Contacts of the helix formed by residues 3658 - 3673 (chain C) in PDB entry 5Y3R
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 ASP3658 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3650C LYS* 3.1 15.6 + - - -
3654C MET* 3.1 24.8 - - - +
3656C LEU* 2.8 15.3 - - + +
3657C SER* 1.3 76.7 + - - +
3659C PHE* 1.3 84.4 + - - -
3660C ASN* 2.8 8.0 + - - +
3661C ASP* 3.0 17.3 + - - +
3662C ILE* 3.7 10.9 + - + +
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Residues in contact with PHE3659 (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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3596C LEU* 3.8 9.4 - - + -
3647C GLY* 4.1 5.2 - - - -
3650C LYS* 3.0 42.4 - - + -
3651C LEU* 3.3 64.6 - - + -
3654C MET* 3.3 21.5 - - + -
3655C LYS* 4.6 1.8 - - - -
3656C LEU 3.4 10.3 - - - -
3657C SER 3.0 1.0 + - - -
3658C ASP* 1.3 97.0 + - - +
3660C ASN* 1.3 53.5 + - - +
3661C ASP 3.1 0.7 - - - -
3662C ILE* 3.4 34.5 - - + -
3663C THR* 2.2 47.3 + - - +
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Residues in contact with ASN3660 (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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3593C ARG* 2.9 45.1 + - + +
3596C LEU* 3.1 23.4 - - - +
3597C ALA 5.3 0.4 - - - +
3657C SER* 2.7 27.7 + - - +
3658C ASP 2.8 1.6 + - - +
3659C PHE* 1.3 74.5 - - - +
3661C ASP* 1.3 52.5 - - - +
3663C THR* 4.0 1.7 - - - -
3664C ASN* 2.2 40.9 + - - +
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Residues in contact with ASP3661 (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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3658C ASP 3.0 10.0 + - - +
3660C ASN* 1.3 75.9 - - - +
3662C ILE* 1.3 64.0 + - + +
3664C ASN* 2.8 38.0 + - + +
3665C MET* 2.9 6.8 + - - +
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Residues in contact with ILE3662 (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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3647C GLY* 5.7 7.4 - - - +
3650C LYS* 4.0 15.5 - - + +
3651C LEU* 6.0 0.2 - - + -
3658C ASP* 4.5 9.4 - - + +
3659C PHE* 2.9 43.3 + - + -
3661C ASP* 1.3 77.3 - - + +
3663C THR* 1.3 50.8 + - - +
3665C MET* 2.9 33.9 + - + +
3666C LEU* 2.4 36.8 + - + +
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Residues in contact with THR3663 (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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3589C SER* 3.5 36.3 - - - +
3592C VAL* 5.6 0.5 - - - +
3593C ARG* 3.6 37.8 + - + +
3651C LEU* 4.5 6.4 - - - +
3659C PHE* 2.2 47.5 + - - +
3660C ASN 4.0 0.2 - - - -
3662C ILE* 1.3 64.7 - - - +
3664C ASN* 1.3 58.8 + - - +
3666C LEU* 3.5 17.7 - - + +
3667C LEU* 2.3 38.4 + - - +
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Residues in contact with ASN3664 (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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3593C ARG* 5.2 6.4 + - - +
3660C ASN* 2.2 40.9 + - - +
3661C ASP* 2.8 26.4 + - - +
3663C THR* 1.3 75.6 - - - +
3665C MET* 1.3 61.8 + - - +
3667C LEU* 4.2 5.1 - - - +
3668C LEU* 3.1 30.9 + - + +
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Residues in contact with MET3665 (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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3647C GLY* 6.3 2.5 - - - -
3661C ASP 2.9 7.7 + - - +
3662C ILE* 2.9 43.6 + - + +
3664C ASN* 1.3 74.0 - - - +
3666C LEU* 1.3 52.8 + - + +
3668C LEU* 3.0 11.1 + - - +
3669C LYS* 2.7 56.9 + - + +
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Residues in contact with LEU3666 (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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3588C TRP* 3.5 31.9 - - + -
