Contacts of the helix formed by residues 784 - 800 (chain B) in PDB entry 2O8C
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 784 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729B ALA* 4.4 18.9 - - - +
730B TYR* 4.5 22.8 - - + +
731B GLN 5.5 0.7 - - - +
782B LEU* 3.8 1.7 - - + +
783B CYS* 1.3 79.1 - - - +
785B HIS* 1.3 77.0 + - - +
786B TYR* 3.6 18.0 + - - +
787B ALA* 3.2 24.6 + - + +
788B ILE* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 785 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783B CYS 4.1 1.8 + - - -
784B ASN* 1.3 84.0 + - - +
786B TYR* 1.3 75.9 + - + +
788B ILE* 4.3 2.6 - - - +
789B ASN* 3.1 39.4 + - - +
1079B ILE* 4.3 33.5 - - + +
1080B LEU 5.7 1.8 - - - -
1081B LEU* 4.0 31.3 - - + +
1169B PRO* 5.5 3.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 786 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784B ASN* 3.2 15.5 + - - +
785B HIS* 1.3 96.8 + - + +
787B ALA* 1.3 63.3 + - + +
789B ASN* 3.8 4.7 - - - +
790B ASP* 3.0 43.1 + - + +
885B LYS* 4.0 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 787 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730B TYR* 4.9 11.7 - - + -
782B LEU* 3.7 25.6 - - + +
784B ASN* 3.2 25.2 + - + +
786B TYR* 1.3 80.2 - - + +
788B ILE* 1.3 64.8 + - - +
790B ASP* 3.3 9.6 + - - +
791B ARG* 3.3 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 788 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782B LEU* 3.7 40.4 - - + +
783B CYS* 3.8 11.0 - - - -
784B ASN 3.0 18.9 + - - +
785B HIS* 4.3 4.0 - - - +
787B ALA* 1.3 74.7 - - - +
789B ASN* 1.3 64.7 - - - +
791B ARG 3.4 1.2 + - - -
792B LEU* 3.2 30.8 + - + +
1079B ILE* 3.6 30.7 - - + -
1154B ALA 3.4 22.4 - - - +
1155B GLN* 3.9 12.1 - - + +
1157B GLY* 3.5 16.5 - - - +
1169B PRO* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 789 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785B HIS* 3.1 32.4 + - - +
786B TYR* 3.9 4.4 - - - +
788B ILE* 1.3 77.8 - - - +
790B ASP* 1.3 57.6 + - - +
791B ARG 3.3 0.2 - - - -
792B LEU* 3.7 13.2 - - - +
793B ASP* 2.8 39.4 + - - +
1076B ARG* 3.2 20.3 + - - +
1077B PRO 4.3 6.6 - - - +
1078B VAL* 5.5 0.5 - - - -
1079B ILE* 4.9 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 790 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786B TYR* 3.0 33.5 + - + +
787B ALA* 3.4 11.7 - - - +
788B ILE 3.2 0.4 - - - -
789B ASN* 1.3 75.8 - - - +
791B ARG* 1.3 60.7 + - + +
793B ASP* 4.4 4.8 - - - +
794B ALA 3.2 17.7 + - - -
884B SER* 3.4 10.0 - - - -
885B LYS* 3.1 31.4 + - - +
886B ILE* 3.4 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 791 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732B ARG* 3.9 11.5 - - - +
777B TRP* 3.3 68.4 + - + +
780B ALA 5.3 0.6 + - - -
782B LEU* 3.5 45.7 - - - +
787B ALA 3.3 8.7 + - - +
788B ILE 3.4 5.8 + - - +
790B ASP* 1.3 75.5 - - + +
792B LEU* 1.3 60.6 + - - +
793B ASP 3.2 0.2 - - - -
794B ALA* 3.0 9.6 + - - +
795B ILE* 2.9 31.9 + - - +
886B ILE* 4.6 8.3 - - + -
1060B LEU* 4.6 8.5 - - + +
1063B LEU* 5.9 0.7 - - + -
1156B MET* 3.4 35.8 + - - +
1157B GLY* 3.8 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 792 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788B ILE* 3.2 28.8 + - + +
789B ASN* 3.8 10.3 - - - +
791B ARG* 1.3 79.5 - - - +
793B ASP* 1.3 61.7 + - - +
795B ILE* 3.3 6.7 + - + +
796B GLU* 3.2 26.5 + - - +
1076B ARG* 3.4 32.5 - - + +
