Contacts of the helix formed by residues 3786 - 3800 (chain H) 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 GLY3786 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3785H THR* 1.3 76.0 - - - +
3787H ALA* 1.3 66.7 + - - -
3788H MET* 3.2 3.4 - - - -
3789H VAL* 3.2 22.7 + - - +
3790H SER* 3.5 10.0 + - - -
3875H PHE* 5.2 4.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3787 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3714H GLU* 5.5 6.7 - - - +
3719H MET* 6.1 0.7 - - - -
3786H GLY* 1.3 73.2 - - - -
3788H MET* 1.3 60.0 + - - +
3790H SER* 2.9 19.2 + - - +
3791H SER* 2.9 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET3788 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3712H LEU* 4.6 8.5 - - + -
3713H ASP* 3.4 27.6 - - + +
3714H GLU 3.9 21.1 - - - +
3715H ASP* 4.0 10.5 - - + +
3718H TYR* 3.7 37.0 - - + -
3719H MET* 5.7 6.1 - - + +
3777H MET* 3.7 27.1 - - + +
3786H GLY* 3.2 0.8 - - - -
3787H ALA* 1.3 76.7 - - - +
3789H VAL* 1.3 68.9 + - + +
3791H SER* 3.3 9.1 + - - -
3792H THR* 3.2 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL3789 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3777H MET* 6.5 0.9 - - + -
3778H ILE* 4.8 10.8 - - + -
3781H CYS* 4.4 17.5 - - + -
3784H GLU* 3.4 25.4 - - + +
3785H THR 4.4 0.4 - - - -
3786H GLY* 3.2 20.3 + - - +
3788H MET* 1.3 84.0 - - + +
3790H SER* 1.3 59.0 + - - +
3792H THR* 3.0 18.7 + - - -
3793H LEU* 3.4 18.8 + - + +
3830H LEU* 4.3 24.5 - - + -
3875H PHE* 4.4 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER3790 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3786H GLY 3.5 6.3 + - - -
3787H ALA* 2.9 19.6 + - - -
3788H MET 3.3 0.2 - - - -
3789H VAL* 1.3 78.5 - - - +
3791H SER* 1.3 63.6 + - - +
3793H LEU* 3.7 6.1 + - - +
3794H LYS* 3.1 22.0 + - - +
3874H GLU 5.1 9.0 - - - -
3875H PHE* 4.3 23.5 - - - -
3878H ASP* 6.0 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER3791 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3718H TYR* 6.5 0.4 - - - -
3719H MET* 4.0 19.6 - - - +
3722H ALA* 4.3 24.4 - - - +
3787H ALA 2.9 16.3 + - - -
3788H MET* 3.3 11.2 + - - -
3789H VAL 3.3 0.8 - - - -
3790H SER* 1.3 77.9 + - - +
3792H THR* 1.3 64.1 + - - +
3794H LYS* 3.3 14.6 + - - +
3795H LEU* 3.3 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR3792 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3718H TYR* 3.4 42.4 - - + +
3722H ALA* 5.8 1.8 - - + -
3774H VAL* 4.7 15.8 - - + +
3777H MET* 3.7 19.2 - - + +
3778H ILE* 4.0 16.4 - - - +
3788H MET* 3.2 11.7 + - + +
3789H VAL* 3.0 19.8 + - - -
3791H SER* 1.3 77.3 - - - +
3793H LEU* 1.3 57.7 + - - +
3795H LEU* 3.4 6.8 + - - +
3796H GLY* 3.1 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3793 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3778H ILE* 3.8 25.6 - - + -
3789H VAL* 3.4 23.6 + - + +
3790H SER* 4.1 5.2 - - - +
3791H SER 3.3 0.2 - - - -
3792H THR* 1.3 76.6 + - - +
3794H LYS* 1.3 64.4 + - - +
3796H GLY* 4.4 1.8 - - - +
3797H ILE* 3.3 29.7 + - + +
3830H LEU* 4.9 5.2 - - + -
3875H PHE* 4.7 19.3 - - + +
3878H ASP* 4.9 15.3 - - + +
3879H LEU* 4.7 29.4 - - + +
3882H PHE* 4.6 27.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3794 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3723H ASP* 6.2 3.4 - - - -
