Contacts of the helix formed by residues 3812 - 3824 (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 LEU3812 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3810C VAL 3.2 2.6 + - - -
3811C THR* 1.3 72.2 - - - +
3813C LYS* 1.3 77.4 + - - +
3814C ASP 2.9 1.4 + - - -
3815C LEU* 3.2 8.0 + - - +
3816C LEU* 3.0 24.5 + - + +
3883C LEU* 6.0 8.5 - - + +
3904C PHE* 5.8 4.5 - - + -
3925C LEU* 3.0 48.5 - - + +
3926C ASN 4.0 0.7 - - - +
3928C PHE* 3.1 35.8 + - + +
3930C VAL* 4.9 6.1 - - + -
3937C VAL* 3.6 26.0 - - + +
3966C GLN* 6.2 0.4 - - - +
3967C PHE* 5.5 14.6 - - + -
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Residues in contact with LYS3813 (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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3811C THR* 3.0 9.3 - - - +
3812C LEU* 1.3 84.2 - - - +
3814C ASP* 1.3 56.5 + - - +
3816C LEU* 3.1 20.4 - - + +
3817C LEU* 2.8 73.6 + - + +
3820C MET* 4.7 0.2 - - - +
3831C ASP* 4.3 3.9 + - - -
3925C LEU* 3.3 20.0 - - + -
3926C ASN* 3.4 26.2 - - + +
4125C GLU* 3.3 27.1 + - - -
4128C MET* 3.4 17.2 - - - +
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Residues in contact with ASP3814 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3810C VAL* 3.3 29.4 - - + +
3811C THR* 2.7 22.4 + - - +
3813C LYS* 1.3 73.6 - - - +
3815C LEU* 1.3 70.8 + - + +
3817C LEU* 2.6 29.3 + - - +
3818C ASN* 2.9 24.7 + - - +
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Residues in contact with LEU3815 (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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887C ASP* 4.4 17.3 - - - +
3810C VAL* 5.9 2.7 - - + +
3811C THR 4.8 3.8 - - - +
3812C LEU* 3.2 6.3 + - - +
3814C ASP* 1.3 85.9 - - + +
3816C LEU* 1.3 65.2 + - - +
3817C LEU 3.0 0.2 + - - -
3818C ASN* 2.5 41.4 - - - +
3819C THR* 2.9 12.2 - - - +
3886C ALA* 3.6 26.2 - - + +
3889C ARG* 4.6 3.6 - - + +
3890C MET* 5.6 8.1 - - + -
3930C VAL* 5.1 14.8 - - + -
3932C MET* 4.9 19.1 - - + -
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Residues in contact with LEU3816 (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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3812C LEU* 3.0 15.8 + - + +
3813C LYS* 3.1 46.2 - - + +
3815C LEU* 1.3 76.8 - - - +
3817C LEU* 1.3 59.9 + - + +
3819C THR* 3.0 8.7 - - - +
3820C MET* 2.9 47.5 + - + +
3879C PRO* 3.9 14.4 - - + +
3882C LEU* 3.7 22.4 - - + -
3883C LEU* 4.3 14.8 - - + +
3886C ALA* 4.6 1.3 - - - +
3925C LEU* 4.4 9.2 - - + -
3966C GLN* 4.5 12.6 - - - +
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Residues in contact with LEU3817 (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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3813C LYS* 2.8 70.0 + - + +
3814C ASP* 2.6 13.0 + - - +
3816C LEU* 1.3 71.8 - - + +
3818C ASN* 1.3 58.3 + - - +
3820C MET* 2.4 38.6 + - + -
3821C SER* 2.8 14.6 + - - -
3829C LEU* 3.3 39.0 - - + +
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Residues in contact with ASN3818 (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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889C GLU* 4.1 10.7 + - - +
3814C ASP* 2.9 17.8 + - - +
3815C LEU* 2.5 47.0 - - - +
3817C LEU* 1.3 74.9 - - - +
3819C THR* 1.3 85.4 + - - +
3821C SER* 5.1 2.5 - - - -
3822C GLN* 3.0 36.3 + - + +
3889C ARG* 3.2 23.8 + - - +
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Residues in contact with THR3819 (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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889C GLU* 6.4 0.9 - - - -
3815C LEU 2.9 23.8 - - - +
3816C LEU* 3.0 12.3 - - - +
3818C ASN* 1.3 92.2 + - - +
3820C MET* 1.3 58.9 + - - +
3822C GLN* 5.3 0.2 - - - -
3823C GLU* 2.8 37.5 + - - +
3882C LEU* 3.2 36.8 - - + +
3885C ARG* 3.9 14.1 - - - +
3886C ALA* 4.1 13.2 - - + -
3889C ARG* 5.5 3.4 - - - +
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Residues in contact with MET3820 (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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3813C LYS* 4.7 3.4 - - - +
3816C LEU* 2.9 48.4 + - + +
3817C LEU* 2.4 31.0 + - + +
3819C THR* 1.3 71.2 - - - +
3821C SER* 1.3 51.4 - - - +
3823C GLU* 3.5 0.5 - - - +
3824C GLU* 2.2 42.3 + - + +
3829C LEU* 3.3 32.3 - - + -
3830C SER* 3.5 18.6 - - - +
3831C ASP* 3.6 8.7 - - - +
3833C ARG* 5.7 2.0 - - - +
3879C PRO* 4.1 12.6 - - + -
3882C LEU* 3.4 18.6 - - + -
4128C MET* 5.0 7.9 - - + +
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Residues in contact with SER3821 (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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3817C LEU 2.8 10.7 + - - -
3818C ASN* 4.4 2.0 - - - -
3820C MET* 1.3 73.1 - - - +
3822C GLN* 1.3 60.3 + - - -
3824C GLU 2.5 32.1 + - - +
3825C LYS 2.7 7.3 - - - +
3826C ALA 2.8 15.0 - - - -
3827C ALA* 2.7 15.7 + - - -
3829C LEU* 2.3 50.3 + - - +
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Residues in contact with GLN3822 (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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889C GLU* 5.4 12.8 - - - +
3818C ASN* 3.0 24.3 + - + +
3819C THR* 5.3 0.4 - - - -
3821C SER* 1.3 77.1 - - - +
3823C GLU* 1.3 60.1 + - - +
3825C LYS 3.5 6.9 - - - +
3826C ALA* 2.6 36.5 + - - +
3827C ALA* 3.8 7.1 - - - +
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Residues in contact with GLU3823 (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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3819C THR* 2.8 29.5 + - - +
3820C MET* 3.5 1.1 - - - +
3821C SER 2.9 4.5 - - - -
3822C GLN* 1.3 78.4 - - - +
3824C GLU* 1.3 62.0 + - + +
3825C LYS* 2.8 15.8 + - - +
3878C VAL* 6.1 4.7 - - + -
3882C LEU* 5.0 7.9 - - + -
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Residues in contact with GLU3824 (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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3820C MET* 2.2 31.7 + - + +
3821C SER* 2.5 14.4 + - - +
3823C GLU* 1.3 70.2 - - + +
3825C LYS* 1.3 105.2 + - + +
3826C ALA 3.3 1.4 + - - -
3828C TYR* 4.2 2.3 + - - +
3829C LEU 2.9 29.0 - - - +
3830C SER* 3.3 23.8 - - - +
3878C VAL* 6.3 3.1 - - + -
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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