Contacts of the helix formed by residues 768 - 786 (chain D) in PDB entry 5MS0
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 ASN 768 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620C ASN* 5.0 17.0 - - + -
1187C PHE* 4.7 7.9 - - - -
761D ALA* 4.9 4.0 - - - +
766D GLY 3.6 5.7 + - - +
767D LEU* 1.3 77.9 - - - +
769D VAL* 1.3 66.2 + - - +
770D LEU* 3.3 9.7 + - + +
771D GLN* 3.9 7.2 + - + +
772D TYR* 3.6 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 769 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657C THR* 5.9 6.1 - - - +
660C VAL* 4.5 22.0 - - + -
1187C PHE* 4.6 13.8 - - + +
768D ASN* 1.3 74.6 - - - +
770D LEU* 1.3 59.4 + - - +
771D GLN 3.5 0.2 - - - -
772D TYR* 3.7 6.0 + - - +
773D PHE* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 770 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768D ASN* 3.3 6.5 - - + +
769D VAL* 1.3 78.6 - - - +
771D GLN* 1.3 57.3 + - - +
773D PHE* 3.1 8.3 + - - +
774D ILE* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 771 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759D ILE* 4.3 23.3 - - + -
761D ALA* 5.1 15.3 - - + +
767D LEU* 6.0 2.9 - - + -
768D ASN* 3.9 11.3 + - + +
770D LEU* 1.3 75.8 - - - +
772D TYR* 1.3 62.0 + - - +
774D ILE* 3.3 8.8 + - - +
775D SER* 2.9 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 772 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671C LEU 5.7 5.2 - - - +
672C GLU* 6.0 4.3 - - - -
676C ALA* 5.5 4.2 - - - +
767D LEU* 6.1 3.0 - - + +
768D ASN 3.6 15.9 + - - +
769D VAL* 3.9 5.8 - - - +
770D LEU 3.3 0.2 - - - -
771D GLN* 1.3 78.8 - - - +
773D PHE* 1.3 60.1 + - - +
775D SER* 3.5 8.3 + - - +
776D THR* 3.5 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 773 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550C VAL* 6.1 0.9 - - - +
554C HIS 6.1 0.9 - - - +
560C PRO* 6.5 0.7 - - - -
769D VAL 3.0 20.0 + - - +
770D LEU* 3.1 8.9 + - - +
772D TYR* 1.3 75.4 - - - +
774D ILE* 1.3 63.3 + - - +
776D THR* 3.6 16.2 + - - -
777D HIS* 4.2 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 774 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747D MET* 4.3 17.9 - - + +
770D LEU 2.9 13.2 + - - +
771D GLN* 3.3 11.4 + - - +
773D PHE* 1.3 76.8 - - - +
775D SER* 1.3 62.3 + - - +
776D THR 3.1 0.4 - - - -
777D HIS* 3.2 23.4 + - - +
778D GLY 4.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 775 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676C ALA* 5.4 6.7 - - - -
747D MET* 5.0 7.8 - - - +
771D GLN 2.9 16.2 + - - -
772D TYR* 3.9 8.7 - - - -
773D PHE 3.4 0.4 - - - -
774D ILE* 1.3 76.2 - - - +
776D THR* 1.3 57.0 + - - +
777D HIS 3.2 0.2 - - - -
778D GLY* 3.5 4.1 + - - +
779D ALA* 2.9 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 776 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550C VAL* 5.6 6.5 - - - -
560C PRO* 4.4 27.1 - - - -
561C ILE* 6.0 2.5 - - - -
676C ALA* 5.0 8.1 - - - -
772D TYR 3.5 10.2 + - - -
773D PHE* 3.8 12.8 - - - -
774D ILE 3.1 1.2 - - - -
775D SER* 1.3 77.0 - - - +
777D HIS* 1.3 59.1 + - - +
779D ALA* 3.5 8.9 - - - +
780D ARG* 2.9 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 777 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C ASP* 6.0 2.2 - - - +
550C VAL* 5.6 9.8 - - - +
748D ALA 3.6 19.6 - - - +
