Contacts of the helix formed by residues 3769 - 3781 (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 GLY3769 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3695D HIS* 3.8 14.3 + - - -
3698D VAL* 3.5 21.2 - - - +
3699D LEU* 5.5 6.1 - - - +
3768D ARG* 1.3 75.1 - - - +
3770D ALA* 1.3 60.3 + - - +
3771D ALA 3.5 1.8 - - - -
3772D GLU* 3.8 16.3 + - - +
3773D MET* 3.6 15.8 + - - +
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Residues in contact with ALA3770 (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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3698D VAL* 4.0 10.0 - - + +
3725D MET* 5.2 6.5 - - - -
3765D LEU* 3.3 42.4 - - + +
3768D ARG* 3.1 6.0 + - + -
3769D GLY* 1.3 76.8 - - - +
3771D ALA* 1.3 63.9 + - - +
3772D GLU 3.2 0.4 - - - -
3773D MET* 3.4 12.4 + - - +
3774D VAL* 3.5 19.8 + - - +
3795D LEU* 5.6 5.6 - - + -
3799D ILE* 6.1 1.8 - - + -
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Residues in contact with ALA3771 (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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3765D LEU 4.6 2.7 + - - +
3766D HIS* 5.4 6.7 - - - +
3768D ARG 4.6 1.9 + - - +
3769D GLY* 3.5 0.6 - - - -
3770D ALA* 1.3 78.5 - - - +
3772D GLU* 1.3 65.1 + - + +
3774D VAL* 3.3 22.9 - - - +
3775D LEU* 3.5 13.2 - - - +
3799D ILE* 6.1 0.9 - - + -
3807D VAL* 3.9 27.4 - - + -
3810D LYS* 4.9 16.2 - - + +
3811D MET* 4.4 9.8 - - + +
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Residues in contact with GLU3772 (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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3769D GLY* 3.8 16.1 + - - +
3770D ALA 3.2 1.0 - - - -
3771D ALA* 1.3 80.4 - - + +
3773D MET* 1.3 63.8 + - - +
3775D LEU* 3.5 5.4 + - - +
3776D GLN* 3.3 36.5 + - - +
3810D LYS* 3.1 38.2 - - + +
3813D ASP* 4.7 0.9 - - - +
3814D TYR* 3.2 42.8 - - - +
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Residues in contact with MET3773 (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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3698D VAL* 4.3 16.8 - - - +
3701D PHE* 5.4 9.6 - - + -
3702D SER* 5.7 5.8 - - - +
3718D TYR* 4.4 10.7 + - - +
3769D GLY 3.6 11.1 + - - +
3770D ALA* 3.4 11.1 + - - +
3771D ALA 3.3 0.8 - - - -
3772D GLU* 1.3 79.8 - - - +
3774D VAL* 1.3 62.6 - - + +
3776D GLN* 3.6 7.5 + - - +
3777D MET* 3.3 26.0 + - - +
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Residues in contact with VAL3774 (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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3718D TYR* 5.3 5.6 - - - +
3770D ALA 3.5 13.2 - - - +
3771D ALA* 3.3 22.2 - - - +
3773D MET* 1.3 78.7 - - + +
3775D LEU* 1.3 69.8 + - + +
3777D MET* 4.2 4.9 - - - +
3778D ILE* 3.2 27.4 + - - +
3792D THR* 4.7 20.0 - - - +
3795D LEU* 3.9 26.5 - - + -
3796D GLY* 4.9 13.2 - - - -
3799D ILE* 6.3 0.9 - - + -
3811D MET* 4.5 8.3 - - + -
3823D PHE* 4.8 0.2 - - - -
3882D PHE* 5.3 6.4 - - + -
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Residues in contact with LEU3775 (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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3771D ALA 3.5 16.4 - - - +
3772D GLU* 3.5 10.2 + - - +
3773D MET 3.2 0.4 - - - -
3774D VAL* 1.3 92.5 - - + +
3776D GLN* 1.3 63.3 + - - +
3777D MET 3.3 0.4 - - - -
