Contacts of the helix formed by residues 461 - 469 (chain C) in PDB entry 5VOT
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 461 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447C ASP* 4.0 7.6 - - - +
449C LYS* 4.2 8.9 - - - +
451C GLY* 3.1 14.5 - - - -
452C ALA* 2.3 48.1 + - - +
454C ASP* 6.1 3.5 - - + +
459C ILE* 5.4 1.6 - - + +
460C TRP* 1.3 72.4 - - - +
462C GLY* 1.3 62.4 + - - +
464C VAL* 3.4 1.2 + - - +
465C GLY* 2.7 20.7 + - - -
652C SER* 3.9 19.8 + - - -
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Residues in contact with GLY 462 (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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445C VAL* 3.6 7.7 - - - +
447C ASP* 3.0 32.9 + - - -
449C LYS* 3.7 8.7 - - - -
451C GLY* 4.3 3.1 - - - -
461C ASN* 1.3 77.0 - - - +
463C MET* 1.3 56.7 + - - -
465C GLY* 2.6 23.2 + - - -
466C GLU* 2.9 12.3 + - - +
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Residues in contact with MET 463 (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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398C THR* 3.7 17.3 - - + +
399C THR* 3.5 34.1 - - - -
400C ILE* 3.8 24.5 - - + -
445C VAL* 3.7 20.4 - - + +
449C LYS 3.5 17.8 + - - +
450C TYR* 3.4 25.2 + - + +
462C GLY* 1.3 67.6 - - - -
464C VAL* 1.3 60.9 + - - +
466C GLU* 2.7 26.1 + - - +
467C LEU* 2.9 18.9 + - - +
475C ALA* 5.4 6.7 - - + -
477C ALA* 4.1 11.7 - - + -
478C PRO 5.9 0.9 - - - +
479C LEU* 5.0 13.7 - - + -
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Residues in contact with VAL 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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450C TYR 3.5 5.1 + - - +
451C GLY* 3.6 24.5 - - - +
460C TRP* 3.5 37.5 - - + -
461C ASN 3.5 7.6 - - - +
462C GLY 3.2 0.4 - - - -
463C MET* 1.3 76.0 - - - +
465C GLY* 1.3 57.3 + - - +
467C LEU* 4.6 2.9 - - - +
468C VAL* 2.9 49.2 + - + +
479C LEU* 5.2 10.3 - - + -
485C ARG* 4.9 17.9 - - + +
488C VAL* 4.8 6.3 - - + -
489C ILE* 6.0 8.3 - - + -
491C PHE* 6.5 1.1 - - + -
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Residues in contact with GLY 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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460C TRP 3.6 10.9 + - - -
461C ASN* 2.7 12.9 + - - -
462C GLY 2.6 18.3 + - - -
464C VAL* 1.3 72.3 - - - +
466C GLU* 1.3 60.6 + - - +
469C TYR* 3.0 41.5 - - - +
471C LYS* 4.6 2.8 - - - +
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Residues in contact with GLU 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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398C THR* 3.9 13.6 - - + +
445C VAL* 3.6 24.4 - - + +
446C GLY 4.7 2.4 + - - -
462C GLY 2.9 13.9 + - - +
463C MET* 2.7 24.2 + - - +
465C GLY* 1.3 74.2 - - - +
467C LEU* 1.3 58.0 + - - +
470C GLY 3.4 1.7 + - - -
471C LYS* 2.6 56.9 + - - +
472C ALA* 3.0 19.2 + - + +
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Residues in contact with LEU 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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398C THR* 4.7 0.9 - - + -
463C MET 2.9 14.4 + - - +
464C VAL* 4.6 1.8 - - - +
466C GLU* 1.3 74.5 - - - +
468C VAL* 1.3 67.9 + - + +
470C GLY* 2.9 14.7 + - - -
472C ALA* 3.3 37.5 - - + +
473C ASP 3.6 4.5 - - - +
474C ILE* 3.5 16.8 - - - +
475C ALA* 3.7 19.5 - - + -
489C ILE* 4.0 21.3 - - + +
735C ALA* 3.7 34.1 - - + +
736C THR* 4.1 3.6 - - - +
737C PRO* 3.9 22.3 - - + +
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Residues in contact with VAL 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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460C TRP* 4.2 14.4 - - + -
464C VAL* 2.9 40.7 + - + +
467C LEU* 1.3 77.9 - - + +
469C TYR* 1.3 79.3 + - + +
470C GLY 3.4 2.4 + - - -
488C VAL* 4.1 16.2 - - + +
489C ILE* 3.9 24.2 - - + -
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Residues in contact with TYR 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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458C LYS 4.1 3.6 + - - -
459C ILE* 3.2 23.3 - - + +
460C TRP* 3.1 48.0 + - + -
465C GLY* 3.0 31.9 + - - +
467C LEU 3.1 0.6 - - - -
468C VAL* 1.3 86.9 - - + +
470C GLY* 1.3 54.7 - - - +
471C LYS* 2.8 41.0 + - + +
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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