3726H ALA* 4.2 11.1 - - + +
3790H SER 3.1 15.1 + - - +
3791H SER* 3.5 12.8 - - - +
3792H THR 3.2 0.6 - - - -
3793H LEU* 1.3 78.4 - - - +
3795H LEU* 1.3 59.2 + - - +
3797H ILE* 3.3 31.7 - - + +
3798H SER* 3.7 8.7 + - - -
3877H GLN* 5.6 8.5 - - - +
3878H ASP* 5.5 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3795 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3722H ALA* 3.5 32.1 - - + +
3725H MET* 3.8 35.0 - - + -
3726H ALA* 3.8 17.7 - - + +
3765H LEU* 5.1 2.7 - - + -
3770H ALA* 5.3 7.0 - - + +
3774H VAL* 3.9 23.8 - - + -
3791H SER 3.3 9.4 + - - +
3792H THR* 3.4 7.6 + - - +
3793H LEU 3.3 0.2 - - - -
3794H LYS* 1.3 78.1 - - - +
3796H GLY* 1.3 65.2 + - - +
3798H SER* 3.4 9.9 + - - -
3799H ILE* 3.5 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY3796 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3774H VAL* 4.9 11.4 - - - -
3792H THR 3.1 14.6 + - - -
3793H LEU* 3.5 2.8 + - - -
3794H LYS 3.4 0.4 - - - -
3795H LEU* 1.3 81.8 - - - +
3797H ILE* 1.3 60.1 + - - +
3798H SER 3.3 0.3 + - - -
3799H ILE* 3.4 12.6 + - - +
3800H LEU* 3.5 21.7 - - - +
3882H PHE* 3.9 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3797 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3793H LEU 3.3 14.1 - - - +
3794H LYS* 3.3 35.4 - - + +
3796H GLY* 1.3 75.0 - - - +
3798H SER* 1.3 61.9 + - - +
3799H ILE 3.3 0.2 - - - -
3800H LEU* 3.8 4.4 + - - +
3801H ASN* 3.3 25.1 + - - +
3877H GLN* 5.6 5.4 - - - +
3878H ASP* 4.1 18.2 - - + +
3881H ARG* 4.5 17.5 - - + -
3882H PHE* 3.8 37.7 - - + +
3885H LEU* 4.5 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER3798 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3726H ALA* 3.2 30.7 + - - -
3729H CYS* 3.2 28.8 - - - +
3730H HIS* 3.8 12.8 + - - -
3758H LEU* 5.8 2.6 - - - +
3794H LYS 3.9 9.4 - - - -
3795H LEU 3.4 11.1 + - - -
3796H GLY 3.2 1.0 - - - -
3797H ILE* 1.3 83.5 - - - +
3799H ILE* 1.3 61.5 + - - +
3801H ASN* 3.9 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3799 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3726H ALA* 6.5 0.4 - - - -
3729H CYS* 3.9 17.5 - - + -
3758H LEU* 5.4 1.9 - - - +
3762H GLN* 3.9 28.5 - - + +
3765H LEU* 3.7 35.2 - - + -
3766H HIS* 5.6 3.6 - - + +
3770H ALA* 6.1 1.8 - - + -
3771H ALA* 6.1 0.7 - - + -
3774H VAL* 6.3 0.4 - - + -
3795H LEU* 3.5 25.4 - - + +
3796H GLY* 3.4 7.5 + - - +
3797H ILE 3.3 0.6 - - - -
3798H SER* 1.3 81.8 - - - +
3800H LEU* 1.3 61.7 + - + +
3801H ASN 3.2 4.8 + - - -
3802H GLY 4.6 2.3 + - - -
3804H ASN* 3.7 11.8 + - - +
3807H VAL* 3.9 31.9 - - + -
3811H MET* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3800 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3796H GLY* 3.5 20.2 + - - +
3797H ILE* 3.8 2.2 + - - +
3798H SER 3.6 0.2 - - - -
3799H ILE* 1.3 79.5 - - + +
3801H ASN* 1.3 64.5 + - - +
3802H GLY 3.3 2.7 - - - -
3803H GLY* 3.1 15.2 + - - -
3804H ASN* 4.2 14.4 - - - +
3807H VAL* 3.7 25.8 - - + -
3808H GLN* 5.0 9.0 - - + -
3811H MET* 4.2 19.5 - - + -
3882H PHE* 4.7 8.7 - - + -
3885H LEU* 3.1 46.1 - - + +
3886H LEU* 3.9 25.1 - - + +
----------------------------------------------------------
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