Contacts of the helix formed by residues 775 - 789 (chain D) in PDB entry 2VE8
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 GLY 775 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769D GLN* 3.5 3.8 - - - -
774D ILE* 1.3 80.9 - - - +
776D TYR* 1.3 67.3 + - - -
777D ASN 3.4 2.5 - - - -
778D ARG* 3.4 8.2 + - - +
779D ALA* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 776 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765D ILE* 3.6 36.3 - - + +
766D SER 6.0 0.2 - - - -
769D GLN* 3.2 32.0 - - - +
775D GLY* 1.3 70.7 - - - -
777D ASN* 1.4 80.2 + - - +
779D ALA* 3.2 3.3 + - - +
780D ALA* 2.8 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 777 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775D GLY 3.4 0.6 - - - -
776D TYR* 1.4 99.5 - - - +
778D ARG* 1.4 58.6 + - - +
780D ALA* 3.5 5.4 - - - +
781D ARG* 2.8 39.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 778 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A LEU 2.9 22.6 + - - -
773A LYS* 2.9 33.7 + - - +
774A ILE* 4.2 9.1 - - - +
744D SER* 5.7 8.3 - - - +
747D ASP* 2.8 43.1 + - - +
748D PRO* 3.9 2.0 - - - +
749D LEU* 3.5 18.8 - - - +
774D ILE* 4.0 26.8 - - + +
775D GLY* 3.4 13.3 + - - +
776D TYR 3.3 0.4 - - - -
777D ASN* 1.4 79.2 - - - +
779D ALA* 1.3 61.9 + - - +
781D ARG* 3.4 5.5 + - - +
782D MET* 3.3 22.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
765D ILE* 3.8 10.1 - - + +
768D VAL* 3.9 22.1 - - + +
769D GLN* 3.7 19.5 - - + -
774D ILE* 3.8 12.0 - - + +
775D GLY 3.1 17.7 + - - +
776D TYR 3.6 3.1 - - - +
778D ARG* 1.3 75.7 - - - +
780D ALA* 1.3 65.5 + - - +
782D MET* 3.1 6.1 + - - +
783D ILE* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 780 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765D ILE* 3.7 31.1 - - + +
776D TYR* 2.8 23.5 + - + +
777D ASN* 3.2 9.8 + - - +
779D ALA* 1.3 78.6 - - - +
781D ARG* 1.4 63.6 + - + +
783D ILE* 3.2 4.6 + - - +
784D GLU* 3.0 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 781 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744D SER* 3.5 38.6 + - - +
745D GLU* 3.4 48.7 + - - +
777D ASN* 2.8 27.2 + - + +
778D ARG* 4.0 4.9 - - - +
779D ALA 3.3 0.2 - - - -
780D ALA* 1.4 74.5 - - + +
782D MET* 1.3 62.2 + - + +
784D GLU* 3.3 29.0 + - - +
785D ALA* 3.0 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 782 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747D ASP* 3.6 32.1 - - + +
749D LEU* 3.6 36.3 - - + +
750D TYR* 3.7 13.0 - - + -
753D ALA* 3.9 6.3 - - + -
768D VAL* 4.6 2.0 - - + -
772D LEU* 4.1 13.0 - - + -
774D ILE* 3.4 33.2 - - + -
778D ARG* 3.3 10.8 + - + +
779D ALA* 3.1 9.0 + - - +
781D ARG* 1.3 77.7 - - + +
783D ILE* 1.3 60.3 + - + +
785D ALA* 3.1 8.3 + - - +
786D MET* 2.9 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 783 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763D ALA* 3.4 24.0 - - + +
764D SER 3.7 4.0 - - - +
765D ILE* 3.5 36.6 - - + +
768D VAL* 4.0 16.6 - - + -
779D ALA 3.0 16.9 + - - +
780D ALA* 3.8 6.1 - - - +
781D ARG 3.2 0.2 - - - -
782D MET* 1.3 77.1 - - - +
784D GLU* 1.3 58.4 + - - +
786D MET* 3.0 17.0 + - + +
787D GLU* 2.9 26.4 + - - +
792D VAL* 4.1 5.6 - - + +
801D ARG* 3.3 40.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 784 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780D ALA* 3.0 27.8 + - - +
781D ARG* 3.5 37.1 + - - +
782D MET 3.2 0.2 - - - -
783D ILE* 1.3 76.3 - - - +
785D ALA* 1.3 60.7 + - - +
787D GLU* 3.1 11.6 + - - +
788D MET* 3.0 21.7 + - - +
801D ARG* 4.9 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 785 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745D GLU 4.5 13.5 - - - +
746D ASP* 5.0 7.6 - - - +
750D TYR* 3.7 21.1 + - + -
781D ARG 3.0 12.9 + - - +
782D MET* 3.1 11.0 + - + +
784D GLU* 1.3 75.7 - - - +
786D MET* 1.3 61.8 + - - +
788D MET* 3.3 9.4 + - - +
789D ALA* 3.0 23.7 + - - +
771G LYS* 6.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 786 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750D TYR* 3.6 21.8 - - + +
753D ALA* 3.4 45.3 - - + +
754D VAL* 3.8 14.1 - - + +
757D VAL* 3.9 32.1 - - + -
763D ALA* 5.9 0.2 - - - -
768D VAL* 5.0 1.3 - - + -
782D MET* 2.9 27.2 + - + +
783D ILE* 3.0 19.5 + - + +
785D ALA* 1.3 76.4 - - - +
787D GLU* 1.3 61.9 + - - +
789D ALA 3.3 0.9 + - - -
790D GLY 3.1 4.0 + - - -
791D VAL* 2.9 35.3 + - + +
792D VAL* 3.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 787 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783D ILE 2.9 8.8 + - - +
784D GLU* 3.1 11.9 + - - +
786D MET* 1.3 76.4 - - - +
788D MET* 1.3 64.5 + - - +
790D GLY* 3.0 14.0 + - - -
792D VAL* 3.7 12.0 - - + +
793D THR 4.0 2.0 - - - +
794D PRO* 3.2 44.1 - - + +
795D MET 4.4 0.7 + - - -
801D ARG* 2.7 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 788 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784D GLU 3.0 12.6 + - - +
785D ALA* 3.6 10.3 - - - +
787D GLU* 1.3 79.7 - - - +
789D ALA* 1.4 58.4 + - - +
790D GLY* 3.2 1.3 + - - -
773G LYS* 5.2 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 789 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750D TYR* 3.5 25.4 - - + +
785D ALA 3.0 11.4 + - - +
786D MET 3.3 2.4 + - - +
787D GLU 3.2 0.2 - - - -
788D MET* 1.4 74.8 - - - +
790D GLY* 1.3 61.2 + - - +
791D VAL* 3.3 7.5 + - + +
773G LYS* 6.0 5.6 - - - +
----------------------------------------------------------
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