Contacts of the helix formed by residues 3581 - 3596 (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 PRO3581 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3580C ASN* 1.3 88.0 - - + +
3582C GLU* 1.3 55.6 + - + +
3583C LEU 3.0 0.7 - - - -
3584C LEU* 2.3 41.8 + - + +
3585C PHE* 2.8 37.1 + - + -
3617C LEU* 3.5 12.1 - - + -
3630C ARG* 3.2 9.4 - - - +
3632C PHE* 4.6 8.5 - - + -
3633C ILE* 3.3 36.1 - - + +
3637C GLY* 5.4 3.1 - - - -
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Residues in contact with GLU3582 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3580C ASN* 2.9 13.5 - - + +
3581C PRO* 1.3 77.8 - - + +
3583C LEU* 1.3 56.1 + - + +
3585C PHE* 3.8 9.2 - - - +
3586C LYS* 2.9 56.4 + - + +
3670C MET 5.1 0.4 - - - +
3671C ASN* 2.7 21.4 - - - +
3674C SER* 2.6 52.2 + - - +
3675C LYS* 4.3 4.2 + - - +
3677C PRO* 5.5 0.2 - - - +
3734C ARG* 3.7 20.5 + - - -
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Residues in contact with LEU3583 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3580C ASN 3.7 6.4 + - - +
3581C PRO 3.0 0.6 - - - -
3582C GLU* 1.3 76.7 - - + +
3584C LEU* 1.3 67.1 + - + +
3585C PHE 3.3 0.4 - - - -
3586C LYS* 3.9 22.4 - - + +
3587C ASP* 2.7 56.2 + - - +
3732C LEU* 3.4 26.9 - - + +
3733C ARG* 3.9 39.3 - - - +
3754C GLY 5.5 0.7 - - - -
3755C GLY* 4.0 12.3 - - - +
4022C LYS 5.9 2.7 - - - +
4023C LYS* 5.2 1.3 - - - +
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Residues in contact with LEU3584 (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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3577C GLN* 3.2 52.9 - - + +
3578C LEU 5.2 2.7 - - - +
3580C ASN 3.7 7.6 - - - +
3581C PRO* 2.3 39.5 + - + +
3583C LEU* 1.3 70.5 - - + +
3585C PHE* 1.3 54.1 + - - +
3588C TRP* 2.9 30.0 + - - +
3616C ALA* 4.0 9.9 - - + -
3617C LEU* 3.4 27.3 - - + +
3754C GLY 5.5 8.3 - - - +
3755C GLY* 6.6 0.2 - - - -
3799C ARG* 3.1 12.4 + - - +
3800C LEU* 6.2 2.7 - - + -
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Residues in contact with PHE3585 (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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3581C PRO* 2.8 45.5 + - + -
3582C GLU* 3.8 9.9 - - + +
3584C LEU* 1.3 73.7 - - - +
3586C LYS* 1.3 61.3 + - + +
3588C TRP* 2.8 21.7 + - - +
3589C SER 2.8 11.4 + - - -
3613C MET* 3.9 9.4 - - + -
3617C LEU* 3.3 26.9 - - + +
3633C ILE* 6.0 0.2 - - + -
3637C GLY* 4.7 12.6 - - - -
3641C ASP* 3.1 33.7 - - + -
3644C PHE* 3.5 27.4 - + - -
3670C MET* 3.2 38.8 - - + +
3674C SER* 6.2 2.0 - - - -
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Residues in contact with LYS3586 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3582C GLU* 2.9 45.5 + - + +
3583C LEU* 3.9 19.1 - - + +
3585C PHE* 1.3 73.6 - - + +
3587C ASP* 1.3 60.8 + - - +
3589C SER* 2.8 24.9 + - - -
3590C ASN* 2.8 26.0 + - - +
3667C LEU* 3.7 20.4 - - + -
3670C MET* 4.5 4.9 - - + -
3671C ASN* 3.2 38.2 - - + +
3732C LEU* 5.2 7.1 + - - +
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Residues in contact with ASP3587 (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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3583C LEU* 2.7 58.6 + - - +
3586C LYS* 1.3 72.9 - - - +
3588C TRP* 1.3 52.6 - - - +
3590C ASN* 3.3 18.2 + - - +
3591C ASP* 2.9 24.5 + - - +
3755C GLY* 3.4 24.7 - - - +
3799C ARG* 2.6 37.4 + - - +
4022C LYS* 5.1 16.2 - - + +
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Residues in contact with TRP3588 (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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3584C LEU 2.9 17.2 + - - +
3585C PHE* 2.8 13.9 + - - +
3587C ASP* 1.3 76.6 - - - +
3589C SER* 1.3 56.6 + - - -
3592C VAL* 2.9 59.4 + - + +
3609C MET* 3.6 30.6 + - + +
3610C TYR* 4.2 9.4 - + - -
3613C MET* 3.7 41.7 - - + +
3614C TYR* 5.8 1.6 - + - -
3644C PHE* 5.3 3.1 - - + -
3648C GLY* 4.4 16.8 - - - -
3651C LEU* 3.6 38.1 - - + -
3666C LEU* 3.5 27.8 - - + -
3670C MET* 3.8 19.5 - - + -
