Contacts of the helix formed by residues 819 - 834 (chain B) in PDB entry 1JQO
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 TRP 819 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615B TRP* 3.5 22.0 - + - -
618B TYR* 4.5 8.1 + + - -
707B VAL* 3.7 13.6 + - - -
709B PRO* 3.3 45.2 - - + +
713B TRP* 4.0 22.8 - + + -
717B MET* 3.5 25.1 - - + -
815B MET* 3.0 28.6 + - - +
817B ASN 3.8 0.2 - - - -
818B GLU* 1.3 75.2 - - - +
820B PRO* 1.3 78.0 - - + +
821B PHE* 3.2 43.7 - + + +
822B PHE* 3.2 27.3 + + + -
823B ARG* 3.0 23.0 + - - +
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Residues in contact with PRO 820 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657B LEU* 4.0 32.5 - - + +
658B SER* 4.7 0.4 - - - -
706B PRO* 3.7 25.6 - - + -
707B VAL* 3.6 18.8 - - + +
818B GLU 3.2 11.4 - - - +
819B TRP* 1.3 90.7 - - + +
821B PHE* 1.3 61.6 + - - +
823B ARG* 3.1 8.8 + - + +
824B VAL* 2.9 32.1 + - + +
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Residues in contact with PHE 821 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B LEU* 5.6 1.6 - - + -
614B ALA* 4.1 18.6 - - + -
615B TRP* 3.5 37.0 - + + -
618B TYR* 4.2 18.6 - + + -
658B SER* 3.8 32.4 - - - +
717B MET* 4.3 8.1 - - - -
819B TRP* 3.2 53.5 - + + +
820B PRO* 1.3 79.9 - - - +
822B PHE* 1.3 71.4 + + - +
824B VAL* 3.5 1.9 + - - +
825B THR* 3.0 47.9 + - + -
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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
----------------------------------------------------------
611B LEU* 6.1 1.1 - - + -
717B MET* 3.7 25.6 - - + -
720B MET* 4.5 0.7 - - + -
798B PHE* 4.2 13.2 - + - -
812B LEU* 4.1 16.4 - - + -
815B MET* 3.3 40.4 - - + +
816B TYR* 3.8 25.8 - - + -
819B TRP* 3.2 32.9 + + + +
821B PHE* 1.3 86.7 - + - +
823B ARG* 1.3 63.8 + - - +
825B THR* 3.8 5.0 + - - -
826B LEU* 3.3 48.2 + - + +
874B ILE* 4.7 2.0 - - + -
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Residues in contact with ARG 823 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816B TYR* 3.5 49.9 + - + +
817B ASN* 4.5 13.9 + - - +
819B TRP 3.0 13.4 + - - +
820B PRO* 3.3 13.2 - - + +
822B PHE* 1.3 73.8 - - - +
824B VAL* 1.3 69.0 + - + +
826B LEU* 2.9 6.2 + - - +
827B ASP* 2.7 69.2 + - - +
877B HIS* 5.7 2.4 + - - -
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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
----------------------------------------------------------
654B LEU* 3.7 56.5 - - + +
655B ALA* 4.6 1.8 - - - +
657B LEU* 4.5 7.6 - - + -
658B SER* 3.8 21.1 - - - +
820B PRO* 2.9 20.9 + - + +
821B PHE 3.9 0.2 - - - +
823B ARG* 1.3 72.8 - - + +
825B THR* 1.3 53.7 + - - +
827B ASP* 3.1 9.5 + - - +
828B LEU* 2.7 59.2 + - + +
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Residues in contact with THR 825 (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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610B ARG* 5.8 5.8 - - + -
611B LEU* 5.5 13.5 - - + -
614B ALA* 4.8 16.1 - - + +
658B SER* 5.6 0.5 - - - -
821B PHE* 3.0 39.2 + - + -
822B PHE* 3.8 6.7 - - - -
823B ARG 3.1 0.6 + - - -
824B VAL* 1.3 79.3 - - - +
826B LEU* 1.3 67.8 + - + +
828B LEU* 3.4 9.5 + - - +
829B LEU* 3.2 31.0 + - + +
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Residues in contact with LEU 826 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B LEU* 6.1 2.0 - - + -
794B VAL* 5.2 0.2 - - + -
798B PHE* 3.7 20.4 - - + -
816B TYR* 3.9 21.5 - - + -
822B PHE* 3.3 39.4 + - + +
823B ARG 2.9 6.7 + - - +
825B THR* 1.3 80.9 - - + +
827B ASP* 1.3 66.2 + - - +
829B LEU* 2.9 19.9 + - + +
830B GLU* 2.9 22.3 + - - +
871B LEU* 3.4 33.6 - - + +
874B ILE* 4.3 17.5 - - + -
875B ALA* 5.3 1.8 - - + +
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Residues in contact with ASP 827 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B LEU* 5.6 7.3 - - + +
816B TYR* 2.9 22.2 + - - -