1077B PRO* 3.7 47.1 - - + +
1079B ILE* 6.1 0.2 - - + -
1157B GLY* 3.6 5.8 - - - -
1158B CYS* 3.5 28.7 - - - +
1159B TYR* 4.1 11.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 793 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789B ASN* 2.8 26.8 + - - +
790B ASP* 3.8 3.3 - - - +
792B LEU* 1.3 73.0 - - - +
794B ALA* 1.3 61.1 + - - +
796B GLU* 3.4 9.2 + - - +
797B ASP* 2.9 34.6 + - - +
883B LYS* 4.7 12.2 - - + +
884B SER* 3.7 23.6 - - - +
1076B ARG* 2.7 32.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 794 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790B ASP 3.2 12.6 + - - +
791B ARG 3.0 9.9 + - - +
793B ASP* 1.3 77.1 - - - +
795B ILE* 1.3 62.0 + - - +
797B ASP* 3.3 4.4 + - - +
798B LEU* 3.2 31.0 + - - +
884B SER* 3.4 20.4 - - - +
886B ILE* 4.1 4.5 - - + -
887B LEU* 4.1 4.8 - - + +
1060B LEU* 3.9 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 795 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791B ARG 2.9 12.6 + - - +
792B LEU* 3.5 10.1 - - - +
793B ASP 3.2 0.2 - - - -
794B ALA* 1.3 76.0 - - - +
796B GLU* 1.3 58.1 + - - +
798B LEU* 3.1 6.4 + - - +
799B MET* 3.0 37.5 + - - +
1060B LEU* 4.4 8.5 - - + +
1063B LEU* 3.7 21.1 - - + +
1064B ALA* 3.7 30.4 - - - +
1067B SER* 3.6 30.1 - - - +
1157B GLY 3.2 25.8 - - - +
1158B CYS* 3.9 6.5 - - - -
1159B TYR* 4.1 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 796 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792B LEU 3.2 9.2 + - - +
793B ASP* 3.8 10.7 - - - +
795B ILE* 1.3 76.2 - - - +
797B ASP* 1.3 62.3 + - - +
799B MET* 3.5 11.9 + - + +
800B VAL* 3.4 30.3 + - + +
1076B ARG* 2.9 38.6 + - - +
1159B TYR* 2.8 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 797 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793B ASP* 2.9 19.5 + - - +
794B ALA 3.4 7.0 - - - +
795B ILE 3.2 0.2 - - - -
796B GLU* 1.3 78.8 - - - +
798B LEU* 1.3 59.3 + - - +
800B VAL* 3.3 18.9 - - - +
801B VAL* 3.5 11.6 - - - +
881B GLY 4.8 0.9 - - - +
882B PHE* 3.4 30.8 - - + +
883B LYS* 2.8 42.3 + - - +
884B SER* 2.9 24.0 + - - -
887B LEU* 3.8 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 798 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794B ALA 3.2 15.3 - - - +
795B ILE 3.1 6.5 + - - +
797B ASP* 1.3 74.3 - - - +
799B MET* 1.3 65.1 + - - +
800B VAL 3.1 1.8 - - - -
801B VAL* 3.0 18.3 + - + +
805B ILE* 3.2 29.7 - - + +
875B MET* 4.6 17.3 - - + -
882B PHE* 4.9 2.5 - - + -
887B LEU* 3.8 26.7 - - + -
1057B LEU* 4.7 2.9 - - + -
1060B LEU* 3.6 43.1 - - + +
1061B LEU* 3.7 24.2 - - + +
1064B ALA* 4.1 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 799 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795B ILE* 3.0 38.6 + - + +
796B GLU* 3.9 11.2 - - + +
797B ASP 3.5 0.4 - - - -
798B LEU* 1.3 75.9 - - - +
800B VAL* 1.3 61.1 + - + +
801B VAL 3.2 2.8 + - - -
802B PRO* 4.2 3.1 - - - +
805B ILE* 5.0 0.9 - - - -
1064B ALA* 4.1 21.3 - - + +
1067B SER* 4.4 17.5 - - - +
1068B ARG* 3.6 49.8 + - + +
1159B TYR* 4.8 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 800 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796B GLU* 3.4 15.3 - - + +
797B ASP* 3.3 22.0 - - - +
798B LEU 3.1 0.2 + - - -
799B MET* 1.3 79.4 - - + +
801B VAL* 1.3 59.1 + - + +
802B PRO* 3.7 7.3 - - - +
882B PHE* 6.0 0.2 - - + -
----------------------------------------------------------
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