Contacts of the helix formed by residues 463 - 473 (chain C) in PDB entry 3VI7
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 GLN 463 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290B ALA* 3.3 32.3 - - + +
293B ASP* 3.6 18.5 - - + +
294B THR* 3.0 29.2 + - - +
297B ASP* 3.0 23.2 + - - -
450C LYS* 5.9 3.8 - - - +
452C PRO 3.9 8.1 + - - -
462C HIS* 1.4 95.3 - - + +
464C SER* 1.3 66.8 + - - +
465C LEU* 3.4 2.2 + - - +
466C ALA* 3.2 6.8 + - + +
467C ILE* 3.0 18.3 + - - +
600C GSH 3.0 37.7 + - - +
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Residues in contact with SER 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414C ARG* 3.1 38.3 + - - +
417C ILE* 4.4 4.1 - - - +
418C ILE* 4.1 12.9 - - - +
452C PRO* 3.6 17.5 - - - +
463C GLN* 1.3 70.9 - - - +
465C LEU* 1.3 64.7 + - - +
467C ILE* 3.5 2.8 + - - +
468C ALA* 3.0 28.1 + - - +
552C TYR* 5.3 0.7 + - - -
600C GSH 2.5 32.8 + - - -
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Residues in contact with LEU 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B ASP* 4.2 16.1 + - - +
414C ARG* 4.7 1.3 - - - +
417C ILE* 4.3 5.4 - - + -
463C GLN* 3.4 1.8 + - - +
464C SER* 1.3 87.6 - - - +
466C ALA* 1.3 61.1 + - - +
467C ILE 3.3 0.2 - - - -
468C ALA* 3.8 3.0 - - - +
469C ARG* 3.0 40.0 + - - +
492C VAL* 3.9 29.4 - - + -
493C ASP* 4.0 13.0 - - - +
496C ASP* 3.6 30.3 - - - +
548C TRP* 3.9 16.6 - - + -
552C TYR* 3.9 25.8 - - + +
600C GSH 4.6 2.0 + - - +
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Residues in contact with ALA 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B CYS* 3.7 19.1 - - - +
289B ASP* 3.6 26.2 - - + +
290B ALA* 3.7 15.7 - - - +
293B ASP* 4.4 5.1 + - - +
462C HIS 3.9 4.5 - - - +
463C GLN* 3.2 12.2 + - + +
465C LEU* 1.3 76.6 - - - +
467C ILE* 1.3 57.6 + - - +
469C ARG* 3.5 13.9 + - - +
470C TYR* 2.9 29.3 + - - +
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Residues in contact with ILE 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B CYS* 4.2 2.5 - - - -
418C ILE* 3.6 28.9 - - + -
452C PRO 4.5 3.4 - - - +
453C ILE 4.5 2.5 - - - -
454C LEU* 3.7 41.3 - - + +
461C LEU* 3.8 27.6 - - + +
462C HIS* 3.6 22.2 - - - +
463C GLN 3.0 18.3 + - - +
464C SER 3.6 6.3 - - - +
466C ALA* 1.3 76.8 - - - +
468C ALA* 1.3 56.9 + - - +
470C TYR* 3.1 8.1 + - - +
471C LEU* 2.8 35.5 + - + +
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Residues in contact with ALA 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417C ILE* 4.0 11.9 - - + -
418C ILE* 4.5 3.1 - - + +
421C ILE* 3.5 26.5 - - + +
464C SER 3.0 17.7 + - - +
465C LEU* 3.8 1.8 - - - +
467C ILE* 1.3 74.5 - - - +
469C ARG* 1.3 64.5 + - - +
471C LEU* 3.4 2.3 + - - -
472C THR* 2.9 31.5 + - - +
548C TRP* 3.6 24.5 - - + -
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Residues in contact with ARG 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B ARG* 3.4 43.2 - - - +
273B LYS* 6.0 2.0 - - - +
289B ASP* 3.0 35.2 + - - +
293B ASP* 5.4 3.0 + - - -
465C LEU* 3.0 28.0 + - - +
466C ALA* 3.7 6.0 - - - +
468C ALA* 1.3 76.4 - - - +
470C TYR* 1.3 64.4 + - - +
472C THR* 3.0 8.8 + - - +
473C LYS* 3.0 26.1 + - + +
489C ASP* 2.8 35.0 + - - +
492C VAL* 5.3 1.0 - - - +
493C ASP* 4.9 8.7 + - - -
548C TRP* 3.9 24.5 - - + +
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Residues in contact with TYR 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B GLU* 3.5 46.8 - - + +
283B MET* 3.6 32.8 - - + +
286B CYS* 3.9 18.6 - - + -
404C TYR* 4.9 6.4 + - - -
456C VAL* 4.9 8.0 - - + +
461C LEU* 3.7 23.8 - - + -
466C ALA 2.9 16.4 + - - +
467C ILE* 3.1 8.3 + - - +
469C ARG* 1.3 77.3 - - - +
471C LEU* 1.3 82.0 + - + +
472C THR 3.3 0.9 + - - -
473C LYS* 3.6 17.4 + - + +
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Residues in contact with LEU 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C TYR* 4.1 22.7 - - + +
418C ILE* 4.0 11.4 - - + -
421C ILE* 3.9 20.9 - - + -
422C PHE* 3.7 40.8 - - + -
425C LEU* 3.5 22.7 - - + +
427C ILE* 6.4 1.3 - - + -
454C LEU* 4.3 2.9 - - + -
467C ILE* 2.8 38.7 + - + +
468C ALA* 3.9 3.4 - - - +
469C ARG 3.2 0.2 - - - -
470C TYR* 1.3 92.0 - - + +
472C THR* 1.3 59.2 + - - +
473C LYS 3.4 1.0 - - - +
475C THR* 3.7 4.9 - - - +
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Residues in contact with THR 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421C ILE* 3.6 33.9 - - + -
425C LEU* 5.2 0.2 - - - -
468C ALA 2.9 18.8 + - - +
469C ARG* 3.1 8.1 + - - +
471C LEU* 1.3 75.4 - - - +
473C LYS* 1.3 67.6 - - - +
474C ASN 3.3 0.3 + - - -
475C THR* 2.8 29.1 + - - -
477C LEU* 3.9 21.8 - - + -
478C ALA* 3.6 11.2 - - - +
548C TRP* 3.4 29.9 + - + -
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Residues in contact with LYS 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B GLU* 3.8 33.7 + - + +
285B GLN* 2.8 35.9 + - - +
469C ARG* 3.0 16.9 + - + +
470C TYR* 3.7 13.8 - - + +
471C LEU 3.4 1.5 - - - +
472C THR* 1.3 80.8 + - - +
474C ASN* 1.3 91.5 + - - +
475C THR* 3.2 6.2 + - - +
478C ALA* 4.9 4.5 - - - -
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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