Contacts of the helix formed by residues 818 - 839 (chain B) in PDB entry 3V53
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 GLU 818 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782B TYR* 4.1 45.8 + - + +
814B VAL 4.9 0.9 - - - +
815B LEU* 3.7 36.7 - - + +
816B ASP* 3.1 9.6 + - - +
817B GLU* 1.3 77.4 - - - +
819B ALA* 1.3 61.4 + - - +
820B GLU 3.5 1.3 - - - -
821B VAL* 4.0 11.7 + - + +
822B PHE* 3.5 18.7 + - - +
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Residues in contact with ALA 819 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808B LEU* 3.8 14.1 - - + +
811B VAL* 3.9 12.8 - - + -
812B ALA* 3.8 24.2 - - + +
815B LEU* 3.0 21.8 + - - +
817B GLU 3.5 1.7 - - - +
818B GLU* 1.3 78.3 - - - +
820B GLU* 1.3 59.5 + - - +
821B VAL 3.4 0.4 - - - -
822B PHE* 3.2 7.9 + - - +
823B ILE* 2.9 33.6 + - - +
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Residues in contact with GLU 820 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749B LYS* 4.1 31.0 + - + +
808B LEU* 3.6 26.6 - - + +
817B GLU* 5.0 5.4 - - - +
818B GLU* 4.5 0.6 - - - +
819B ALA* 1.3 78.0 - - - +
821B VAL* 1.3 62.1 + - + +
823B ILE* 3.2 1.2 + - - +
824B VAL* 2.8 48.0 + - + +
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Residues in contact with VAL 821 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782B TYR* 4.2 9.4 - - + +
817B GLU 4.9 4.5 - - - +
818B GLU* 4.0 16.6 + - + +
819B ALA 3.4 0.4 - - - -
820B GLU* 1.3 79.7 - - + +
822B PHE* 1.3 62.6 + - - +
824B VAL* 4.2 4.6 - - - +
825B LYS* 3.1 31.0 + - + +
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Residues in contact with PHE 822 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774B TRP* 3.7 20.0 - + - -
775B ILE* 3.8 28.0 - - + -
778B LYS* 3.7 23.6 - - + -
779B ILE* 4.3 13.0 - - + -
782B TYR* 3.4 29.8 + + + -
794B VAL* 4.0 24.5 - - + -
811B VAL* 4.0 19.7 - - + -
815B LEU* 4.6 2.5 - - + -
818B GLU 3.5 14.5 + - - +
819B ALA* 3.2 9.6 + - - +
820B GLU 3.2 0.2 - - - -
821B VAL* 1.3 79.8 - - - +
823B ILE* 1.3 76.4 + - + +
825B LYS* 3.9 3.1 - - - +
826B MET* 3.0 30.4 + - + +
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Residues in contact with ILE 823 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753B PHE* 3.7 15.9 - - + -
794B VAL* 5.1 2.7 - - + -
804B PRO* 3.5 31.4 - - + +
807B ILE* 4.0 18.8 - - + -
808B LEU* 3.7 25.4 - - + +
811B VAL* 4.7 6.7 - - + -
819B ALA 2.9 22.0 + - - +
820B GLU 3.2 1.5 + - - +
822B PHE* 1.3 92.0 - - + +
824B VAL* 1.3 61.5 + - - +
826B MET* 3.2 21.2 + - - +
827B TRP* 2.8 33.2 + - + +
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Residues in contact with VAL 824 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747B THR 6.0 2.2 - - - +
749B LYS* 4.4 15.9 - - + -
752B LEU* 3.7 22.3 - - + +
753B PHE* 3.9 19.7 - - + -
820B GLU* 2.8 39.8 + - + +
821B VAL* 4.2 4.5 - - - +
823B ILE* 1.3 70.4 - - - +
825B LYS* 1.3 59.5 + - - +
827B TRP* 3.0 4.7 + - - +
828B ARG* 2.8 37.9 + - + +
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Residues in contact with LYS 825 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774B TRP* 3.9 19.5 - - + -
778B LYS* 5.7 2.7 - - + -