823B ARG* 2.7 60.6 + - - +
824B VAL* 3.4 11.2 + - - +
826B LEU* 1.3 73.7 - - - +
828B LEU* 1.3 65.5 + - + +
830B GLU* 3.3 23.1 + - - +
831B MET* 3.3 27.6 + - + +
877B HIS* 5.1 1.4 - - - -
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Residues in contact with LEU 828 (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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645B VAL* 3.5 20.7 - - + +
649B GLY 3.4 23.6 - - - +
650B GLY* 4.7 1.1 - - - -
651B PRO* 4.1 19.7 - - + -
654B LEU* 4.5 3.1 - - + -
824B VAL* 2.7 46.2 + - + +
825B THR* 3.6 8.7 - - - +
827B ASP* 1.3 72.8 - - + +
829B LEU* 1.3 64.7 - - + +
831B MET* 2.9 36.5 + - + +
832B VAL* 3.1 14.9 + - - +
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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
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610B ARG* 5.3 4.7 - - + -
611B LEU* 6.4 0.4 - - + -
790B VAL* 3.4 39.0 - - + +
791B TRP* 4.3 12.6 - - + -
794B VAL* 4.1 22.9 - - + -
825B THR* 3.2 15.8 + - + +
826B LEU* 2.9 35.1 + - + +
828B LEU* 1.3 78.6 - - + +
830B GLU* 1.3 56.2 + - - +
832B VAL* 2.7 30.7 + - + +
833B PHE* 2.9 18.6 + - + -
871B LEU* 3.6 18.2 - - + -
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Residues in contact with GLU 830 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816B TYR* 4.6 1.4 + - - -
826B LEU 2.9 11.5 + - - +
827B ASP* 3.5 19.4 - - - +
828B LEU 3.2 0.2 - - - -
829B LEU* 1.3 74.9 - - - +
831B MET* 1.3 57.6 - - + +
833B PHE* 3.6 4.1 + - - +
834B ALA* 2.8 27.5 + - - +
871B LEU* 4.0 12.2 - - + +
872B LEU* 3.9 9.9 - - + +
875B ALA* 5.2 2.6 - - - +
877B HIS* 3.0 38.0 + - - -
879B ASP 3.5 2.6 - - - +
880B ILE* 3.0 29.3 - - + +
881B LEU* 2.9 29.2 + - + +
882B GLU 3.9 0.3 + - - -
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Residues in contact with MET 831 (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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645B VAL* 6.2 2.9 - - + -
651B PRO* 5.0 12.6 - - + -
654B LEU* 4.8 11.2 - - + -
827B ASP* 3.3 32.9 + - + +
828B LEU* 2.9 27.1 + - + +
830B GLU* 1.3 74.1 - - + +
832B VAL* 1.3 62.4 + - + +
834B ALA* 2.7 33.6 + - - +
835B LYS* 3.1 14.9 + - + +
881B LEU* 4.1 21.5 - - + -
887B LEU* 4.8 11.9 - - + -
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Residues in contact with VAL 832 (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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645B VAL* 3.6 32.5 - - + +
787B HIS* 3.6 34.1 - - + +
790B VAL* 4.1 21.5 - - + -
791B TRP* 5.0 7.2 - - + -
828B LEU 3.3 15.3 - - - +
829B LEU* 2.7 22.4 + - + +
831B MET* 1.3 70.3 - - - +
833B PHE* 1.3 56.6 + - + +
835B LYS* 2.6 32.0 + - - +
836B GLY 3.1 8.8 + - - -
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Residues in contact with PHE 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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787B HIS* 5.4 0.4 - + - -
791B TRP* 3.6 35.9 - + + -
829B LEU* 2.9 21.9 + - + -
830B GLU* 3.9 5.2 - - - +
832B VAL* 1.3 74.9 - - + +
834B ALA* 1.3 58.6 + - - +
835B LYS 2.9 5.1 + - - -
836B GLY* 3.3 20.5 + - - +
864B TYR* 3.6 41.5 - + - -
867B THR* 3.8 12.6 - - + -
868B GLN* 3.2 56.3 + - + +
871B LEU* 3.7 32.1 - - + -
880B ILE* 3.8 10.8 - - + +
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Residues in contact with ALA 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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830B GLU 2.8 16.5 + - - +
831B MET* 2.7 24.8 + - - +
833B PHE* 1.3 72.2 - - - +
835B LYS* 1.3 57.5 + - + +
880B ILE* 3.4 19.3 - - + -
881B LEU* 3.7 22.9 - - + -
891B LEU* 2.9 29.1 - - + +
895B ASN* 5.4 1.2 - - - +
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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
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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