3799C ARG* 3.2 11.4 - - - +
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Residues in contact with SER3589 (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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3585C PHE 2.8 5.1 + - - -
3586C LYS 2.8 16.2 + - - -
3588C TRP* 1.3 77.1 - - - +
3590C ASN* 1.3 58.1 + - - +
3592C VAL* 4.7 1.1 - - - -
3593C ARG* 2.4 44.5 + - - +
3663C THR* 3.5 23.4 - - - +
3666C LEU* 3.9 2.1 - - - +
3667C LEU* 4.1 9.2 - - - -
3670C MET* 2.4 40.4 - - - +
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Residues in contact with ASN3590 (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* 2.8 23.6 + - - +
3587C ASP* 3.3 25.1 + - - +
3588C TRP 3.1 0.2 - - - -
3589C SER* 1.3 78.2 - - - +
3591C ASP* 1.3 56.0 + - - +
3593C ARG* 2.2 37.3 + - - +
3594C ALA* 2.5 38.6 + - - +
3667C LEU* 4.9 3.6 - - - +
4021C LEU* 4.2 23.1 - - + +
4022C LYS* 5.6 6.4 + - + +
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Residues in contact with ASP3591 (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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3587C ASP* 2.9 8.3 + - - +
3590C ASN* 1.3 76.8 - - - +
3592C VAL* 1.3 65.0 + - - +
3594C ALA* 3.2 5.3 + - - +
3595C GLU* 2.9 28.5 + - - +
3609C MET* 3.5 23.0 - - + +
3799C ARG* 2.4 42.7 + - - +
4018C GLN* 3.5 27.7 + - - +
4021C LEU* 4.3 14.7 - - - +
4022C LYS* 4.3 4.1 - - - +
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Residues in contact with VAL3592 (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* 2.9 55.8 + - + +
3589C SER* 4.6 1.6 - - - +
3591C ASP* 1.3 74.1 - - - +
3593C ARG* 1.3 56.9 + - - +
3595C GLU* 2.7 31.0 + - - +
3596C LEU* 3.4 9.7 + - + +
3606C ILE* 3.4 35.6 - - + +
3609C MET* 3.4 17.3 - - + -
3651C LEU* 3.9 25.6 - - + -
3663C THR* 5.6 1.3 - - - +
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Residues in contact with ARG3593 (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* 2.4 39.2 + - - +
3590C ASN* 2.2 39.9 + - - +
3592C VAL* 1.3 76.7 - - - +
3594C ALA* 1.3 60.0 + - - +
3596C LEU* 3.3 16.0 - - - +
3597C ALA 4.4 0.7 + - - -
3660C ASN* 2.9 46.4 + - - +
3663C THR* 3.6 37.3 + - + +
3664C ASN* 5.2 5.8 + - - +
3667C LEU* 3.3 33.5 - - - +
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Residues in contact with ALA3594 (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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3590C ASN 2.5 26.8 + - - +
3591C ASP* 3.3 8.3 - - - +
3592C VAL 3.0 0.2 - - - -
3593C ARG* 1.3 73.7 - - - +
3595C GLU* 1.3 57.6 + - + +
3596C LEU 3.0 10.1 + - - -
3597C ALA* 3.1 16.5 + - - +
3598C LYS* 2.9 19.4 + - - +
4021C LEU* 4.6 17.5 - - + -
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Residues in contact with GLU3595 (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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3591C ASP* 2.9 17.4 + - - +
3592C VAL 2.7 14.9 + - - +
3594C ALA* 1.3 71.1 - - - +
3596C LEU* 1.3 60.1 + - - +
3597C ALA 3.2 0.9 - - - -
3598C LYS* 3.0 52.6 + - - +
3602C ASN* 3.8 11.0 - - - +
3605C ASN* 2.9 38.0 - - + +
3606C ILE* 3.4 13.2 - - + -
3609C MET* 3.5 24.2 - - + +
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Residues in contact with LEU3596 (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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3592C VAL* 3.8 12.3 - - + +
3593C ARG* 3.3 15.5 - - + +
3594C ALA 3.0 1.2 + - - -
3595C GLU* 1.3 79.3 - - - +
3597C ALA* 1.3 56.4 + - - +
3598C LYS 3.3 4.6 + - - +
3602C ASN* 5.3 4.9 - - - +
3606C ILE* 5.3 8.1 - - + -
3651C LEU* 5.8 0.9 - - + -
3655C LYS* 4.9 4.7 - - - -
3656C LEU* 3.3 29.6 - - - +
3657C SER* 3.1 27.5 - - - +
3659C PHE* 3.8 15.5 - - + -
3660C ASN* 3.1 60.5 - - - +
3663C THR* 4.7 0.4 - - - +
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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
------------------------------------------------------------
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