Contacts of the helix formed by residues 741 - 762 (chain D) in PDB entry 5UHE
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 ARG 741 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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739D PRO* 3.5 2.2 - - - +
740D PRO* 1.3 100.8 - - + +
742D LYS* 1.3 66.3 + - - +
743D LYS 3.6 1.3 - - - -
744D GLU* 3.7 31.6 - - + +
745D ILE* 3.1 43.7 + - + +
788D ALA* 3.2 33.7 + - - +
791D GLU* 2.8 33.3 + - - +
792D HIS* 5.4 2.0 - - - +
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Residues in contact with LYS 742 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738D VAL* 5.5 2.0 - - + -
739D PRO* 3.6 36.4 + - + +
740D PRO 3.0 6.2 + - - +
741D ARG* 1.3 80.7 - - - +
743D LYS* 1.3 70.1 + - + +
745D ILE* 4.1 1.8 - - - +
746D LEU* 3.3 51.2 + - + +
785D VAL* 4.9 8.6 - - + +
819D GLY 3.2 26.1 + - - +
820D MET* 4.9 2.2 - - - -
837D LYS 3.4 11.2 + - - -
839D SER 4.2 0.4 - - - +
842D GLU* 2.7 42.2 + - - +
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Residues in contact with LYS 743 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740D PRO 5.1 0.2 + - - -
742D LYS* 1.3 85.5 - - + +
744D GLU* 1.3 63.5 + - + +
746D LEU* 4.0 7.0 - - + -
747D ASP* 2.8 42.9 + - - +
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Residues in contact with GLU 744 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740D PRO 5.5 1.1 - - - +
741D ARG* 3.7 33.6 - - + +
742D LYS 3.2 0.8 - - - -
743D LYS* 1.3 80.6 - - - +
745D ILE* 1.3 62.3 + - + +
747D ASP* 3.9 5.1 - - - +
748D HIS* 3.5 16.6 + - - +
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Residues in contact with ILE 745 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739D PRO* 6.3 0.2 - - + -
741D ARG* 3.1 44.1 + - + +
742D LYS* 4.1 2.0 - - - +
744D GLU* 1.3 73.3 - - + +
746D LEU* 1.3 66.8 + - + +
748D HIS* 3.1 15.6 + - + +
749D TYR* 3.1 42.0 - - + -
781D ALA 4.6 6.1 - - - +
784D GLU* 3.9 47.8 - - + +
785D VAL* 4.7 12.3 - - + -
788D ALA* 4.5 9.6 - - + -
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Residues in contact with LEU 746 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742D LYS* 3.3 44.8 + - + +
743D LYS* 4.3 6.1 - - + +
745D ILE* 1.3 80.6 - - + +
747D ASP* 1.3 60.7 + - - +
749D TYR* 3.5 3.9 + - - +
750D GLU* 3.0 29.0 + - - +
778D TRP* 4.4 21.1 - - + -
781D ALA* 5.0 5.6 - - + -
785D VAL* 4.9 8.3 - - + -
820D MET* 4.1 28.3 - - + -
837D LYS* 3.9 36.0 + - + +
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Residues in contact with ASP 747 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743D LYS* 2.8 33.2 + - - +
744D GLU* 3.9 6.5 - - - +
746D LEU* 1.3 79.4 - - - +
748D HIS* 1.3 57.6 + - - +
750D GLU* 3.6 6.7 - - - +
751D GLU* 3.0 30.5 + - - +
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Residues in contact with HIS 748 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744D GLU 3.5 9.4 + - - +
745D ILE* 3.1 12.6 + - - +
747D ASP* 1.3 79.9 - - - +
749D TYR* 1.3 84.3 + + - +
751D GLU* 3.5 9.9 + - - +
752D ARG* 3.0 54.6 + - + +
780D GLU* 5.9 0.4 + - - -
784D GLU* 5.1 3.4 - - - -
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Residues in contact with TYR 749 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745D ILE* 3.1 38.2 + - + -
746D LEU* 3.5 2.9 + - - +
747D ASP 3.4 0.2 - - - -
748D HIS* 1.3 94.8 + + - +
750D GLU* 1.3 60.2 + - - +
751D GLU 3.3 0.4 - - - -
752D ARG* 3.7 16.2 - - - -
753D ALA* 3.0 26.3 + - - +
777D ILE* 3.4 35.0 - - + +
778D TRP* 3.8 22.9 - - + -
780D GLU* 3.6 41.3 + - + +
781D ALA* 3.7 22.9 - - + -
784D GLU* 2.2 33.0 + - - -
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Residues in contact with GLU 750 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570C TYR* 5.6 5.7 - - - -
746D LEU 3.0 18.9 + - - +
747D ASP* 3.6 9.2 - - - +
749D TYR* 1.3 80.0 - - - +
751D GLU* 1.3 57.3 + - - +
753D ALA* 4.3 3.5 - - - +
754D ASP* 3.0 29.7 + - + +
778D TRP* 3.3 19.6 - - - -
837D LYS* 2.6 33.0 + - - +
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Residues in contact with GLU 751 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747D ASP 3.0 16.0 + - - +
748D HIS* 3.8 11.2 + - - +
750D GLU* 1.3 75.4 - - - +
752D ARG* 1.3 64.9 + - + +
