Contacts of the helix formed by residues 839 - 858 (chain B) in PDB entry 3JWR
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 CYS 839 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559B PHE* 4.5 10.3 - - + -
628B ALA* 4.4 6.5 - - - -
632B GLY* 3.6 22.9 - - - -
634B ILE* 4.2 16.2 - - - -
829B TYR 5.4 0.2 - - - +
832B LEU* 3.7 29.9 - - + +
833B THR* 3.7 6.3 + - - +
836B SER* 3.2 27.8 + - - +
837B GLU 2.8 1.6 + - - -
838B ASP* 1.3 77.1 - - - +
840B PHE* 1.3 62.1 + - - +
841B PRO* 3.0 7.0 - - - -
842B LEU* 3.2 23.4 + - + +
843B LEU 4.0 0.2 + - - -
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Residues in contact with PHE 840 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A PRO* 2.9 48.5 - - + -
833B THR* 3.4 16.8 + - + -
837B GLU* 2.9 15.9 + - - +
839B CYS* 1.3 75.9 - - - +
841B PRO* 1.3 75.8 - - + +
843B LEU* 2.7 30.2 + - + -
844B ASP* 2.8 54.5 + - + -
847B ARG* 4.8 6.5 - - - -
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Residues in contact with PRO 841 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B PHE* 3.6 34.8 - - + -
769B THR 4.9 1.2 - - - +
838B ASP 3.3 14.6 - - - +
839B CYS* 3.0 7.6 - - - +
840B PHE* 1.3 97.6 - - + +
842B LEU* 1.3 54.9 + - - +
844B ASP* 3.5 7.9 - - + +
845B GLY* 2.8 29.3 + - - -
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Residues in contact with LEU 842 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B PHE* 3.8 39.3 - - + +
624B CYS* 4.3 22.0 - - - -
628B ALA* 5.8 3.8 - - + -
762B ALA* 5.2 2.0 - - + +
763B CYS* 6.4 0.4 - - - -
766B SER* 4.9 0.9 - - - -
769B THR* 3.0 39.2 - - + +
829B TYR* 4.0 23.6 - - + -
832B LEU* 3.9 24.5 - - + -
839B CYS* 3.2 10.9 + - + +
841B PRO* 1.3 80.5 - - - +
843B LEU* 1.3 62.1 + - - +
846B CYS* 3.0 24.7 + - - +
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Residues in contact with LEU 843 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A PRO* 5.4 3.6 - - + -
826B THR* 4.0 14.4 - - + +
829B TYR* 3.8 19.8 + - + +
830B GLU* 3.6 53.4 - - + +
833B THR* 4.2 11.2 - - + +
839B CYS 4.0 0.6 + - - -
840B PHE* 2.7 26.9 + - + +
842B LEU* 1.3 73.1 - - - +
844B ASP* 1.3 65.6 + - - +
846B CYS* 3.4 3.1 - - + +
847B ARG* 2.9 54.8 + - - +
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Residues in contact with ASP 844 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A PHE* 4.7 11.1 - - - -
840B PHE* 2.8 45.5 + - + +
841B PRO* 3.5 9.6 - - + +
843B LEU* 1.3 78.7 - - - +
845B GLY* 1.3 63.2 + - - +
847B ARG* 3.3 13.0 - - - +
848B LYS* 3.0 51.4 + - - +
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Residues in contact with GLY 845 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769B THR* 3.8 19.9 - - - -
770B LYS 4.3 2.5 - - - +
841B PRO 2.8 18.6 + - - -
842B LEU 4.0 0.2 - - - -
844B ASP* 1.3 72.6 - - - +
846B CYS* 1.3 60.0 + - - +
848B LYS* 3.6 15.0 - - - +
849B ASN* 3.2 29.1 + - - -
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Residues in contact with CYS 846 (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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768B ILE* 3.7 16.5 - - - +
769B THR* 3.9 4.2 - - + +
821B ILE* 4.1 10.7 - - - +
825B CYS* 4.1 9.6 - - - -
826B THR* 4.0 33.4 - - - -
829B TYR* 4.0 21.1 - - + -
842B LEU 3.0 18.8 + - - +
843B LEU* 3.4 7.9 - - + +
844B ASP 3.1 0.2 - - - -
845B GLY* 1.3 71.7 - - - +
847B ARG* 1.3 66.9 + - - +
848B LYS 3.0 1.1 - - - -
849B ASN* 3.0 6.8 + - - +
850B ARG* 2.9 19.2 + - - +
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Residues in contact with ARG 847 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A SER* 4.1 15.1 + - - -
564A PHE* 4.5 17.4 - - + -
565A GLU* 2.9 45.0 + - + +
773A PRO* 5.2 1.6 - - - +
774A ILE* 4.0 25.1 - - - +
777A ARG* 5.2 2.4 - - - +
826B THR* 4.5 10.3 - - + +
830B GLU* 3.6 29.9 + - - +
840B PHE* 4.8 9.4 - - - -
843B LEU* 2.9 40.9 + - - +
844B ASP* 3.3 17.9 - - - +
846B CYS* 1.3 79.4 - - - +
848B LYS* 1.3 56.3 + - - +
850B ARG* 3.5 8.3 - - - +
851B GLN* 2.9 28.4 + - - +
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Residues in contact with LYS 848 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A PHE* 4.2 22.2 - - + -
844B ASP* 3.0 46.4 + - - +
845B GLY* 3.6 15.7 - - - +
846B CYS 3.0 0.2 - - - -
847B ARG* 1.3 78.3 - - - +
849B ASN* 1.3 61.6 + - - +
851B GLN* 3.2 21.3 - - - +
852B LYS* 3.3 14.6 - - - +
