Contacts of the helix formed by residues 807 - 829 (chain B) in PDB entry 2X36
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 GLY 807 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806B LEU* 1.3 79.4 - - - +
808B GLU* 1.3 57.2 + - - -
809B VAL* 2.3 23.8 + - - +
810B MET 2.7 13.3 + - - -
811B LYS* 3.6 3.4 + - - -
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Residues in contact with GLU 808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A GLN* 3.2 26.9 - - + +
807B GLY* 1.3 70.6 - - - -
809B VAL* 1.3 63.5 + - + +
810B MET 3.3 0.2 - - - -
811B LYS* 2.3 51.2 + - - +
812B GLU* 2.9 24.0 + - + +
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Residues in contact with VAL 809 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A GLN* 3.7 18.4 - - - +
807B GLY* 2.3 16.5 + - - +
808B GLU* 1.3 74.4 - - + +
810B MET* 1.3 65.1 + - + +
812B GLU* 3.6 1.7 + - - +
813B SER* 3.2 21.3 + - - -
850B PRO 4.9 8.7 - - - +
853B GLY* 5.8 0.2 - - - -
854B PRO* 4.4 23.6 - - + -
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Residues in contact with MET 810 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802B VAL* 6.0 2.2 - - + -
806B LEU* 3.2 44.0 - - + -
807B GLY 2.7 7.5 + - - -
809B VAL* 1.3 77.3 - - + +
811B LYS* 1.3 56.9 + - - +
813B SER* 3.1 6.4 + - - +
814B ALA* 2.8 33.7 + - + +
842B LEU* 5.6 0.2 - - + -
844B VAL* 4.0 27.1 - - + -
853B GLY* 3.2 41.7 - - - +
854B PRO 4.3 0.9 - - - -
856B ALA* 5.2 0.2 - - + -
860B ILE* 4.0 25.4 - - + -
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Residues in contact with LYS 811 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802B VAL* 4.7 24.9 - - + +
806B LEU 3.9 17.0 - - - +
807B GLY 4.2 1.3 - - - +
808B GLU* 2.3 66.2 + - - +
810B MET* 1.3 77.6 - - + +
812B GLU* 1.3 58.0 + - + +
814B ALA* 3.3 8.3 + - - +
815B ARG* 2.9 32.8 + - + +
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Residues in contact with GLU 812 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A VAL 4.6 2.3 - - - +
803A THR* 3.3 21.7 - - + +
804A GLY* 2.7 29.0 + - - -
805A GLN* 3.0 44.6 + - - +
806A LEU 5.2 0.2 + - - -
843A HIS* 4.8 1.2 + - - -
808B GLU* 2.9 12.8 + - + +
809B VAL 4.3 2.7 - - - +
811B LYS* 1.3 72.6 - - + +
813B SER* 1.3 66.8 + - - +
814B ALA 3.0 1.8 - - - -
815B ARG* 3.0 6.6 + - + +
816B ILE* 2.9 36.7 + - + +
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Residues in contact with SER 813 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809B VAL 3.2 18.4 + - - -
810B MET* 3.1 11.2 + - - +
812B GLU* 1.3 76.8 - - - +
814B ALA* 1.3 59.2 + - - +
816B ILE* 3.4 9.5 + - - +
817B ALA* 2.9 28.9 + - - +
853B GLY 4.6 1.0 + - - -
854B PRO* 3.3 41.2 + - - +
857B GLY* 4.6 7.7 + - - -
860B ILE* 5.1 2.3 - - - +
883B VAL* 5.4 2.3 - - - +
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Residues in contact with ALA 814 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B LEU* 4.5 8.2 - - + +
802B VAL* 4.9 7.6 - - + -
810B MET* 2.8 17.4 + - + +
811B LYS* 3.6 8.5 - - - +
813B SER* 1.3 78.6 + - - +
815B ARG* 1.3 52.2 + - + +
817B ALA* 3.1 6.5 + - - +
818B TYR* 2.6 38.1 + - - +
842B LEU* 3.6 29.8 - - + -
860B ILE* 4.4 11.8 - - + +
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Residues in contact with ARG 815 (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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785A ARG* 2.6 35.0 - - - +