749D LYS* 4.7 2.6 - - - -
750D PRO* 4.5 25.6 - - + +
773D PHE 4.2 3.8 + - - +
774D ILE* 3.2 15.7 + - - +
776D THR* 1.3 80.5 - - - +
778D GLY* 1.3 58.7 + - - +
780D ARG* 4.1 7.9 + - - +
781D LYS* 4.4 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 778 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747D MET* 5.8 3.6 - - - +
748D ALA 4.4 6.7 + - - -
774D ILE 4.1 1.0 + - - -
775D SER* 3.5 7.2 + - - +
777D HIS* 1.3 77.7 - - - +
779D ALA* 1.3 62.0 + - - +
780D ARG 3.3 1.2 + - - -
781D LYS* 3.8 15.7 + - - +
782D GLY 4.2 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 779 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676C ALA* 4.1 21.1 - - + +
677C ASN* 4.7 16.3 - - + +
775D SER 2.9 18.9 + - - +
776D THR* 3.2 12.0 + - - -
778D GLY* 1.3 75.6 - - - +
780D ARG* 1.3 61.8 - - - +
781D LYS 3.4 0.4 - - - -
782D GLY* 4.2 1.6 + - - -
783D LEU* 3.9 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 780 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548C ARG* 4.8 15.7 - - + +
549C ASP* 4.9 11.0 - - + -
550C VAL 5.6 1.1 - - - +
776D THR 2.9 15.0 + - - +
777D HIS* 4.4 6.1 - - - +
778D GLY 3.3 0.4 - - - -
779D ALA* 1.3 77.1 - - - +
781D LYS* 1.3 56.9 + - - +
783D LEU* 5.4 1.1 - - - -
784D ALA* 2.7 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 781 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777D HIS 4.4 5.9 + - - +
778D GLY* 3.8 12.8 + - - +
779D ALA 3.4 0.8 - - - -
780D ARG* 1.3 79.2 - - - +
782D GLY* 1.3 58.5 + - - +
784D ALA* 4.8 1.1 - - - -
785D ASP* 2.8 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 782 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778D GLY 4.2 5.4 + - - -
779D ALA 4.2 3.2 + - - -
781D LYS* 1.3 80.7 - - - +
783D LEU* 1.3 59.2 + - - +
785D ASP* 3.4 14.8 - - - +
786D THR* 3.6 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 783 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569C ILE* 3.5 15.9 - - + +
677C ASN* 6.0 7.9 - - + +
779D ALA 3.9 14.6 + - - +
780D ARG* 3.9 1.7 + - - -
781D LYS 3.5 0.2 - - - -
782D GLY* 1.3 72.9 - - - +
784D ALA* 1.3 64.3 + - - +
785D ASP 3.2 1.6 - - - -
786D THR* 3.3 7.4 + - - +
787D ALA 3.2 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 784 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548C ARG* 4.9 13.2 - - + -
569C ILE* 3.8 25.9 - - + +
570C GLY* 5.7 0.4 - - - -
780D ARG* 2.7 25.7 + - + +
781D LYS* 4.6 1.1 - - - +
783D LEU* 1.3 73.9 - - - +
785D ASP* 1.3 63.4 + - - +
787D ALA* 3.5 13.2 - - - +
788D LEU 4.7 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 785 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781D LYS 2.8 23.5 + - - +
782D GLY* 3.4 10.3 - - - +
784D ALA* 1.3 78.2 - - - +
786D THR* 1.3 57.1 + - - +
787D ALA 3.2 3.7 + - - -
788D LEU* 4.5 1.0 + - - +
789D LYS* 3.5 15.8 + - - +
930D LEU 5.6 2.9 - - - +
931D THR* 5.9 2.0 - - - -
932D MET* 4.9 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 786 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566C GLY 4.3 2.6 - - - +
782D GLY 3.6 10.0 + - - -
783D LEU* 3.3 10.8 + - - -
785D ASP* 1.3 76.3 - - - +
787D ALA* 1.3 63.5 + - - +
789D LYS* 3.7 17.0 - - - -
790D THR* 3.4 20.0 + - - -
----------------------------------------------------------
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