Contacts of the helix formed by residues 3805 - 3822 (chain A) in PDB entry 5NUG
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 SER3805 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3709A GLN* 3.6 22.4 - - - +
3712A CYS* 3.6 3.6 - - - +
3713A LEU* 3.0 38.6 + - - +
3716A VAL* 4.9 2.6 - - - +
3801A TYR 3.1 5.1 + - - -
3802A LEU* 3.0 23.4 + - - -
3804A LEU* 1.3 77.1 - - - +
3806A THR* 1.3 57.7 + - - +
3808A CYS* 3.2 12.4 + - - +
3809A SER* 2.9 28.8 + - - -
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Residues in contact with THR3806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3709A GLN* 3.6 32.5 + - - +
3802A LEU* 2.6 23.7 + - - +
3803A PRO* 3.2 13.0 - - + +
3805A SER* 1.3 72.2 - - - +
3807A ALA* 1.3 59.1 + - - +
3809A SER* 3.2 4.2 + - - -
3810A SER* 2.9 37.7 + - - +
3893A LYS* 5.0 13.9 - - + -
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Residues in contact with ALA3807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3803A PRO 2.5 23.0 + - - +
3804A LEU* 3.3 11.7 - - + +
3806A THR* 1.3 75.7 - - - +
3808A CYS* 1.3 57.6 + - - +
3810A SER* 3.2 9.4 + - - -
3811A ILE* 2.9 33.9 + - - +
3860A THR* 5.7 3.1 - - + -
3864A PHE* 4.6 19.7 - - + -
3890A ILE* 4.0 8.9 - - + +
3891A LYS* 6.3 0.4 - - - -
3893A LYS* 6.6 0.2 - - - -
3894A GLY* 5.7 7.0 - - - +
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Residues in contact with CYS3808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3708A LEU* 4.4 0.2 - - - -
3712A CYS* 3.9 13.2 - - - -
3804A LEU* 2.9 51.5 + - - -
3805A SER* 3.2 10.1 - - - +
3807A ALA* 1.3 75.9 - - - +
3809A SER* 1.3 58.0 + - - +
3811A ILE* 3.2 8.5 + - - +
3812A TYR 2.9 24.9 + - - -
3832A PHE* 3.2 14.2 - - + -
3836A TYR* 2.3 37.0 - - - +
3863A LEU* 3.9 6.7 - - - -
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Residues in contact with SER3809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3705A ARG* 3.4 40.4 + - - +
3708A LEU* 3.0 26.6 - - - +
3709A GLN* 4.0 9.2 - - - -
3805A SER 2.9 12.3 + - - -
3806A THR* 3.4 9.0 - - - -
3808A CYS* 1.3 77.0 - - - +
3810A SER* 1.3 56.5 + - - +
3812A TYR* 3.2 2.6 + - - +
3813A PHE* 2.9 33.7 + - - -
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Residues in contact with SER3810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3705A ARG* 6.5 0.4 - - - -
3806A THR* 2.9 23.1 + - - +
3807A ALA* 3.2 10.1 + - - -
3809A SER* 1.3 75.5 - - - +
3811A ILE* 1.3 53.8 + - - +
3813A PHE* 3.2 8.8 + - - +
3814A THR* 2.8 36.7 + - - -
3890A ILE* 3.7 23.1 - - - +
3893A LYS* 4.2 19.9 + - - +
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Residues in contact with ILE3811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3807A ALA 2.9 19.4 + - - +
3808A CYS* 3.3 10.5 - - - +
3810A SER* 1.3 75.5 - - - +
3812A TYR* 1.3 58.8 + - - +
3814A THR* 3.2 4.7 + - - -
3815A MET* 2.9 34.6 + - + +
3832A PHE* 3.9 15.9 - - + -
3863A LEU* 5.7 4.9 - - + -
3864A PHE* 3.6 39.9 - - + -
3867A ALA* 4.7 16.8 - - + -
3883A PHE* 5.3 1.5 - - + -
3887A LEU* 2.9 43.3 - - + -
3890A ILE* 4.1 13.0 - - + +
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Residues in contact with TYR3812 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3703A VAL* 4.4 12.5 - - + +
3708A LEU* 3.4 28.3 - - + -
3808A CYS 2.9 6.1 + - - -
3811A ILE* 1.3 76.1 - - - +
3813A PHE* 1.3 74.2 + + - +
3815A MET* 3.2 8.5 + - + +
3816A GLU* 2.9 65.5 + - + -
3827A TYR* 4.0 11.2 + - + -
3828A SER* 3.8 18.8 - - - -
3829A LEU* 3.5 39.2 + - + +
3832A PHE* 3.6 36.3 - + + -
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Residues in contact with PHE3813 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3703A VAL* 3.4 26.7 - - + -
3704A THR* 3.9 12.6 - - - -
3705A ARG* 3.7 48.0 - - + -
3708A LEU* 4.6 2.7 - - + -
3809A SER* 2.9 24.1 + - - +
3810A SER* 3.5 10.5 - - - +
3812A TYR* 1.3 96.2 - + - +
3814A THR* 1.3 55.7 + - - +
3816A GLU* 3.2 11.2 + - - +
3817A SER* 2.9 30.2 + - - -
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Residues in contact with THR3814 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3810A SER 2.8 14.7 + - - -
