Contacts of the helix formed by residues 789 - 802 (chain A) in PDB entry 5J3V
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 MET 789 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751A LEU* 3.5 32.5 - - + -
752A HIS* 4.0 30.5 - - + +
755A VAL* 4.9 8.7 - - + -
785A GLU 5.6 1.6 - - - +
786A VAL 3.2 8.3 + - - +
787A ALA 3.1 0.8 - - - -
788A PRO* 1.3 86.2 - - + +
790A LEU* 1.3 63.7 + - - +
791A GLN 3.1 3.1 - - - +
792A GLN* 3.2 51.7 - - + +
793A PHE* 3.0 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 790 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786A VAL 3.6 1.8 + - - -
787A ALA* 3.0 20.4 + - - +
788A PRO 3.4 0.2 - - - -
789A MET* 1.3 78.8 - - - +
791A GLN* 1.3 61.7 + - - +
792A GLN 3.2 1.2 + - - -
793A PHE* 3.5 18.8 - - + -
794A ILE* 3.4 34.6 + - + +
817A ILE* 3.7 31.2 - - + -
820A MET* 3.2 28.0 - - + +
821A ILE* 3.8 18.4 - - + -
824A ASN 4.0 11.9 - - - +
827A GLY* 4.3 7.9 - - - +
828A VAL* 4.3 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 791 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A PRO* 4.0 19.2 + - - +
789A MET 3.1 0.8 - - - -
790A LEU* 1.3 77.8 - - - +
792A GLN* 1.3 59.9 + - + +
794A ILE* 4.3 9.2 - - - +
795A ARG* 5.8 1.9 - - - +
824A ASN* 4.2 11.4 + - - +
826A SER* 4.2 12.0 + - - -
827A GLY* 3.5 40.2 - - - +
831A ASP* 4.5 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 792 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A VAL* 4.3 14.1 - - + +
759A ASN* 3.0 26.2 + - - +
788A PRO 4.8 1.4 - - - +
789A MET* 3.2 56.5 - - + +
790A LEU 3.1 0.2 - - - -
791A GLN* 1.3 81.6 - - + +
793A PHE* 1.3 59.1 + - - +
794A ILE 3.7 0.4 - - - -
795A ARG* 5.2 2.0 - - - -
796A PRO* 4.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 793 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751A LEU* 5.8 1.1 - - + -
755A VAL* 4.0 30.5 - - + -
758A ILE* 3.9 15.8 - - + +
759A ASN* 4.2 7.2 - - - +
775A ILE* 3.8 24.9 - - + -
786A VAL* 4.2 10.8 - - + -
789A MET* 3.0 31.9 - - + -
790A LEU* 3.5 28.9 - - + -
792A GLN* 1.3 77.7 - - - +
794A ILE* 1.3 65.3 + - - +
795A ARG 3.3 2.7 - - - -
796A PRO* 3.1 7.0 - - - +
797A TRP* 3.1 38.1 + + + +
817A ILE* 4.1 14.1 - - + -
820A MET* 3.8 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 794 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790A LEU* 3.4 36.3 + - + +
791A GLN 4.3 11.0 - - - +
793A PHE* 1.3 82.9 - - - +
795A ARG* 1.3 66.8 + - + +
797A TRP* 3.8 6.3 - - + -
798A CYS* 3.1 41.3 + - - -
817A ILE* 4.7 8.7 - - + -
821A ILE* 5.1 0.4 - - + -
827A GLY 4.4 7.6 - - - +
828A VAL* 3.6 34.1 - - + -
831A ASP* 4.6 22.4 - - + +
834A PHE* 4.7 1.4 - - + +
835A PHE* 4.6 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 795 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A GLN 5.8 2.0 - - - +
792A GLN 5.2 1.9 - - - +
793A PHE 3.3 0.2 - - - -
794A ILE* 1.3 84.5 - - + +
796A PRO* 1.3 69.2 - - + +
799A THR* 3.2 25.5 + - - +
831A ASP* 3.2 48.0 + - + +
834A PHE* 3.2 45.9 - - + -
141B ASP* 3.8 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 796 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758A ILE* 3.5 30.1 - - + +
759A ASN* 3.4 26.7 - - - +
768A LEU* 6.0 2.6 - - + +
792A GLN 4.7 0.2 - - - +
793A PHE 3.1 17.5 - - - +
795A ARG* 1.3 93.4 - - + +
797A TRP* 1.3 61.0 + - - -
799A THR* 3.1 16.7 + - - +
800A SER* 3.2 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 797 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758A ILE* 4.2 8.9 - - + +
772A ALA* 2.9 41.6 + - + -
775A ILE* 4.7 2.8 - - + +
776A GLY* 4.3 6.1 - - - +
793A PHE* 3.1 38.3 + + - +
794A ILE* 3.6 8.3 - - - +
795A ARG 3.2 0.2 - - - -
796A PRO* 1.3 78.4 - - - +
798A CYS* 1.3 80.8 + - - +
800A SER* 3.4 4.0 + - - -
801A LEU* 3.3 46.3 + - + +
813A ALA* 3.6 22.0 - - + -
814A PHE* 4.1 27.8 - + - -
817A ILE* 3.5 46.3 - - + +
835A PHE* 5.6 0.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 798 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A ILE* 3.1 36.0 + - - +
795A ARG 4.5 0.2 - - - +
797A TRP* 1.3 93.0 - - - +
799A THR* 1.3 60.1 + - - +
801A LEU* 3.3 1.5 + - - +
802A ARG* 3.0 36.2 + - - +
834A PHE* 3.5 37.5 - - + +
835A PHE* 3.8 17.0 - - - -
838A ALA* 3.8 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 799 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A ARG 3.2 17.7 + - - +
796A PRO* 3.1 18.7 + - - +
798A CYS* 1.3 77.1 - - - +
800A SER* 1.3 59.8 + - - +
802A ARG* 3.5 34.1 + - - +
803A ASN* 3.6 12.6 + - - -
834A PHE* 3.6 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 800 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A LYS* 5.9 0.5 - - - -
768A LEU* 3.6 21.9 - - - +
769A GLU* 3.6 33.4 + - - +
772A ALA* 4.8 1.6 - - - -
796A PRO 3.2 18.9 + - - -
797A TRP* 3.7 6.3 - - - -
798A CYS 3.1 0.6 - - - -
799A THR* 1.3 79.8 + - - +
801A LEU* 1.3 62.7 + - - +
802A ARG 3.5 0.2 - - - -
803A ASN* 2.8 21.5 + - - +
804A ILE* 3.8 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 801 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769A GLU* 4.2 9.6 - - - +
772A ALA* 3.8 21.5 - - + -
773A ILE* 4.5 5.4 - - + -
797A TRP* 3.3 50.6 + - + +
798A CYS 4.4 1.3 - - - +
800A SER* 1.3 82.3 - - - +
802A ARG* 1.3 63.4 + - - +
803A ASN 3.2 3.3 + - - -
804A ILE* 3.5 35.6 + - + +
810A LYS* 3.5 25.2 - - + +
813A ALA* 3.8 19.7 - - + -
814A PHE* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 802 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A CYS* 3.0 15.1 + - - +
799A THR* 3.5 38.2 + - - +
801A LEU* 1.3 78.8 - - - +
803A ASN* 1.3 65.3 + - + +
804A ILE 3.4 2.7 - - - +
810A LYS* 4.7 0.2 + - - -
834A PHE* 5.9 0.9 - - - -
837A ASP* 3.2 49.9 + - - +
838A ALA* 4.1 6.5 - - - +
841A SER* 3.2 27.0 - - - -
----------------------------------------------------------
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