Contacts of the helix formed by residues 3748 - 3767 (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 PHE3748 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3747D SER* 1.3 81.0 + - - +
3749D GLU* 1.3 59.9 + - - +
3751D LYS* 3.9 6.2 - - + -
3752D GLU* 3.0 35.2 + - + +
4714D TRP* 3.7 31.9 - - + +
4715D ASP* 4.4 8.3 - - + -
4716D LYS 5.3 0.9 - - - -
4717D PHE* 4.4 26.5 - + - -
4994D ILE* 5.6 19.1 - - + -
5009D TRP* 5.6 13.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU3749 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3747D SER* 3.3 8.4 + - - +
3748D PHE* 1.3 84.7 - - - +
3750D GLU* 1.3 56.4 + - - +
3752D GLU* 4.0 3.3 - - - +
3753D MET* 3.1 29.1 + - - +
4714D TRP 5.3 2.9 + - - +
4716D LYS* 4.2 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU3750 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3747D SER* 3.5 22.1 + - - +
3748D PHE 3.3 0.4 - - - -
3749D GLU* 1.3 76.7 - - - +
3751D LYS* 1.3 64.5 + - - +
3753D MET* 3.5 5.6 + - - +
3754D GLU* 3.2 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3751 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3747D SER 3.0 18.6 + - - +
3748D PHE* 3.9 8.3 - - + +
3750D GLU* 1.3 77.8 - - - +
3752D GLU* 1.3 61.7 + - - +
3754D GLU* 3.5 4.5 + - - +
3755D LYS* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU3752 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3748D PHE* 3.0 28.8 + - + +
3749D GLU* 4.2 4.5 - - - +
3751D LYS* 1.3 76.5 - - - +
3753D MET* 1.3 62.3 + - - +
3755D LYS* 3.6 6.8 + - - +
3756D GLN* 3.2 22.0 + - - +
4717D PHE* 4.4 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET3753 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3749D GLU 3.1 19.1 + - - +
3750D GLU* 3.8 7.0 - - - +
3751D LYS 3.2 0.2 - - - -
3752D GLU* 1.3 77.4 - - - +
3754D GLU* 1.3 60.2 + - + +
3756D GLN* 3.3 6.7 + - - +
3757D ARG* 3.0 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU3754 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3750D GLU* 3.2 18.2 + - + +
3751D LYS* 4.1 4.5 - - - +
3753D MET* 1.3 76.0 - - + +
3755D LYS* 1.3 64.9 + - - +
3757D ARG* 3.4 38.5 + - - +
3758D LEU* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3755 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3751D LYS 3.1 18.2 + - - +
3752D GLU* 3.8 7.6 - - - +
3753D MET 3.3 0.4 - - - -
3754D GLU* 1.3 78.5 - - - +
3756D GLN* 1.3 61.2 + - - +
3758D LEU* 3.5 10.3 + - - +
3759D LEU* 3.2 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN3756 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3752D GLU 3.2 15.0 + - - +
3753D MET* 3.7 5.4 - - - +
3755D LYS* 1.3 77.4 - - - +
3757D ARG* 1.3 65.6 + - + +
3759D LEU* 3.0 17.3 + - - +
3760D TYR* 3.0 24.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3757 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3753D MET* 3.0 25.1 + - + +
3754D GLU* 3.4 37.8 + - - +
3755D LYS 3.4 0.2 - - - -
3756D GLN* 1.3 76.1 - - + +
3758D LEU* 1.3 61.7 + - - +
3760D TYR* 3.4 7.6 + - - +
3761D GLN* 2.9 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3758 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3729D CYS* 4.6 10.6 - - - +
3730D HIS* 5.2 12.1 - - - +
3754D GLU 3.1 17.4 + - - +
3755D LYS* 3.7 9.2 - - - +
3756D GLN 3.2 0.2 - - - -
3757D ARG* 1.3 77.7 - - - +
3759D LEU* 1.3 65.7 + - + +
3761D GLN* 3.4 8.3 + - - +
3762D GLN* 3.1 23.7 + - + +
3798D SER 5.8 3.6 - - - +
3799D ILE 5.4 2.0 - - - +
3801D ASN* 4.7 16.6 - - + +