782B TYR* 5.9 0.7 - - - +
821B VAL* 3.1 20.8 + - + +
822B PHE* 3.9 3.1 - - - +
824B VAL* 1.3 80.8 - - - +
826B MET* 1.3 56.8 + - - +
828B ARG* 3.4 13.2 - - - +
829B LEU* 3.0 23.9 + - - +
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Residues in contact with MET 826 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771B ILE* 4.1 9.9 - - + -
774B TRP* 3.7 24.2 - - + -
775B ILE* 3.5 31.4 - - + -
794B VAL* 3.6 15.3 - - + -
798B VAL* 3.3 33.0 - - + -
822B PHE* 3.0 21.8 + - + +
823B ILE* 3.5 20.6 - - + +
824B VAL 3.1 0.4 - - - -
825B LYS* 1.3 76.1 - - - +
827B TRP* 1.3 59.9 + - - +
829B LEU* 3.1 9.3 + - + +
830B LEU* 2.7 41.9 + - + +
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Residues in contact with TRP 827 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752B LEU* 3.5 36.8 + - + -
753B PHE* 4.4 9.1 + + + -
755B TYR 4.8 7.5 + - - -
757B LEU* 3.8 16.0 - - + +
759B TRP* 3.5 28.7 - + - -
798B VAL* 5.2 7.9 - - + -
802B SER 3.4 21.8 - - - -
803B SER 5.0 0.2 - - - -
804B PRO* 3.5 45.2 - - + +
807B ILE* 5.6 4.9 - - + -
823B ILE* 2.8 21.9 + - + +
824B VAL* 3.6 3.6 - - - +
826B MET* 1.3 78.6 - - - +
828B ARG* 1.3 61.0 + - - +
829B LEU 3.1 0.2 - - - -
830B LEU* 3.6 23.1 - - + +
831B ILE* 2.9 54.9 + - + +
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Residues in contact with ARG 828 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742B ILE* 5.6 12.7 - - - +
745B ILE* 3.6 47.2 + - + +
746B PRO 3.7 11.1 + - - -
747B THR* 4.7 11.9 + - - +
752B LEU* 4.2 12.4 - - + +
824B VAL* 2.8 20.2 + - - +
825B LYS* 3.4 17.3 - - - +
827B TRP* 1.3 77.6 - - - +
829B LEU* 1.3 59.3 + - - +
831B ILE* 4.9 0.2 - - - -
832B TYR* 3.4 21.8 + - - +
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Residues in contact with LEU 829 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770B ARG* 5.3 7.6 - - + +
771B ILE* 4.4 27.4 - - + -
774B TRP* 3.7 54.5 - - + +
825B LYS 3.0 14.1 + - - +
826B MET* 3.2 12.8 - - + +
827B TRP 3.1 0.2 - - - -
828B ARG* 1.3 75.4 - - - +
830B LEU* 1.3 60.0 + - + +
832B TYR* 3.2 5.7 + - + +
833B GLU* 2.8 40.4 + - + +
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Residues in contact with LEU 830 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757B LEU* 3.8 12.9 - - + +
759B TRP* 4.5 6.1 - - + -
762B VAL* 4.1 20.6 - - + -
771B ILE* 4.1 24.5 - - + -
798B VAL* 3.9 34.3 - - + -
826B MET* 2.7 27.1 + - + +
827B TRP* 3.2 42.4 + - + +
829B LEU* 1.3 74.1 - - + +
831B ILE* 1.3 61.0 + - - +
833B GLU* 4.2 3.4 - - + +
834B THR* 3.1 27.9 + - - +
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Residues in contact with ILE 831 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744B LYS* 4.1 3.4 - - + +
745B ILE* 3.8 22.4 - - + -
746B PRO* 4.3 4.0 - - + -
752B LEU* 3.7 26.9 - - + -
755B TYR* 3.6 63.9 - - + +
757B LEU* 3.8 13.7 - - + -
827B TRP* 2.9 32.9 + - + +
828B ARG 4.4 0.2 - - - +
830B LEU* 1.3 71.1 - - - +
832B TYR* 1.3 64.9 + - - +
834B THR* 3.1 4.4 - - - +
835B GLU* 3.0 27.3 + - + +
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Residues in contact with TYR 832 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734B LYS* 3.3 48.3 + - + +