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Residues in contact with ASN 849 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768B ILE 2.9 25.0 + - - +
770B LYS 2.6 30.5 + - - +
772B TRP* 3.7 26.5 + - + +
775B GLN* 3.3 28.7 - - + +
821B ILE* 5.0 2.7 - - + -
845B GLY 3.2 6.8 + - - +
846B CYS 3.0 7.6 + - - +
848B LYS* 1.3 76.3 - - - +
850B ARG* 1.3 68.1 + - - +
851B GLN 3.1 1.1 - - - -
852B LYS* 2.9 3.9 + - - +
853B TRP* 2.9 31.7 + - + -
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Residues in contact with ARG 850 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A GLU* 2.9 43.5 + - - -
566A LEU* 4.0 11.7 - - - +
570A GLU* 3.0 36.1 + - - -
818B VAL* 3.7 19.5 - - + +
821B ILE* 3.8 36.6 - - + +
822B ASP* 2.9 39.4 + - - -
826B THR* 5.6 3.6 - - - -
846B CYS 2.9 12.0 + - - +
847B ARG* 3.5 11.0 - - - +
849B ASN* 1.3 76.0 - - - +
851B GLN* 1.3 63.4 + - - +
853B TRP* 3.3 2.6 + - - +
854B GLN* 2.9 34.4 + - - +
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Residues in contact with GLN 851 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A PHE* 2.8 34.9 + - + +
565A GLU* 3.6 14.8 + - - +
566A LEU 3.5 20.2 + - - +
567A SER* 4.7 5.2 + - - -
847B ARG 2.9 14.2 + - - +
848B LYS* 3.2 16.6 - - - +
850B ARG* 1.3 76.4 - - - +
852B LYS* 1.3 61.0 + - + +
854B GLN* 3.3 3.5 + - - +
855B ALA* 3.1 26.7 + - - +
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Residues in contact with LYS 852 (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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772B TRP* 3.5 61.4 - - + +
848B LYS 3.3 16.2 - - - +
849B ASN* 2.9 6.9 + - - +
851B GLN* 1.3 77.7 - - + +
853B TRP* 1.3 65.7 + - - +
855B ALA* 3.6 7.0 + - - +
856B LEU* 3.2 26.2 + - - +
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Residues in contact with TRP 853 (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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772B TRP* 3.8 21.5 - + - -
775B GLN* 3.0 22.8 + - + -
776B GLN* 4.5 11.0 - - - -
779B ALA* 3.8 28.3 - - + -
780B GLU* 5.1 2.2 - - - -
813B LEU* 3.3 32.3 - - + -
814B PRO* 3.4 39.0 - - + +
817B GLN* 3.8 19.6 - - + +
818B VAL* 4.0 8.3 - - + +
821B ILE* 4.0 20.4 - - + -
849B ASN* 2.9 24.8 + - + +
850B ARG 3.8 3.4 - - - +
852B LYS* 1.3 73.6 - - - +
854B GLN* 1.3 61.7 + - - +
856B LEU* 3.2 22.5 + - + +
857B ALA* 2.8 29.6 + - - +
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Residues in contact with GLN 854 (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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565A GLU 4.6 1.6 - - - +
567A SER* 3.8 14.4 - - - +
570A GLU* 2.9 40.2 + - - +
815B LYS* 5.5 0.5 - - - +
818B VAL* 3.3 26.8 - - + +
850B ARG* 2.9 26.8 + - - +
851B GLN* 3.5 5.6 - - - +
853B TRP* 1.3 76.7 - - - +
855B ALA* 1.3 66.6 + - - +
857B ALA* 3.1 16.6 + - - +
858B GLU* 3.2 37.6 + - - +
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Residues in contact with ALA 855 (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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567A SER* 5.6 0.9 - - - -
851B GLN* 3.1 13.9 + - - +
852B LYS* 3.7 13.0 - - - +
854B GLN* 1.3 78.1 - - - +
856B LEU* 1.3 58.4 + - + +
858B GLU* 2.9 38.7 + - - +
859B GLN 3.5 5.7 + - - +
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Residues in contact with LEU 856 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772B TRP* 4.1 19.5 - - + -
776B GLN* 5.1 4.3 - - - +
814B PRO* 3.9 15.0 - - + +
852B LYS* 3.2 9.0 + - - +
853B TRP* 3.2 35.3 + - + +
855B ALA* 1.3 79.1 - - + +
857B ALA* 1.3 55.6 + - - +
859B GLN* 2.6 43.5 + - - +
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Residues in contact with ALA 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814B PRO* 3.6 7.6 - - - +
815B LYS* 3.7 52.9 + - + +
853B TRP 2.8 16.3 + - - +
854B GLN* 3.1 21.0 + - - +
856B LEU* 1.3 72.5 - - - +
858B GLU* 1.3 59.5 + - + +
859B GLN* 3.1 11.0 + - - +
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Residues in contact with GLU 858 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A SER* 2.9 33.5 + - - -
569A LEU* 3.6 17.3 - - - +
570A GLU* 4.6 0.3 - - - +
854B GLN* 3.2 32.2 + - - +
855B ALA* 2.9 15.4 + - - +
857B ALA* 1.3 78.0 - - + +
859B GLN* 1.3 71.4 + - - +
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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