3802D GLY* 3.6 38.4 - - - +
3804D ASN* 5.6 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3759 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3755D LYS 3.2 10.9 + - - +
3756D GLN* 3.0 27.2 + - - +
3758D LEU* 1.3 77.8 - - + +
3760D TYR* 1.3 60.3 + - - +
3762D GLN* 3.3 8.0 + - - +
3763D ALA* 2.7 30.5 + - - +
3804D ASN* 4.7 15.4 + - + +
3806D ASP* 5.7 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR3760 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3756D GLN* 3.0 14.8 + - + +
3757D ARG* 3.7 11.2 - - - +
3758D LEU 3.2 0.6 - - - -
3759D LEU* 1.3 74.8 - - - +
3761D GLN* 1.3 83.4 + - - +
3763D ALA* 3.3 9.2 + - + +
3764D ARG* 3.0 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN3761 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3728D SER 3.5 22.4 - - - +
3729D CYS* 3.4 32.5 - - - +
3731D LEU 5.2 5.3 - - - +
3757D ARG* 2.9 26.4 + - - +
3758D LEU* 3.4 6.4 + - - +
3760D TYR* 1.3 107.8 - - - +
3762D GLN* 1.3 60.7 + - - +
3764D ARG* 3.5 37.4 + - - +
3765D LEU* 4.0 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN3762 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3729D CYS* 4.0 13.6 - - - -
3758D LEU* 3.1 19.8 + - + +
3759D LEU* 3.7 5.2 - - - +
3761D GLN* 1.3 76.4 - - - +
3763D ALA* 1.3 59.0 + - - +
3765D LEU* 3.3 5.2 + - - +
3766D HIS* 2.9 27.8 + - + +
3799D ILE* 3.9 33.8 - - + +
3804D ASN* 4.1 15.5 - - - +
3806D ASP* 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3763 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3759D LEU 2.7 22.1 + - - +
3760D TYR* 3.3 12.3 + - + +
3762D GLN* 1.3 70.1 - - - +
3764D ARG* 1.3 64.4 + - - +
3765D LEU 3.2 0.2 - - - -
3766D HIS* 3.6 13.6 - - + -
3767D ASN* 3.1 25.5 + - - +
3806D ASP* 5.2 6.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3764 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3670D ILE* 3.6 28.2 - - - +
3671D ASP* 3.5 35.2 + - - +
3674D SER* 4.9 11.1 + - - +
3694D LEU* 4.4 16.7 - - + +
3760D TYR* 3.0 45.1 + - + +
3761D GLN* 3.5 33.1 - - - +
3762D GLN 3.2 0.4 - - - -
3763D ALA* 1.3 78.8 - - - +
3765D LEU* 1.3 64.5 + - + +
3767D ASN* 4.4 5.1 + - - +
3768D ARG* 4.5 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3765 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3670D ILE* 5.5 2.9 - - + -
3694D LEU* 4.7 17.3 - - + -
3725D MET* 3.6 51.8 - - + +
3726D ALA* 6.0 0.4 - - - -
3729D CYS* 4.7 7.0 - - + -
3761D GLN 4.4 7.0 - - - +
3762D GLN 3.3 5.6 + - - +
3763D ALA 3.2 0.2 - - - -
3764D ARG* 1.3 83.9 - - + +
3766D HIS* 1.3 64.7 + - - +
3767D ASN 3.3 1.8 - - - -
3768D ARG* 3.3 20.2 + - + +
3770D ALA* 3.3 28.6 + - + +
3771D ALA 4.6 0.9 + - - -
3795D LEU* 5.1 4.7 - - + -
3799D ILE* 3.7 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS3766 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3762D GLN 2.9 18.8 + - - +
3763D ALA* 3.4 13.2 + - + -
3765D LEU* 1.3 74.8 - - - +
3767D ASN* 1.3 66.6 + - - +
3768D ARG 3.2 6.6 - - - +
3771D ALA* 5.4 7.2 - - - +
3799D ILE* 5.6 3.3 - - + +
3806D ASP* 3.1 54.7 + - + +
3807D VAL* 3.9 19.5 - - + +
3809D GLN* 5.0 3.6 + - - -
3810D LYS* 3.5 27.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN3767 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3695D HIS* 5.4 1.0 - - - -
3763D ALA 3.1 16.6 + - - +
3764D ARG 4.6 4.3 - - - +
3765D LEU 3.3 0.2 - - - -
3766D HIS* 1.3 80.7 - - - +
3768D ARG* 1.3 62.9 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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