801A GLU* 2.5 29.2 + - - +
803A THR* 4.5 11.0 - - + -
841A HIS* 4.1 3.2 + - - +
799B SER* 5.9 0.2 - - - +
800B LEU* 4.3 21.4 + - + +
811B LYS* 2.9 25.6 + - + +
812B GLU* 3.0 6.9 + - - +
814B ALA* 1.3 71.1 - - + +
816B ILE* 1.3 61.8 + - - +
818B TYR* 3.5 29.8 - - + +
819B THR* 2.9 31.6 + - - -
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Residues in contact with ILE 816 (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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803A THR* 3.6 22.7 - - - +
841A HIS* 4.2 9.4 - - + +
843A HIS* 3.6 33.2 - - + +
812B GLU* 2.9 33.6 + - + +
813B SER* 3.8 6.7 - - - +
815B ARG* 1.3 74.8 - - - +
817B ALA* 1.4 63.1 + - - +
820B PHE* 2.9 27.4 + - - +
883B VAL 4.1 9.6 - - - +
884B SER* 3.8 6.1 - - - +
885B LEU* 3.3 39.5 - - + +
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Residues in contact with ALA 817 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813B SER 2.9 15.2 + - - +
814B ALA* 3.5 6.7 - - - +
816B ILE* 1.4 75.0 - - - +
818B TYR* 1.3 53.4 - - - +
820B PHE* 3.2 3.4 + - - +
821B ALA* 2.8 36.2 + - - +
857B GLY* 3.9 18.2 - - - +
860B ILE* 3.7 25.1 - - + -
861B VAL* 4.3 7.3 - - + +
864B LEU* 4.2 2.5 - - - -
883B VAL* 4.2 16.3 - - + +
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Residues in contact with TYR 818 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A ARG* 4.2 3.6 - - - -
799B SER* 2.9 24.4 + - - -
800B LEU* 3.5 45.8 - - + -
814B ALA 2.6 20.7 + - - +
815B ARG* 3.5 35.0 - - - +
817B ALA* 1.3 72.3 - - - +
819B THR* 1.3 55.7 + - - +
821B ALA* 3.3 1.6 + - - +
822B ARG* 2.9 73.0 + - + +
835B LEU* 3.6 19.5 + - + -
838B SER 4.3 0.3 + - - -
840B ILE* 5.1 3.5 - - + +
864B LEU* 3.6 25.0 - - + +
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Residues in contact with THR 819 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A SER* 3.9 3.8 + - - +
784A LEU 3.7 18.7 - - - +
785A ARG* 3.4 26.1 + - + -
801A GLU* 4.0 1.7 + - - -
841A HIS* 3.0 36.4 - - + -
815B ARG* 2.9 15.1 + - - -
817B ALA 3.3 0.2 - - - -
818B TYR* 1.3 69.1 - - - +
820B PHE* 1.3 67.1 + - - +
822B ARG* 3.5 7.8 + - - +
823B ALA* 3.2 19.8 + - - +
885B LEU* 3.5 22.9 - - + -
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Residues in contact with PHE 820 (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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816B ILE 2.9 18.8 + - - +
817B ALA* 3.6 4.9 - - - +
819B THR* 1.3 79.5 - - - +
821B ALA* 1.3 61.2 + - - +
823B ALA* 4.0 5.1 - - + -
824B PHE* 3.0 52.2 + + + +
861B VAL* 4.0 15.3 - - + -
883B VAL* 4.4 10.5 - - + -
884B SER 4.3 8.7 - - - +
885B LEU* 3.4 25.7 - - - +
886B THR 3.6 18.4 - - - -
887B GLY* 3.8 7.2 - - - -
938B HIS* 4.1 8.1 - + - -
939B TYR* 3.4 44.6 - + + -
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Residues in contact with ALA 821 (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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817B ALA 2.8 20.2 + - - +
818B TYR 3.6 4.9 - - - +
820B PHE* 1.3 71.0 - - - +
822B ARG* 1.3 65.5 + - - +
824B PHE* 3.2 7.7 + - - +
825B LEU* 3.1 24.3 + - - +
835B LEU* 4.0 7.9 - - + -
861B VAL* 4.1 19.7 - - + +
864B LEU* 3.6 30.7 - - + -
865B LEU* 3.7 6.4 - - + +
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Residues in contact with ARG 822 (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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785A ARG* 2.9 48.7 + - - +
