3.3 18.8 + - - +
472D ALA* 3.5 7.9 - - - +
473D LYS 3.1 0.6 - - - -
474D ARG* 1.3 82.0 - - - +
476D VAL* 1.3 57.8 + - - +
480D ARG* 3.3 65.0 + - + +
482D GLN* 4.9 7.4 - - - +
483D VAL* 3.7 18.3 - - + +
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Residues in contact with VAL 476 (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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449D LEU* 3.3 33.9 - - + +
450D GLU* 5.7 0.9 - - - +
453D LYS* 4.0 27.8 - - + -
456D VAL* 3.7 27.4 - - + -
457D MET* 4.1 10.8 - - + -
460D LEU* 3.8 10.1 - - + -
472D ALA 3.2 13.0 + - - +
473D LYS 3.0 7.2 + - - +
475D MET* 1.3 76.6 - - - +
477D GLU* 1.3 65.2 + - - +
478D ARG 3.4 0.2 - - - -
479D GLN* 3.0 19.5 + - - +
483D VAL* 4.3 5.8 - - + -
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Residues in contact with GLU 477 (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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788C ARG* 2.9 17.9 + - - -
789C ASP 5.2 0.6 - - - +
453D LYS* 3.9 17.7 - - - +
473D LYS* 2.9 50.7 + - - +
474D ARG* 3.2 14.9 + - + +
476D VAL* 1.3 78.4 - - - +
478D ARG* 1.3 59.4 + - - +
479D GLN* 3.3 8.8 + - - +
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Residues in contact with ARG 478 (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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153A LYS* 4.1 18.2 + - - +
154A ALA* 5.8 0.8 - - - +
788C ARG* 3.5 29.0 + - - +
474D ARG* 2.9 56.9 + - + +
477D GLU* 1.3 74.2 - - - +
479D GLN* 1.3 71.7 + - - +
480D ARG* 3.4 13.8 + - + +
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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
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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