738B ILE* 3.4 18.5 - - - +
741B LEU* 3.8 28.5 - - + +
742B ILE* 3.7 24.7 - - + +
745B ILE* 3.7 21.3 - - + -
828B ARG 3.4 17.9 + - - +
829B LEU* 3.2 5.3 + - + +
831B ILE* 1.3 80.1 - - - +
833B GLU* 1.3 60.7 + - - +
835B GLU* 3.2 5.1 + - - +
836B ALA* 2.8 35.2 + - + +
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Residues in contact with GLU 833 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734B LYS* 5.9 5.8 - - - +
766B LEU* 6.3 2.7 - - + -
770B ARG* 5.6 8.1 - - + -
771B ILE* 5.4 12.8 - - + -
829B LEU* 2.8 30.5 + - + +
830B LEU* 4.2 4.5 - - + +
832B TYR* 1.3 76.5 - - - +
834B THR* 1.3 61.6 + - - +
836B ALA* 3.4 8.2 + - - +
837B LYS* 3.2 24.9 + - - +
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Residues in contact with THR 834 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755B TYR* 5.6 0.9 - - + -
757B LEU* 3.6 21.8 - - + -
758B ASP* 3.2 19.4 + - + +
761B ILE* 3.2 39.9 - - - +
762B VAL* 4.3 9.6 - - - +
830B LEU 3.1 18.8 + - - +
831B ILE* 3.1 14.8 - - - +
833B GLU* 1.3 75.3 - - - +
835B GLU* 1.3 72.0 + - + +
837B LYS* 3.4 2.6 + - - +
838B LYS* 2.9 25.6 + - + +
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Residues in contact with GLU 835 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B LEU* 5.7 11.2 - - + +
744B LYS* 5.1 12.5 - - + +
755B TYR* 3.0 28.7 + - - +
758B ASP* 5.3 1.7 + - - +
831B ILE* 3.0 25.7 + - + +
832B TYR* 3.7 4.7 - - - +
834B THR* 1.3 78.8 - - + +
836B ALA* 1.3 61.9 + - - +
838B LYS* 2.9 52.7 + - - +
839B ILE* 3.1 27.6 + - + +
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Residues in contact with ALA 836 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733B MET* 4.9 13.1 - - - +
734B LYS* 4.4 33.0 - - + -
741B LEU* 5.9 3.3 - - - +
832B TYR* 2.8 22.3 + - + +
833B GLU* 3.5 9.9 - - - +
835B GLU* 1.3 77.3 - - - +
837B LYS* 1.3 60.0 + - + +
839B ILE* 3.8 16.8 + - - +
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Residues in contact with LYS 837 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761B ILE* 3.7 27.1 + - + +
763B ASP* 3.7 21.0 + - - -
765B ILE* 4.3 13.3 - - - +
766B LEU* 3.8 24.1 - - + +
833B GLU 3.2 14.3 + - - +
834B THR 3.7 6.7 - - - +
835B GLU 3.2 0.4 - - - -
836B ALA* 1.3 75.5 - - - +
838B LYS* 1.3 63.2 + - - +
839B ILE 3.2 2.3 + - - -
840B GLY* 3.6 11.6 + - - -
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Residues in contact with LYS 838 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756B PRO 5.5 2.8 + - - -
758B ASP* 3.6 36.7 + - + +
761B ILE* 3.9 15.5 - - + -
834B THR 2.9 12.8 + - - +
835B GLU* 2.9 46.7 + - - +
837B LYS* 1.3 78.0 - - - +
839B ILE* 1.3 61.4 + - + +
840B GLY 3.0 6.9 + - - -
841B LEU 4.4 3.1 + - - +
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Residues in contact with ILE 839 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733B MET* 5.2 9.1 - - + +
737B HIS* 5.8 16.8 - - + -
835B GLU* 3.1 23.1 + - - +
836B ALA* 3.8 12.1 + - - +
837B LYS 3.2 4.4 - - - -
838B LYS* 1.3 79.1 - - + +
840B GLY* 1.3 59.6 + - - +
841B LEU 3.9 14.4 - - - +
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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