Contacts of the helix formed by residues 749 - 765 (chain A) in PDB entry 3B2T
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 THR 749 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A GLN* 4.0 19.7 - - - +
747A ARG 5.0 1.8 - - - +
748A PRO* 1.3 77.5 - - - +
750A PHE* 1.3 65.2 + - - +
751A LYS* 3.4 10.7 + - - +
752A GLN* 2.9 41.3 + - - +
753A LEU* 2.9 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 750 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A ALA* 4.4 6.5 - - - -
614A MET* 3.5 54.5 - - + -
615A GLU* 3.6 20.6 - - + +
618A ALA* 4.3 14.6 - - + -
682A HIS* 3.9 7.0 - - + -
683A GLN* 5.0 0.8 - - - +
685A ASP* 3.6 33.9 - - + -
686A VAL* 3.6 18.6 - - + +
689A PHE* 3.7 26.7 - + + -
748A PRO 4.2 0.2 + - - -
749A THR* 1.3 75.2 - - - +
751A LYS* 1.3 63.0 + - - +
753A LEU* 3.6 17.7 - - + +
754A VAL* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 751 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A GLU* 3.5 27.1 + - + +
749A THR* 3.1 9.7 + - - +
750A PHE* 1.3 78.6 - - - +
752A GLN* 1.3 64.3 + - + +
754A VAL* 3.3 2.8 + - - +
755A GLU* 3.1 49.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 752 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A ARG 4.5 0.7 - - - +
748A PRO* 3.3 16.7 - - + +
749A THR* 2.9 40.6 + - - +
751A LYS* 1.3 79.7 - - + +
753A LEU* 1.3 62.4 + - - +
755A GLU* 3.3 15.5 + - - +
756A ASP* 3.1 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 753 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A ALA* 4.5 9.9 - - + -
686A VAL* 4.2 9.9 - - + -
689A PHE* 3.7 27.8 - - + -
735A MET* 3.5 37.0 - - + -
739A CYS* 4.1 14.1 - - - -
748A PRO* 3.7 19.5 - - + -
749A THR 2.9 15.8 + - - +
750A PHE* 3.2 27.1 + - + +
752A GLN* 1.3 76.5 - - - +
754A VAL* 1.3 59.3 + - - +
756A ASP* 4.0 4.2 - - - +
757A LEU* 3.0 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 754 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A TYR* 3.7 21.3 - - + +
611A ALA* 3.4 36.6 - - + +
612A ARG* 3.7 10.8 - - + +
615A GLU* 3.3 28.3 - - - +
750A PHE 2.9 21.6 + - - +
751A LYS 3.6 4.9 - - - +
752A GLN 3.2 0.2 - - - -
753A LEU* 1.3 75.2 - - - +
755A GLU* 1.3 62.8 + - + +
757A LEU* 3.4 1.8 + - - -
758A ASP* 2.9 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 755 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751A LYS* 3.1 40.9 + - + +
752A GLN* 3.3 19.2 + - - +
754A VAL* 1.3 79.4 - - + +
756A ASP* 1.3 63.5 + - - +
758A ASP* 3.5 6.3 + - - +
759A ARG* 3.3 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 756 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735A MET* 3.8 21.8 - - + +
748A PRO* 5.9 1.9 - - - +
752A GLN* 3.1 25.3 + - - +
753A LEU* 4.0 4.0 - - - +
755A GLU* 1.3 77.4 - - - +
757A LEU* 1.3 58.9 + - - +
759A ARG* 2.8 43.0 + - - +
760A ILE* 3.1 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 757 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A VAL* 4.5 10.6 - - + +
607A THR* 3.7 36.8 - - + +
608A TYR* 3.9 18.2 - - + +
611A ALA* 3.6 25.6 - - + -
689A PHE* 4.2 5.8 - - + -
732A LEU* 4.0 17.7 - - + -
735A MET* 3.8 28.3 - - + -
753A LEU* 3.0 24.1 + - + +
756A ASP* 1.3 74.3 - - - +
758A ASP* 1.3 61.7 + - - +
760A ILE* 3.9 3.1 - - + +
761A LEU* 2.8 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 758 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A TYR* 3.6 30.5 + - + -
754A VAL* 2.9 20.3 + - + +
755A GLU* 3.7 7.2 - - - +
756A ASP 3.3 0.2 - - - -
757A LEU* 1.3 76.0 - - - +
759A ARG* 1.3 57.8 + - - +
761A LEU* 3.7 4.9 - - - +
762A THR* 2.9 42.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 759 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A GLU* 3.5 24.9 + - - +
735A MET* 5.6 0.2 - - - +
755A GLU 3.3 9.8 + - - +
756A ASP* 2.8 48.7 + - - +
757A LEU 3.2 0.2 - - - -
758A ASP* 1.3 80.4 + - - +
760A ILE* 1.3 65.0 + - - +
762A THR* 3.4 4.9 + - - -
763A LEU* 3.1 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 760 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A PHE* 5.6 1.3 - - + -
604A VAL* 4.1 20.0 - - + -
731A GLU* 3.5 43.7 - - + +
732A LEU* 4.1 22.0 - - + -
735A MET* 3.8 25.4 - - + -
756A ASP 3.1 18.0 + - - +
757A LEU* 3.9 5.6 - - - +
759A ARG* 1.3 81.7 - - - +
761A LEU* 1.3 59.5 + - - +
763A LEU* 3.3 7.7 + - - +
764A THR* 2.7 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 761 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A LYS* 4.1 15.7 - - + +
604A VAL* 3.7 14.1 - - + +
605A SER* 3.9 35.9 - - - +
608A TYR* 3.7 36.8 - - + -
757A LEU 2.8 23.2 + - - +
758A ASP* 3.7 6.3 - - - +
760A ILE* 1.3 74.2 - - - +
762A THR* 1.3 63.8 + - - +
764A THR* 3.0 3.7 + - - -
765A THR* 2.8 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 762 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758A ASP* 2.9 28.9 + - - -
759A ARG* 3.7 6.1 - - - -
761A LEU* 1.3 76.7 - - - +
763A LEU* 1.3 63.6 + - + +
765A THR* 3.2 15.2 + - - +
767A GLN* 3.2 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 763 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A ARG* 3.1 20.1 + - + +
760A ILE* 3.8 6.3 - - - +
761A LEU 3.2 0.2 - - - -
762A THR* 1.3 80.9 - - + +
764A THR* 1.3 60.5 + - - +
765A THR 4.7 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 764 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A PHE* 3.5 37.1 - - + -
601A LYS* 3.9 25.1 - - + +
604A VAL* 4.7 2.6 - - - +
760A ILE* 2.7 30.7 + - - +
761A LEU* 3.0 8.6 + - - -
763A LEU* 1.3 78.5 - - - +
765A THR* 1.3 60.8 + - - +
766A ASN 3.7 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 765 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A LYS* 3.7 31.1 - - - -
761A LEU* 2.8 29.0 + - - +
762A THR* 3.2 10.3 + - - +
763A LEU 4.7 1.9 - - - +
764A THR* 1.3 76.8 - - - +
766A ASN* 1.3 71.1 + - - +
767A GLN* 2.8 34.8 + - - +
----------------------------------------------------------
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