Contacts of the helix formed by residues 3822 - 3833 (chain D) in PDB entry 6X34
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 GLY3822 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3779D SER* 3.7 19.8 - - - +
3782D LYS* 5.8 0.7 - - - -
3821D VAL* 1.3 78.3 - - - +
3823D PHE* 1.3 62.8 + - - +
3824D PHE* 3.5 1.7 - - - +
3825D GLN* 3.8 24.5 - - - +
3826D SER* 3.2 24.3 + - - -
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Residues in contact with PHE3823 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3775D LEU* 3.2 55.0 - - + -
3778D ILE* 3.8 23.8 - - + -
3779D SER* 3.7 14.6 - - - +
3815D LEU* 4.7 23.3 - - + -
3820D GLU 4.6 6.0 + - - +
3821D VAL* 3.6 2.8 - - - +
3822D GLY* 1.3 77.0 - - - +
3824D PHE* 1.3 94.7 + + + +
3826D SER* 3.2 18.4 + - - -
3827D ILE* 3.3 22.3 - - + +
3882D PHE* 5.2 13.2 - + - -
3886D LEU* 6.6 0.2 - - + -
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Residues in contact with PHE3824 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3815D LEU* 4.1 11.9 - - + -
3821D VAL* 5.8 0.2 - - - +
3822D GLY 4.5 1.4 - - - +
3823D PHE* 1.3 102.6 - + + +
3825D GLN* 1.3 65.1 + - - +
3826D SER 3.3 0.2 - - - -
3827D ILE* 3.3 27.8 + - + +
3828D GLN* 3.5 17.0 + - - +
3894D PHE* 6.3 1.1 - + - -
3897D TYR* 3.5 39.7 - + - -
3898D LEU* 5.0 14.4 - - + -
3901D GLN* 4.1 14.6 - - + -
3908D ILE* 3.6 48.2 - - + +
3910D ILE* 5.5 8.7 - - + -
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Residues in contact with GLN3825 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3821D VAL* 3.4 31.1 - - + +
3822D GLY* 3.7 26.3 + - - +
3823D PHE 3.3 0.8 - - - -
3824D PHE* 1.3 80.5 - - + +
3826D SER* 1.3 60.7 + - - +
3827D ILE 3.4 0.3 + - - -
3828D GLN* 3.4 21.3 + - - +
3829D ALA* 3.6 10.0 + - - +
3906D THR* 5.3 10.3 + - + +
3908D ILE* 5.5 6.5 - - + -
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Residues in contact with SER3826 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3778D ILE* 3.1 37.9 + - - +
3781D CYS* 3.7 16.6 - - - -
3782D LYS* 4.7 3.8 - - - -
3783D GLY* 3.9 15.4 - - - +
3822D GLY 3.2 13.2 + - - -
3823D PHE 3.2 10.7 + - - -
3824D PHE 3.3 0.4 - - - -
3825D GLN* 1.3 75.1 - - - +
3827D ILE* 1.3 67.2 + - - +
3829D ALA* 3.5 3.3 + - - +
3830D LEU* 3.3 27.0 + - - +
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Residues in contact with ILE3827 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3778D ILE* 4.8 7.4 - - + -
3823D PHE* 3.3 27.1 - - + +
3824D PHE* 3.3 36.8 + - + +
3825D GLN 3.2 0.6 - - - -
3826D SER* 1.3 78.1 - - - +
3828D GLN* 1.3 64.8 + - + +
3830D LEU* 3.2 11.8 + - + +
3831D MET* 3.0 32.5 + - + +
3879D LEU* 5.7 5.4 - - + -
3883D LEU* 4.6 21.1 - - + -
3910D ILE* 3.9 29.8 - - + -
3913D CYS* 6.2 0.4 - - - -
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Residues in contact with GLN3828 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3824D PHE 3.5 11.2 + - - +
3825D GLN* 3.4 14.1 + - - +
3826D SER 3.3 0.4 - - - -
3827D ILE* 1.3 78.5 - - + +
3829D ALA* 1.3 60.3 + - - +
3831D MET* 3.4 13.6 + - - +
3832D GLN* 3.4 23.7 + - - +
3908D ILE* 3.3 34.0 - - + +
3910D ILE* 6.1 0.7 - - + -
3913D CYS* 4.1 25.9 - - + -
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Residues in contact with ALA3829 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3783D GLY* 3.7 36.3 - - - +
3825D GLN 3.6 6.9 + - - +
3826D SER 3.5 3.5 + - - +
3827D ILE 3.2 0.4 - - - -
3828D GLN* 1.3 79.4 - - - +
3830D LEU* 1.3 63.1 + - - +
3832D GLN* 3.4 6.7 + - - +
3833D THR* 3.1 28.4 + - + +
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Residues in contact with LEU3830 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3778D ILE* 5.4 8.5 - - + -
3781D CYS* 5.3 5.8 - - - -
3783D GLY 5.4 1.1 - - - -
3784D GLU 4.2 16.4 - - - +
3785D THR* 3.9 21.3 - - + -
3789D VAL* 4.3 19.1 - - + -
3793D LEU* 4.9 7.0 - - + -
3826D SER* 3.3 20.1 + - - +
3827D ILE* 3.2 11.5 + - + +
3829D ALA* 1.3 78.3 - - - +
3831D MET* 1.3 62.4 + - - +
3833D THR* 3.0 14.2 + - - -
3834D CYS* 3.6 15.1 - - - -
3875D PHE* 3.9 22.2 - - + -
3879D LEU* 3.7 29.5 - - + +
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Residues in contact with MET3831 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3827D ILE* 3.0 31.2 + - + +
3828D GLN* 3.7 9.4 - - - +
3829D ALA 3.2 0.2 - - - -
3830D LEU* 1.3 79.3 - - - +
3832D GLN* 1.3 64.7 + - + +
3834D CYS* 3.8 13.8 + - - +
3879D LEU* 3.7 25.4 - - + -
3880D PHE* 3.6 28.9 - - + -
3883D LEU* 5.3 9.4 - - + -
3910D ILE* 5.4 2.7 - - + -
3913D CYS* 3.6 37.0 - - + +
3914D THR* 3.7 21.3 - - + +
3917D TYR* 4.3 7.7 - - + -
3920D ARG* 3.3 17.4 + - - -
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Residues in contact with GLN3832 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3828D GLN* 3.4 15.8 + - - +
3829D ALA* 3.4 8.6 + - - +
3830D LEU 3.3 0.6 - - - -
3831D MET* 1.3 81.1 - - - +
3833D THR* 1.3 61.1 + - + +
3834D CYS 3.2 8.0 + - - +
3913D CYS* 5.4 10.7 + - - +
3916D ASP* 5.7 6.7 - - - +
3920D ARG* 3.9 29.2 + - - +
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Residues in contact with THR3833 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3783D GLY 6.1 0.7 - - - +
3785D THR* 3.7 29.4 - - + +
3829D ALA* 3.1 15.7 + - + +
3830D LEU* 3.0 22.2 + - - +
3832D GLN* 1.3 76.8 - - + +
3834D CYS* 1.3 63.5 + - - +
3835D SER* 3.2 5.5 + - - -
3875D PHE* 4.8 6.4 - - - -
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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
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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