3589C SER* 3.9 4.7 - - - +
3644C PHE* 3.8 28.7 - - + +
3648C GLY* 6.3 2.0 - - - +
3651C LEU* 5.3 5.8 - - + -
3662C ILE* 2.4 34.8 + - + +
3663C THR* 2.9 19.1 + - + +
3665C MET* 1.3 69.2 - - + +
3667C LEU* 1.3 52.7 + - - +
3669C LYS* 2.9 12.9 + - - +
3670C MET* 2.3 68.8 + - + +
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Residues in contact with LEU3667 (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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3586C LYS* 3.7 38.4 - - + +
3589C SER* 4.1 13.9 - - - +
3590C ASN* 4.9 2.5 - - - +
3593C ARG* 3.3 28.7 - - - +
3663C THR* 2.3 33.8 + - + +
3664C ASN* 4.2 4.0 - - - +
3666C LEU* 1.3 67.8 - - - +
3668C LEU* 1.3 67.3 + - + +
3670C MET* 3.4 7.6 - - - +
3671C ASN* 2.8 33.3 + - + +
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Residues in contact with LEU3668 (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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3664C ASN* 3.1 25.7 + - + +
3665C MET* 3.0 6.3 + - - +
3667C LEU* 1.3 81.2 - - + +
3669C LYS* 1.3 61.6 + - - +
3671C ASN* 5.1 1.6 - - - -
3672C LYS* 3.1 57.4 + - + +
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Residues in contact with LYS3669 (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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3643C HIS* 3.2 57.1 + - + +
3644C PHE* 3.5 20.6 - - + -
3647C GLY* 6.3 0.6 - - - -
3665C MET* 2.7 39.4 + - + +
3666C LEU* 3.3 15.9 - - - +
3668C LEU* 1.3 73.4 - - - +
3670C MET* 1.3 63.6 + - - +
3671C ASN 3.0 1.9 + - - -
3672C LYS* 3.0 14.2 + - - +
3673C ASP* 3.4 27.5 + - - +
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Residues in contact with MET3670 (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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3582C GLU* 5.1 1.2 - - - +
3585C PHE* 3.2 53.0 - - + +
3586C LYS* 4.6 2.9 - - + -
3588C TRP* 3.8 16.6 - - + -
3589C SER* 2.4 31.9 - - - +
3613C MET* 5.4 0.2 - - + -
3644C PHE* 3.2 28.7 - - + -
3666C LEU* 2.3 53.8 + - + +
3667C LEU* 3.4 18.6 - - + +
3669C LYS* 1.3 68.6 - - - +
3671C ASN* 1.3 62.4 + - - +
3674C SER* 3.4 16.6 + - - -
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Residues in contact with ASN3671 (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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3582C GLU* 2.7 19.8 - - - +
3586C LYS* 3.2 37.1 - - + +
3667C LEU* 2.8 20.0 + - + +
3668C LEU* 4.5 2.2 - - - +
3670C MET* 1.3 76.0 - - - +
3672C LYS* 1.3 61.7 + - + +
3673C ASP 3.2 2.0 - - - -
3674C SER* 2.3 32.5 + - - -
3675C LYS* 3.6 20.3 + - - +
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Residues in contact with LYS3672 (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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3668C LEU* 3.1 50.6 + - + +
3669C LYS* 3.0 7.6 + - - +
3671C ASN* 1.3 79.6 - - + +
3673C ASP* 1.3 65.7 + - - +
3674C SER 3.3 0.2 - - - -
3675C LYS* 3.2 45.1 - - - +
3676C PRO* 5.0 1.2 - - - +
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Residues in contact with ASP3673 (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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3636C PHE* 4.9 8.0 - - - +
3640C PHE* 3.0 68.9 - - + -
3643C HIS* 4.8 1.7 + - - -
3644C PHE* 5.3 1.3 - - + -
3669C LYS* 3.4 22.7 + - - +
3670C MET 5.0 0.2 - - - -
3671C ASN 3.2 0.4 - - - -
3672C LYS* 1.3 83.1 - - - +
3674C SER* 1.3 56.8 + - - +
3675C LYS 3.4 4.4 + - - -
3676C PRO* 4.5 7.4 - - - +
3677C PRO* 5.0 0.5 - - - +
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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