3778D ILE 3.5 0.5 + - - -
3779D SER* 3.5 9.0 + - - -
3811D MET* 3.8 53.2 - - + +
3814D TYR* 4.5 18.2 - - + -
3815D LEU* 4.4 19.5 - - + -
3823D PHE* 3.2 46.5 - - + -
3882D PHE* 5.2 5.6 - - + -
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Residues in contact with GLN3776 (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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462D GLU* 4.1 17.2 + - - +
3702D SER* 4.1 22.6 - - - -
3705D ALA* 4.4 6.6 - - + +
3706D LEU* 3.4 32.2 - - + +
3772D GLU* 3.3 26.1 + - - +
3773D MET* 4.3 4.6 - - - +
3774D VAL 3.6 0.2 - - - -
3775D LEU* 1.3 76.3 - - - +
3777D MET* 1.3 59.3 + - - +
3779D SER* 3.5 6.9 + - - +
3780D ALA* 3.1 25.8 + - - +
3814D TYR* 2.9 41.0 + - + +
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Residues in contact with MET3777 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3701D PHE* 5.9 1.1 - - - +
3704D THR* 5.8 2.5 - - - -
3705D ALA* 4.5 15.8 - - + +
3712D LEU* 5.8 4.5 - - + -
3718D TYR* 3.8 20.4 - - + +
3773D MET 3.3 19.5 + - - +
3774D VAL 4.6 3.1 - - - +
3775D LEU 3.3 0.2 - - - -
3776D GLN* 1.3 75.9 - - - +
3778D ILE* 1.3 64.9 + - - +
3780D ALA* 3.2 26.4 + - + +
3781D CYS* 3.4 14.2 + - + +
3788D MET* 3.7 29.2 - - + +
3789D VAL* 6.5 0.9 - - + -
3792D THR* 3.7 31.9 - - + +
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Residues in contact with ILE3778 (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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3774D VAL 3.2 19.0 + - - +
3775D LEU 3.5 1.2 + - - +
3776D GLN 3.3 0.6 - - - -
3777D MET* 1.3 78.1 - - + +
3779D SER* 1.3 60.3 + - - +
3781D CYS* 3.2 19.9 - - - -
3789D VAL* 4.8 12.3 - - + -
3792D THR* 4.0 19.1 - - - +
3793D LEU* 3.8 31.9 - - + -
3823D PHE* 3.8 30.7 - - + +
3826D SER* 3.1 31.5 + - - +
3827D ILE* 4.8 6.7 - - + -
3830D LEU* 5.4 8.5 - - + -
3882D PHE* 6.3 2.9 - - + -
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Residues in contact with SER3779 (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 3.5 8.1 + - - -
3776D GLN* 3.5 10.1 + - - -
3777D MET 3.3 0.4 - - - -
3778D ILE* 1.3 79.9 - - - +
3780D ALA* 1.3 60.9 + - - +
3781D CYS 3.3 0.7 + - - -
3782D LYS* 3.6 10.5 + - - +
3821D VAL 4.6 2.6 + - - -
3822D GLY* 3.7 26.5 - - - +
3823D PHE* 3.7 23.0 + - - +
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Residues in contact with ALA3780 (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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3705D ALA* 3.9 25.1 - - + +
3710D SER 4.5 3.8 - - - +
3711D LYS 2.9 20.1 - - - +
3776D GLN 3.1 17.0 + - - +
3777D MET* 3.2 24.8 + - + +
3779D SER* 1.3 76.0 - - - +
3781D CYS* 1.3 61.2 + - - +
3782D LYS* 3.2 4.9 + - - +
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Residues in contact with CYS3781 (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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3711D LYS* 4.1 9.9 - - - +
3712D LEU* 5.2 5.3 - - + +
3777D MET* 3.4 14.7 + - + +
3778D ILE* 3.2 22.9 - - - +
3779D SER 3.3 1.2 - - - -
3780D ALA* 1.3 79.1 - - - +
3782D LYS* 1.3 63.9 + - - +
3783D GLY* 3.2 18.6 + - - -
3784D GLU* 3.4 39.7 + - + +
3789D VAL* 4.4 19.5 - - + -
3826D SER* 3.7 11.4 - - - -
3830D LEU* 5.3 5.4 - - - -
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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