Contacts of the helix formed by residues 784 - 805 (chain B) in PDB entry 4XUF
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 THR 784 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783B LEU* 1.3 76.1 - - - +
785B PHE* 1.3 68.8 + - - +
786B GLU* 2.9 32.6 + - + +
787B ASP* 3.0 39.2 + - - +
788B LEU* 3.3 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 785 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784B THR* 1.3 80.7 + - - +
786B GLU* 1.3 71.3 + - - +
788B LEU* 3.2 15.3 + - + +
789B LEU* 3.0 45.8 + - + +
882B PHE* 3.5 24.5 - + - -
913B TYR* 3.2 27.1 - - + -
914B ALA* 4.6 2.0 - - - -
915B THR* 3.9 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 786 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784B THR* 2.9 29.0 + - + -
785B PHE* 1.3 86.1 + - + +
787B ASP* 1.3 53.5 + - - +
789B LEU* 3.2 12.4 + - + +
790B CYS* 2.6 35.0 + - - +
946B GLN 6.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 787 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782B VAL* 4.3 7.8 - - - +
783B LEU* 3.6 24.5 + - + -
784B THR* 3.0 38.4 + - - +
786B GLU* 1.3 75.2 - - - +
788B LEU* 1.3 61.2 + - - +
790B CYS* 3.3 10.6 + - - +
791B PHE* 2.9 42.1 + - + -
823B LYS* 4.8 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 788 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B LEU* 4.3 15.5 - - + -
783B LEU* 4.8 12.8 - - + -
784B THR 3.3 11.3 + - - +
785B PHE* 3.2 19.6 + - + +
787B ASP* 1.3 76.4 - - - +
789B LEU* 1.3 62.7 + - - +
791B PHE* 3.3 21.5 + - + +
792B ALA* 3.3 17.0 + - - +
881B ILE* 3.7 39.0 - - + +
882B PHE* 4.0 23.5 - - + -
884B LEU* 4.8 10.5 - - + -
913B TYR* 4.8 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 789 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785B PHE* 3.0 40.2 + - + +
786B GLU* 3.4 15.5 - - + +
788B LEU* 1.3 73.2 - - - +
790B CYS* 1.3 59.7 + - - +
792B ALA* 3.2 3.5 + - - +
793B TYR* 2.9 31.5 + - - +
882B PHE* 3.5 22.7 - - + -
915B THR* 6.1 0.4 - - + -
918B ILE* 3.6 25.1 - - + -
943B LEU* 4.1 13.4 - - + +
946B GLN* 3.6 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 790 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786B GLU 2.6 21.3 + - - +
787B ASP* 3.4 15.5 - - - +
788B LEU 3.2 0.2 - - - -
789B LEU* 1.3 74.6 - - - +
791B PHE* 1.3 62.4 - - + +
793B TYR* 3.5 11.3 + - - +
794B GLN* 2.9 40.6 + - - +
823B LYS* 5.3 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 791 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B LEU* 4.0 26.0 - - + -
702B TYR* 4.3 11.7 - + - -
703B LEU* 4.7 2.2 - - + -
783B LEU* 4.2 15.3 - - + -
787B ASP* 2.9 22.3 + - + -
788B LEU* 3.5 22.9 - - + +
789B LEU 3.2 0.2 - - - -
790B CYS* 1.3 79.2 - - + +
792B ALA* 1.3 61.0 + - - +
794B GLN* 3.1 31.9 - - - +
795B VAL* 3.2 16.9 - - + +
819B VAL* 4.9 5.2 - - + -
823B LYS* 3.1 54.3 - - + -
825B VAL* 3.8 16.4 - - + -
881B ILE* 4.5 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 792 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788B LEU 3.3 7.4 + - - +
789B LEU* 3.2 6.5 + - - +
791B PHE* 1.3 79.4 - - - +
793B TYR* 1.3 61.0 + - - +
795B VAL* 3.5 3.2 + - - +
796B ALA 3.1 10.4 + - - -
874B TYR* 2.3 25.8 + - - -
878B LEU* 3.6 25.4 - - + -
881B ILE* 3.8 16.5 - - + +
882B PHE* 4.5 7.4 - - + -
943B LEU* 3.6 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 793 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789B LEU 2.9 17.9 + - - +
790B CYS* 3.7 12.8 - - - +
791B PHE 3.2 0.2 - - - -
792B ALA* 1.3 78.5 - - - +
794B GLN* 1.3 63.2 + - + +
796B ALA* 3.2 6.6 + - - +
797B LYS* 2.7 66.2 + - + +
940B THR* 3.2 39.3 + - + +
943B LEU* 3.5 16.4 - - + +
944B GLY* 4.1 20.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 794 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B ASN* 3.3 28.3 + - - +
790B CYS* 2.9 30.4 + - - +
791B PHE* 3.1 37.2 - - - +
793B TYR* 1.3 79.8 - - + +
795B VAL* 1.3 55.3 + - - +
797B LYS* 3.3 10.4 - - + +
798B GLY 2.7 29.6 + - - -
823B LYS 3.7 10.3 + - - -
824B VAL* 3.2 17.2 - - - +
825B VAL* 3.1 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 795 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B LEU* 5.6 2.5 - - + -
791B PHE* 3.2 20.9 + - + +
792B ALA* 3.7 6.3 - - - +
793B TYR 3.3 0.2 - - - -
794B GLN* 1.3 78.0 - - - +