786A ARG* 3.3 43.0 - - - +
798B GLY 3.5 10.3 + - - -
818B TYR* 2.9 63.2 + - + +
819B THR* 3.8 6.5 - - - +
820B PHE 3.3 0.2 - - - -
821B ALA* 1.3 73.8 - - - +
823B ALA* 1.3 63.5 + - - +
825B LEU* 3.1 5.7 + - - +
826B MET* 3.1 28.5 + - + +
835B LEU* 3.8 34.0 + - + +
836B VAL* 3.7 16.2 + - + +
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Residues in contact with ALA 823 (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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783A SER* 4.3 8.3 - - - +
784A LEU* 3.8 23.8 - - + +
819B THR 3.2 9.8 + - - +
820B PHE* 4.1 7.0 - - + +
822B ARG* 1.3 78.1 - - - +
824B PHE* 1.4 58.2 - - - +
826B MET* 3.3 17.5 + - - +
827B GLN* 2.9 30.1 + - - +
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Residues in contact with PHE 824 (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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820B PHE* 3.0 48.5 + + + +
821B ALA* 3.6 6.5 - - - +
822B ARG 3.1 0.2 - - - -
823B ALA* 1.4 78.6 - - - +
825B LEU* 1.3 52.1 + - - +
827B GLN* 3.4 6.8 + - + +
828B HIS* 2.8 51.1 + + + +
865B LEU* 3.9 18.8 - - + -
938B HIS* 5.8 0.9 - + - -
939B TYR* 4.3 3.1 - + - -
940B ARG* 4.0 28.0 - - + -
943B PHE* 3.4 48.2 - + + -
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Residues in contact with LEU 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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821B ALA 3.1 12.5 + - - +
822B ARG 3.5 8.3 - - - +
824B PHE* 1.3 74.7 - - + +
826B MET* 1.3 60.1 + - - +
827B GLN 3.3 0.2 - - - -
828B HIS* 4.5 6.3 - - - +
829B ALA* 2.9 40.7 + - + +
832B ASN* 3.9 36.6 - - + +
835B LEU* 3.3 38.6 - - + +
836B VAL* 6.4 0.7 - - + -
865B LEU* 4.1 12.8 - - + -
868B ALA* 3.6 24.0 - - + -
869B MET* 4.2 20.2 - - + -
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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
----------------------------------------------------------
784A LEU* 4.9 9.0 - - - -
785A ARG* 2.9 44.9 - - - +
786A ARG* 3.0 24.9 - - - +
787A PRO* 3.5 17.9 - - + -
822B ARG* 3.1 17.8 + - + +
823B ALA* 3.4 12.3 - - - +
825B LEU* 1.3 75.3 - - + +
827B GLN* 1.3 61.0 + - - +
829B ALA 4.8 0.2 - - - -
830B PRO* 3.2 32.2 - - - +
832B ASN 5.2 4.0 + - - +
836B VAL* 3.5 19.3 - - + -
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Residues in contact with GLN 827 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823B ALA 2.9 16.7 + - - +
824B PHE* 3.8 7.9 - - + +
826B MET* 1.3 77.7 - - - +
828B HIS* 1.3 65.3 + - - +
830B PRO* 3.8 6.8 - - - +
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Residues in contact with HIS 828 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824B PHE* 2.8 40.9 + + + +
825B LEU* 4.3 5.2 - - - +
827B GLN* 1.3 79.7 - - - +
829B ALA* 1.3 70.7 + - + +
830B PRO* 3.4 5.2 - - - +
869B MET* 4.0 18.1 - - - -
943B PHE* 3.3 39.1 - + - -
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Residues in contact with ALA 829 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825B LEU* 2.9 24.5 + - + +
828B HIS* 1.3 91.6 - - + +
830B PRO* 1.3 55.5 - - - +
831B ALA* 2.4 23.9 + - + +
832B ASN* 2.6 29.8 + - + +
869B MET* 6.3 1.1 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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