3811A ILE* 3.2 8.3 + - - -
3813A PHE* 1.3 75.0 - - - +
3815A MET* 1.3 58.5 + - - +
3817A SER* 3.2 8.3 + - - -
3818A LEU* 2.9 27.4 + - - +
3883A PHE* 4.4 10.8 - - + -
3886A LEU* 3.6 45.3 - - + -
3887A LEU* 5.8 1.3 - - + -
3890A ILE* 3.0 19.6 - - + +
4346A MET* 4.6 4.1 - - + +
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Residues in contact with MET3815 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3811A ILE* 2.9 19.6 + - + +
3812A TYR* 3.2 10.0 + - + +
3814A THR* 1.3 77.8 - - - +
3816A GLU* 1.3 57.4 + - - +
3818A LEU* 2.9 28.9 - - + +
3819A LYS 4.1 1.0 + - - -
3825A TYR 5.4 0.2 - - - +
3826A GLN* 5.8 0.3 - - - -
3827A TYR* 3.6 33.4 + - + -
3831A PHE* 3.7 27.6 - - + -
3832A PHE* 5.2 13.0 - - - -
3835A ILE* 5.2 2.0 - - + -
3867A ALA* 4.1 13.9 - - + +
3871A VAL* 2.1 46.4 - - + -
3883A PHE* 3.5 17.4 - - + -
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Residues in contact with GLU3816 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3684A PRO* 6.1 0.7 - - - +
3703A VAL* 5.2 7.3 - - - +
3812A TYR* 2.9 49.7 + - + +
3813A PHE* 3.2 15.4 + - - +
3815A MET* 1.3 74.9 - - - +
3817A SER* 1.3 62.0 + - - +
3819A LYS* 3.4 47.6 + - + +
3827A TYR 5.2 7.6 - - - +
4140A ARG* 4.8 9.9 + - - +
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Residues in contact with SER3817 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3813A PHE 2.9 14.8 + - - -
3814A THR* 3.2 7.8 + - - -
3816A GLU* 1.3 71.9 - - - +
3818A LEU* 1.3 55.6 + - - +
3819A LYS* 3.1 3.1 - - - -
3820A GLN* 2.8 32.1 + - - +
4346A MET* 3.6 19.5 - - - +
4349A LEU* 2.1 43.4 - - - +
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Residues in contact with LEU3818 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3814A THR 2.9 10.0 + - - +
3815A MET* 2.9 17.3 - - + +
3817A SER* 1.3 75.0 - - - +
3819A LYS* 1.3 56.4 + - - +
3820A GLN 3.1 0.2 - - - -
3821A ILE* 3.0 28.4 - - + +
3822A HIS 4.0 0.3 + - - -
3825A TYR* 3.7 22.2 - - + +
3827A TYR* 4.0 19.1 - - + -
3871A VAL* 4.1 7.6 - - + -
3875A MET* 4.0 21.3 - - + -
3883A PHE* 3.6 32.5 - - + -
4342A LYS* 3.4 29.8 - - - +
4346A MET* 3.7 15.2 - - + +
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Residues in contact with LYS3819 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3167A ARG* 4.5 11.2 - - - +
3684A PRO* 5.2 4.8 - - - +
3685A THR* 4.1 20.2 - - + +
3815A MET 4.1 0.8 + - - -
3816A GLU* 3.4 38.5 + - - +
3817A SER* 3.1 1.2 - - - -
3818A LEU* 1.3 74.7 - - - +
3820A GLN* 1.3 68.5 - - - +
3821A ILE 3.4 0.2 - - - -
3823A PHE* 3.7 18.7 + - - +
3825A TYR 3.5 19.7 + - - +
3826A GLN* 4.1 21.2 + - + +
4140A ARG* 3.8 30.5 - - - +
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Residues in contact with GLN3820 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3164A ARG 5.3 7.9 + - - +
3165A GLY 5.3 4.2 - - - +
3817A SER 2.8 16.6 + - - +
3819A LYS* 1.3 85.1 - - + +
3821A ILE* 1.3 62.8 + - - +
3823A PHE* 4.6 1.6 + - - +
4345A LYS* 3.8 43.0 - - + +
4346A MET* 5.1 2.2 - - - -
4349A LEU* 4.4 22.0 - - + +
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Residues in contact with ILE3821 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3817A SER 4.2 0.4 + - - -
3818A LEU* 3.0 21.5 + - + +
3820A GLN* 1.3 83.4 - - + +
3822A HIS* 1.3 68.1 + - + +
3823A PHE* 3.7 2.7 - - - -
3825A TYR* 3.6 17.5 - - + +
3879A ASP* 4.0 17.9 - - - +
4338A ASP 5.5 0.4 - - - +
4342A LYS* 2.6 70.0 - - + +
4345A LYS* 6.2 3.6 - - + -
4346A MET* 4.7 3.3 - - + +
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Residues in contact with HIS3822 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3818A LEU 4.0 1.4 + - - -
3821A ILE* 1.3 80.7 - - + +
3823A PHE* 1.3 101.8 - + - +
3824A LEU* 2.6 49.0 + - + +
3825A TYR* 3.0 36.3 - + + +
3876A LEU* 2.8 29.5 - - + +
3879A ASP* 4.3 4.9 - - - +
4130A ILE* 3.7 13.3 - - + +
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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