Contacts of the helix formed by residues 748 - 763 (chain A) in PDB entry 3BG5
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 LYS 748 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A ASP* 3.0 37.1 + - - +
711A LEU* 4.3 20.4 - - + +
746A LEU 2.8 12.1 + - - +
747A LEU* 1.3 71.7 - - - +
749A PRO* 1.3 76.9 - - + +
750A LYS 4.7 0.4 - - - +
751A ALA* 2.9 18.2 + - + +
752A ALA* 3.0 10.4 + - - +
862A TYR* 3.7 51.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 749 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A LYS* 1.3 84.9 - - + -
750A LYS* 1.3 62.0 + - - +
752A ALA* 3.1 14.8 + - + +
753A TYR 3.2 8.7 + - - -
778A ASN* 4.2 18.2 - - + +
781A LEU* 3.7 50.3 - - + +
782A THR* 3.5 20.8 - - - +
785A GLN* 3.3 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 750 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A LEU* 3.8 21.5 - - + -
748A LYS* 3.3 1.4 - - - +
749A PRO* 1.3 77.1 - - - +
751A ALA* 1.3 64.2 + - - +
753A TYR* 3.0 33.4 + - + +
754A GLU* 2.9 44.9 + - + +
785A GLN* 4.5 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 751 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A TYR* 3.8 22.4 - - - +
709A ASP* 4.4 2.9 - - - +
710A ILE* 3.5 17.7 - - + +
711A LEU* 3.8 21.3 - - + +
747A LEU* 4.0 7.4 - - + -
748A LYS* 2.9 18.0 + - + +
750A LYS* 1.3 78.0 - - - +
752A ALA* 1.3 53.5 + - - +
754A GLU* 3.5 0.8 + - - -
755A LEU* 2.7 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 752 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A LEU* 3.7 32.4 - - + +
748A LYS 3.0 6.4 + - - +
749A PRO 3.1 10.7 + - - +
751A ALA* 1.3 77.6 - - - +
753A TYR* 1.3 56.8 + - - +
755A LEU* 4.6 0.9 - - - -
756A ILE* 3.0 36.7 + - - +
782A THR* 3.6 29.2 - - + +
786A ALA* 4.4 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 753 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A PRO 3.2 3.9 + - - +
750A LYS* 3.0 34.8 + - + +
752A ALA* 1.3 74.9 - - - +
754A GLU* 1.3 70.8 + - + +
757A GLY* 3.1 21.1 + - - -
785A GLN* 3.3 43.7 - - + +
788A ASP* 4.1 19.5 - - + -
789A ALA* 3.5 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 754 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A ILE* 4.0 21.1 - - + +
711A LEU* 3.5 25.7 - - - +
720A LEU* 4.6 13.3 - - + +
750A LYS* 2.9 33.4 + - + +
751A ALA 3.8 3.6 - - - +
753A TYR* 1.3 82.3 - - + +
755A LEU* 1.3 61.4 + - - +
757A GLY* 4.0 0.3 - - - -
758A GLU* 3.2 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 755 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A TYR* 4.1 15.7 - - + -
710A ILE* 3.9 10.5 - - + +
720A LEU* 4.2 13.0 - - + -
723A TYR* 3.8 33.7 - - + -
724A VAL* 6.3 0.2 - - + -
740A ILE* 4.2 21.3 - - + -
747A LEU* 3.7 26.5 - - + -
751A ALA 2.7 23.0 + - - +
752A ALA 4.1 1.8 - - - +
754A GLU* 1.3 74.8 - - - +
756A ILE* 1.3 65.9 + - + +
758A GLU* 3.4 1.6 + - - +
759A LEU* 3.1 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 756 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740A ILE* 4.6 12.8 - - + -
747A LEU* 5.7 0.7 - - + -
752A ALA* 3.0 26.7 + - - +
755A LEU* 1.3 76.2 - - + +
757A GLY* 1.3 58.9 + - - +
759A LEU* 3.2 6.7 + - + +
760A LYS* 2.9 36.5 + - + +
768A ILE* 3.8 27.6 - - + -
770A LEU* 4.7 12.1 - - + -
786A ALA* 3.8 22.0 - - + +
789A ALA* 3.8 13.2 - - + +
791A VAL* 3.7 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 757 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A TYR 3.1 17.1 + - - -
754A GLU 4.0 0.4 - - - -
756A ILE* 1.3 76.4 - - - +
758A GLU* 1.3 62.0 + - - +
760A LYS* 3.6 3.1 + - - +
761A SER* 3.2 23.4 + - - -
789A ALA* 3.8 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 758 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A LEU* 3.4 41.6 - - + +
724A VAL* 4.1 15.8 - - + +
754A GLU* 3.2 20.9 + - + +
755A LEU 3.7 4.5 - - - +
757A GLY* 1.3 73.9 - - - +
759A LEU* 1.3 59.3 - - - +
761A SER* 3.3 7.9 + - - -
762A ALA* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 759 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A ILE* 5.1 1.3 - - + -
723A TYR* 3.9 18.2 - - + +
724A VAL* 4.3 9.9 - - + +
727A ALA* 3.5 30.7 - - + -
738A LEU* 4.2 9.6 - - + -
740A ILE* 3.9 27.8 - - + -
755A LEU* 3.1 40.9 + - + +
756A ILE* 3.7 5.2 - - + +
758A GLU* 1.3 77.2 - - + +
760A LYS* 1.3 59.5 + - - +
762A ALA* 2.8 20.0 + - + +
763A VAL* 2.8 20.8 + - + +
768A ILE* 3.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 760 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A LYS* 4.8 9.7 + - - +
756A ILE* 2.9 26.0 + - + +
757A GLY 3.8 5.2 - - - +
759A LEU* 1.3 71.3 - - - +
761A SER* 1.3 56.6 + - - +
763A VAL 3.1 18.2 - - - +
765A ASP* 5.3 1.4 - - - +
766A LEU 4.5 7.6 + - - -
767A PRO* 4.7 3.2 - - - +
768A ILE* 3.6 17.7 - - + +
789A ALA 4.0 13.7 - - - +
790A GLY* 3.2 23.2 + - - +
792A ASP* 2.8 40.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 761 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757A GLY 3.2 14.5 + - - -
758A GLU* 3.6 7.2 - - - -
759A LEU 3.1 0.8 - - - -
760A LYS* 1.3 80.5 - - - +
762A ALA* 1.3 57.9 + - - +
763A VAL 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 762 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A VAL* 4.0 18.6 - - + +
728A LYS* 3.1 41.5 + - - +
731A GLU* 4.5 2.1 - - - +
758A GLU* 2.9 16.6 + - - +
759A LEU* 2.8 9.4 + - + +
761A SER* 1.3 79.7 - - - +
763A VAL* 1.3 67.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 763 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A ALA* 3.9 10.5 - - + +
728A LYS* 3.8 29.8 - - + +
731A GLU* 3.5 26.0 - - + +
738A LEU* 4.0 24.7 - - + -
759A LEU* 2.8 21.1 + - - +
760A LYS* 3.1 19.9 - - - +
761A SER 5.3 0.2 - - - -
762A ALA* 1.3 84.1 - - + +
765A ASP* 1.3 65.5 + - - +
766A LEU* 3.3 20.3 - - + +
768A ILE* 5.0 1.3 - - + -
----------------------------------------------------------
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