796B ALA* 1.3 56.5 + - - +
798B GLY 3.3 0.5 + - - -
799B MET* 3.0 28.4 + - + +
812B LEU* 4.8 7.9 - - + -
817B VAL* 4.5 15.7 - - + -
825B VAL* 3.7 20.0 - - + -
827B ILE* 3.5 18.4 - - + +
874B TYR* 3.6 22.4 - - + -
877B LEU* 4.4 26.0 - - + -
881B ILE* 5.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 796 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792B ALA 3.1 6.2 + - - +
793B TYR* 3.5 9.2 - - - +
795B VAL* 1.3 76.0 - - - +
797B LYS* 1.3 57.4 + - - +
799B MET* 3.5 6.0 + - - +
800B GLU* 3.1 27.0 + - - +
874B TYR* 3.2 32.7 - - + +
936B PHE* 4.4 7.5 - - + +
939B LEU* 3.9 23.6 - - + +
940B THR* 3.6 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 797 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B HIS* 3.7 15.2 + - + +
672B GLU* 5.4 7.9 - - + +
673B ASN* 3.4 18.2 - - - +
793B TYR* 2.7 53.4 + - + +
794B GLN* 3.1 11.9 + - + +
796B ALA* 1.3 78.3 - - - +
798B GLY* 1.3 58.7 + - - +
800B GLU* 3.5 25.0 + - - +
801B PHE 3.5 4.9 + - - -
940B THR* 3.4 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 798 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B HIS* 3.7 18.7 + - - -
673B ASN* 4.0 5.8 - - - -
674B ILE* 5.7 0.8 - - - +
794B GLN 2.7 18.7 + - - -
797B LYS* 1.3 71.4 - - - +
799B MET* 1.3 65.0 + - - +
801B PHE* 3.2 12.3 + - - +
802B LEU* 3.3 19.6 + - - +
827B ILE* 3.6 17.3 - - - -
----------------------------------------------------------
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 VAL* 3.0 16.8 + - + +
796B ALA* 3.9 1.3 - - - +
797B LYS 3.4 0.2 - - - -
798B GLY* 1.3 74.0 - - - +
800B GLU* 1.3 60.1 + - - +
802B LEU* 3.1 22.7 + - - +
803B GLU* 2.9 27.9 + - - +
807B CYS 5.7 0.2 - - - +
809B HIS* 4.6 6.1 - - + -
812B LEU* 3.7 36.8 - - + -
827B ILE* 3.6 28.1 - - + +
867B ILE* 4.9 2.5 - - + -
870B ASP* 4.5 13.0 - - - +
874B TYR* 5.5 0.4 - - + -
936B PHE* 2.6 57.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 800 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B HIS* 5.8 0.5 + - - -
796B ALA 3.1 13.5 + - - +
797B LYS* 3.5 23.4 + - - +
798B GLY 3.2 0.2 - - - -
799B MET* 1.3 77.4 - - - +
801B PHE* 1.3 56.5 + - - +
803B GLU* 3.3 4.1 + - - +
804B PHE* 2.9 30.9 + - + +
936B PHE* 4.1 14.7 - - + +
937B PRO* 3.9 30.7 - - + +
940B THR* 4.4 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 801 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B LEU* 3.2 46.9 - - + -
669B GLY* 4.2 3.8 - - - -
670B SER 4.5 8.7 - - - -
671B HIS* 3.5 53.2 - + + +
674B ILE* 5.2 0.2 - - + -
797B LYS 3.5 2.2 + - - +
798B GLY 3.2 10.5 + - - +
799B MET 3.2 0.6 - - - -
800B GLU* 1.3 81.0 + - - +
802B LEU* 1.3 60.9 + - + +
804B PHE* 3.6 15.1 + + + +
805B LYS* 3.2 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 802 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B LEU* 4.3 16.8 - - + -
674B ILE* 3.7 26.7 - - + -
798B GLY 3.3 13.7 + - - +
799B MET* 3.1 35.3 + - + +
801B PHE* 1.3 81.8 - - + +
803B GLU* 1.3 56.4 + - - +
804B PHE 3.2 0.2 - - - -
805B LYS* 3.2 4.9 + - - +
806B SER 2.9 8.8 + - - -
807B CYS* 2.7 53.0 + - + +
809B HIS* 4.7 10.1 - - + +
827B ILE* 5.0 4.0 - - + -
867B ILE* 5.5 0.2 - - + -
1001B P30 4.4 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 803 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799B MET 2.9 15.0 + - - +
800B GLU 3.3 5.4 + - - +
802B LEU* 1.3 75.6 - - - +
804B PHE* 1.3 59.6 + - - +
806B SER* 3.0 19.1 + - - +
807B CYS 4.4 1.9 + - - +
867B ILE* 3.7 41.6 - - + +
868B LYS* 6.0 0.5 - - - +
935B SER* 4.4 10.2 - - - -
936B PHE* 2.9 34.0 + - - +
937B PRO* 3.3 16.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 804 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B GLU* 2.9 20.4 + - + +
801B PHE* 3.7 17.0 - + - +
802B LEU 3.2 0.2 - - - -
803B GLU* 1.3 78.5 - - - +
805B LYS* 1.3 75.8 + - + +
806B SER* 3.2 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 805 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667B GLN 4.1 11.0 + - - +
668B LEU* 3.3 36.7 + - + +
669B GLY* 5.4 1.6 - - - -
801B PHE* 3.2 37.1 + - + +
802B LEU* 3.2 6.8 + - - +
803B GLU 3.2 0.4 - - - -
804B PHE* 1.3 87.7 - - + +
806B SER* 1.3 70.7 + - - +
807B CYS* 3.4 19.6 - - - -
----------------------------------------------------------
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