Contacts of the helix formed by residues 753 - 765 (chain A) in PDB entry 3T6A
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 ALA 753 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A PHE* 2.9 31.4 + - + +
750A MET 3.3 2.9 - - - +
752A GLU* 1.3 76.0 - - - +
754A ALA* 1.3 64.6 + - - +
755A ASP* 2.8 6.3 + - - -
756A SER* 2.9 30.6 + - - +
757A TYR* 3.7 5.9 - - + -
697C SER 4.0 20.9 - - - +
698C THR* 4.1 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 754 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A ILE* 5.4 1.0 - - - +
581A SER* 3.7 32.7 + - - +
583A LEU* 4.2 9.3 - - + +
584A GLU* 4.5 10.1 - - - +
750A MET 2.7 15.9 + - - +
751A ALA 3.4 16.5 + - - +
752A GLU 3.4 1.2 + - - -
753A ALA* 1.3 71.8 - - - +
755A ASP* 1.3 62.8 + - - +
757A TYR* 3.3 25.5 + - - +
758A ARG* 3.7 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 755 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A SER* 5.6 5.9 - - - -
581A SER* 6.1 0.7 - - - -
752A GLU 5.2 0.6 + - - +
753A ALA 2.8 6.2 + - - -
754A ALA* 1.3 76.6 - - - +
756A SER* 1.3 62.2 + - - +
758A ARG* 2.6 50.5 + - - +
759A MET* 3.0 34.5 + - + +
698C THR 5.8 3.6 - - - +
699C CYS* 6.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 756 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A VAL 5.3 0.4 - - - -
753A ALA* 2.9 26.9 + - - +
755A ASP* 1.3 78.6 - - - +
757A TYR* 1.3 64.6 + - - +
759A MET* 3.0 25.2 - - - +
760A ASN* 3.0 13.3 + - - +
698C THR 6.2 0.4 - - - -
700C VAL* 3.4 41.6 + - - +
704C ASN* 5.0 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 757 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A ILE* 4.1 5.4 - - + -
583A LEU* 3.4 22.0 - - + -
696A GLU* 5.5 0.9 + - - -
705A VAL* 3.6 42.6 - - + -
706A SER 3.6 20.9 - - - +
708A PRO* 3.7 17.9 - - + +
746A THR* 5.8 3.3 - - - +
749A PHE* 5.0 10.8 - + - -
750A MET* 3.8 46.1 - - + +
753A ALA* 3.7 12.1 - - + -
754A ALA* 3.5 13.0 - - - +
755A ASP 3.1 0.6 - - - -
756A SER* 1.3 80.2 + - - +
758A ARG* 1.3 65.2 + - - +
760A ASN* 3.0 4.9 + - - +
761A ALA* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 758 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A ILE* 3.0 38.6 - - + +
567A LEU* 3.9 8.0 - - + +
581A SER* 6.5 0.4 - - - -
754A ALA 3.7 3.0 + - - +
755A ASP* 2.6 53.3 + - - +
757A TYR* 1.3 77.7 - - - +
759A MET* 1.3 74.8 + - - +
761A ALA* 3.3 2.6 + - - +
762A GLU* 2.9 69.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 759 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A ASP* 3.0 25.2 + - + +
756A SER* 3.0 19.5 - - - +
758A ARG* 1.3 98.4 - - - +
760A ASN* 1.3 58.6 + - - +
762A GLU* 3.5 4.0 + - - +
763A ARG* 3.1 22.9 + - - +
700C VAL* 3.2 24.7 - - + +
701C PRO* 3.7 7.4 - - + +
702C PRO* 3.2 51.1 - - + +
704C ASN* 5.1 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 760 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A ASN 3.0 21.0 + - - -
704A ASN* 3.3 5.8 + - - +
705A VAL 3.4 26.9 + - - +
706A SER* 3.0 20.6 + - - +
756A SER 3.0 11.2 + - - +
757A TYR 3.0 5.6 + - - +
759A MET* 1.3 75.0 - - - +
761A ALA* 1.3 59.3 + - - +
763A ARG* 2.9 26.9 + - - +
764A ILE* 3.0 41.7 + - - +
704C ASN* 3.2 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 761 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A LEU* 4.7 3.4 - - + -
561A CYS* 3.7 30.1 - - - -
566A ILE* 4.6 1.1 - - + -
567A LEU* 3.9 13.2 - - + -
706A SER* 3.8 15.2 + - - -
757A TYR 2.9 15.6 + - - +
758A ARG* 3.3 5.6 + - - +
760A ASN* 1.3 77.7 - - - +
762A GLU* 1.3 58.4 + - - +
764A ILE* 3.5 2.8 + - - +
765A LEU* 3.0 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 762 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A LEU* 4.1 18.0 - - + +
758A ARG* 2.9 55.0 + - - +
759A MET* 3.8 5.1 - - - +
761A ALA* 1.3 75.4 - - - +
763A ARG* 1.3 57.4 + - - +
765A LEU* 3.7 2.4 - - - -
766A ALA* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 763 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A ASN* 2.9 48.2 + - - +
704A ASN* 4.7 0.2 - - - +
759A MET 3.1 13.7 + - - +
760A ASN* 2.9 38.0 + - - +
762A GLU* 1.3 76.2 - - - +
764A ILE* 1.3 68.8 + - - +
765A LEU 3.4 0.2 + - - -
766A ALA* 3.4 15.5 + - - +
702C PRO 4.3 11.7 + - - +
703C ASN* 3.4 25.8 - - - +
704C ASN* 4.3 6.5 + - - +
763C ARG* 3.3 30.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 764 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A GLN* 5.3 5.9 + - - -
557A LEU* 3.9 20.6 - - + -
640A SER 3.2 25.1 - - - +
641A MET* 3.3 24.0 - - + +
703A ASN* 3.7 19.1 - - - +
706A SER* 3.3 24.9 - - - +
760A ASN* 3.0 27.4 + - - +
761A ALA 4.0 2.7 - - - +
763A ARG* 1.3 86.9 - - - +
765A LEU* 1.3 63.2 + - + +
766A ALA 3.7 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 765 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A GLN* 4.2 25.4 - - + +
557A LEU* 4.1 26.5 - - + -
558A SER* 3.9 29.2 - - - -
567A LEU* 4.2 17.9 - - + -
761A ALA* 3.0 21.6 + - + +
762A GLU* 3.7 3.6 - - - +
764A ILE* 1.3 82.4 - - + +
766A ALA* 1.3 67.8 + - - +
767A GLY 3.1 0.7 + - - -
768A PHE* 2.9 37.9 + - + +
----------------------------------------------------------
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