753D ALA 3.1 1.1 - - - -
754D ASP* 3.5 5.9 + - + +
755D LYS* 3.2 37.2 + - + +
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Residues in contact with ARG 752 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748D HIS* 3.0 50.4 + - + +
749D TYR* 3.9 17.3 - - - +
750D GLU 3.4 0.2 - - - -
751D GLU* 1.3 78.1 - - + +
753D ALA* 1.3 58.1 + - - +
755D LYS* 3.9 20.2 - - + +
756D VAL* 3.2 26.4 + - - +
777D ILE* 3.7 27.0 - - + +
780D GLU* 3.4 33.1 + - - -
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Residues in contact with ALA 753 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749D TYR 3.0 19.0 + - - +
750D GLU* 3.8 7.2 - - - +
751D GLU 3.1 0.4 - - - -
752D ARG* 1.3 76.0 - - - +
754D ASP* 1.3 60.4 + - - +
755D LYS 3.1 1.8 - - - -
756D VAL* 3.1 4.3 + - - +
757D GLU* 2.8 34.3 + - + +
774D LEU* 4.0 16.7 - - + +
777D ILE* 3.9 11.2 - - + -
778D TRP* 4.0 19.7 - - + +
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Residues in contact with ASP 754 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750D GLU* 3.0 21.6 + - + +
751D GLU* 3.5 7.2 + - + +
753D ALA* 1.3 75.4 - - - +
755D LYS* 1.3 57.7 + - + +
757D GLU* 4.1 11.4 - - - +
758D LYS* 3.0 51.7 + - - +
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Residues in contact with LYS 755 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751D GLU* 3.2 34.3 + - + +
752D ARG* 3.9 18.6 - - + +
753D ALA 3.1 0.6 - - - -
754D ASP* 1.3 78.1 - - + +
756D VAL* 1.3 57.7 + - + +
758D LYS* 3.6 5.0 + - - +
759D GLN* 3.1 27.7 + - - +
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Residues in contact with VAL 756 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752D ARG* 3.2 17.2 + - - +
753D ALA 3.1 7.0 + - - +
755D LYS* 1.3 75.4 - - + +
757D GLU* 1.3 65.0 + - - +
759D GLN* 3.2 13.8 + - - +
760D PHE* 3.1 21.5 + - - +
765D LEU* 3.7 16.8 - - + +
770D ARG* 4.4 13.0 - - + +
773D ALA* 4.7 12.6 - - + -
774D LEU* 4.2 19.7 - - + -
777D ILE* 3.6 18.4 - - + -
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Residues in contact with GLU 757 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753D ALA* 2.8 22.6 + - + +
754D ASP* 3.7 14.8 - - - +
755D LYS 3.3 0.2 - - - -
756D VAL* 1.3 78.1 - - - +
758D LYS* 1.3 57.8 + - + +
760D PHE* 3.2 9.7 + - - +
761D GLN* 3.0 25.3 + - - +
770D ARG* 2.8 38.4 + - - +
774D LEU* 3.6 15.8 - - + +
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Residues in contact with LYS 758 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754D ASP* 3.0 45.0 + - - +
755D LYS* 4.1 5.6 - - - +
757D GLU* 1.3 74.2 - - + +
759D GLN* 1.3 59.9 + - - +
760D PHE 3.2 3.1 - - - -
761D GLN* 3.4 18.6 + - + +
762D ARG* 3.5 15.2 + - - +
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Residues in contact with GLN 759 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755D LYS 3.1 17.0 + - - +
756D VAL* 3.6 14.9 - - - +
757D GLU 3.2 0.4 - - - -
758D LYS* 1.3 76.4 - - - +
760D PHE* 1.3 57.9 + - - +
762D ARG* 3.6 37.7 - - - +
764D ALA* 3.5 22.5 + - + +
765D LEU* 3.3 41.0 - - + +
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Residues in contact with PHE 760 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756D VAL 3.1 11.3 + - - +
757D GLU* 3.6 9.2 - - - +
758D LYS 3.2 0.2 - - - -
759D GLN* 1.3 77.5 - - - +
761D GLN* 1.3 61.8 + - - +
762D ARG 3.2 2.5 - - - -
763D GLY* 3.0 19.6 + - - +
765D LEU* 3.1 35.7 - - + +
766D ASN 3.9 4.5 - - - -
767D HIS* 3.6 41.3 - + + -
770D ARG* 3.4 35.7 - - + -
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Residues in contact with GLN 761 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757D GLU 3.0 14.0 + - - +
758D LYS* 3.5 18.2 - - + +
760D PHE* 1.3 81.6 - - - +
762D ARG* 1.3 59.6 + - - +
763D GLY 3.6 0.3 + - - -
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Residues in contact with ARG 762 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758D LYS 3.5 10.3 + - - +
759D GLN* 3.6 36.9 - - - +
761D GLN* 1.3 77.9 - - - +
763D GLY* 1.3 61.7 + - - +
764D ALA* 3.3 26.6 + - + +
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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) + - + + + + + -
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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