Contacts of the helix formed by residues 878 - 895 (chain B) in PDB entry 3H44
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 THR 878 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876B ASP 3.5 3.2 + - - -
877B MET* 1.3 81.6 - - - +
879B GLU* 1.3 68.9 + - - +
880B GLU* 3.4 11.8 + - - +
881B ALA* 3.0 29.6 + - + +
882B PHE* 3.5 14.9 + - - +
933B LYS* 4.9 0.3 - - - +
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Residues in contact with GLU 879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878B THR* 1.3 81.1 + - - +
880B GLU* 1.3 65.8 + - + +
881B ALA 3.1 0.2 - - - -
882B PHE* 3.0 28.2 + - - +
883B GLN* 3.4 21.1 + - - +
933B LYS* 5.4 8.3 - - - +
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Residues in contact with GLU 880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878B THR* 3.4 7.6 + - - +
879B GLU* 1.3 80.7 - - + +
881B ALA* 1.3 63.8 + - - +
883B GLN* 3.6 15.6 - - + +
884B LYS* 3.1 46.4 + - - +
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Residues in contact with ALA 881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLU* 4.9 6.5 - - - +
877B MET* 3.9 17.5 - - + -
878B THR* 3.0 42.7 + - + +
880B GLU* 1.3 77.1 + - - +
882B PHE* 1.3 62.0 + - - +
884B LYS* 3.0 30.2 + - - +
885B HIS* 3.3 11.1 + - + -
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Residues in contact with PHE 882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810B LEU* 3.9 21.3 - - + -
814B ILE* 4.3 15.7 - - + -
874B ILE* 5.3 0.7 - - + -
877B MET* 3.5 13.7 - - - -
878B THR 3.5 6.7 + - - +
879B GLU* 3.0 20.2 + - - +
881B ALA* 1.3 78.0 - - - +
883B GLN* 1.3 72.3 + - - -
885B HIS* 3.0 18.0 + - - +
886B ILE* 3.1 31.2 + - + +
931B LEU 3.6 10.3 - - - -
932B THR* 3.5 7.4 - - - -
933B LYS* 3.2 57.9 - - + -
936B ILE* 4.0 15.0 - - + -
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Residues in contact with GLN 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879B GLU* 3.4 19.9 + - - +
880B GLU* 3.5 18.8 + - + +
881B ALA 3.3 1.0 - - - -
882B PHE* 1.3 92.7 - - - +
884B LYS* 1.3 56.7 + - - +
886B ILE* 3.6 24.8 + - - +
887B GLN* 3.0 26.9 + - - +
929B LYS* 4.4 17.2 + - - +
931B LEU 5.5 0.5 + - - +
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Residues in contact with LYS 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLU* 3.4 40.7 + - + +
134B HIS* 3.6 28.4 - - + +
880B GLU* 3.1 38.3 + - - +
881B ALA* 3.0 19.3 + - - +
883B GLN* 1.3 76.7 - - - +
885B HIS* 1.3 51.8 + - - +
887B GLN* 3.2 8.1 + - + +
888B ALA* 2.7 34.5 + - - +
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Residues in contact with HIS 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B SER* 5.3 4.7 - - - -
133B GLU* 3.9 33.1 + - + +
810B LEU* 4.2 6.3 - - + -
813B GLN* 3.4 32.5 + - + +
814B ILE* 3.6 46.7 + - + +
817B GLU* 6.5 0.4 - - + -
818B PRO* 6.1 2.0 - - + -
877B MET* 3.6 31.4 - - + +
881B ALA 3.3 12.5 + - - -
882B PHE* 3.0 8.6 + - - +
884B LYS* 1.3 77.6 - - - +
886B ILE* 1.3 59.8 + - - +
888B ALA* 3.7 1.4 - - - +
889B LEU* 2.9 30.3 + - - +
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Residues in contact with ILE 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810B LEU* 4.0 21.1 - - + -
882B PHE* 3.1 39.9 + - + +
883B GLN* 3.7 23.8 - - + +
885B HIS* 1.3 76.6 - - - +
887B GLN* 1.3 59.4 + - - +
889B LEU 3.3 0.7 + - - -
890B ALA* 2.8 31.5 + - + +
928B LEU* 3.5 35.4 - - + +
929B LYS* 3.9 27.4 - - + +
931B LEU 3.6 15.0 - - - +
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Residues in contact with GLN 887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLU 5.7 0.4 - - - +
156B GLU* 6.3 0.6 - - - -
157B HIS* 5.9 4.9 - - - +
883B GLN 3.0 19.0 + - - +
884B LYS* 3.4 9.2 - - - +
886B ILE* 1.3 77.9 - - - +
888B ALA* 1.3 61.6 - - - +
890B ALA* 3.4 10.0 + - - +
891B ILE* 3.0 55.9 + - + +
929B LYS* 5.0 10.6 + - - +
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Residues in contact with ALA 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B SER 3.6 24.0 - - - +
133B GLU 3.7 6.5 + - - +
134B HIS* 4.9 0.7 - - - +
135B ALA* 3.5 27.1 - - - +
813B GLN* 3.7 13.0 - - - +
884B LYS 2.7 19.7 + - - +
885B HIS 3.7 0.2 - - - +
886B ILE 3.3 0.2 - - - -
887B GLN* 1.3 73.4 - - - +
889B LEU* 1.3 64.8 + - - +
891B ILE* 3.4 1.1 + - - -
892B ARG* 3.2 28.0 + - - +
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Residues in contact with LEU 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806B MET* 3.6 26.7 - - + -
809B GLU* 3.9 21.8 - - + +
810B LEU* 3.9 22.0 - - + +
813B GLN* 4.4 15.5 - - + +
885B HIS 2.9 18.1 + - - +
886B ILE* 3.6 4.0 - - - +
888B ALA* 1.3 76.1 - - - +
890B ALA* 1.3 64.0 + - - +
892B ARG* 3.1 17.1 + - + +
893B ARG* 3.0 39.9 + - + +
928B LEU* 3.7 19.3 - - + -
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Residues in contact with ALA 890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886B ILE* 2.8 18.2 + - + +
887B GLN* 3.5 17.5 - - - +
889B LEU* 1.3 74.9 - - - +
891B ILE* 1.3 63.3 + - + +
893B ARG* 3.1 3.3 + - - +
894B LEU* 3.0 31.9 + - + +
925B VAL* 4.1 29.6 - - + -
928B LEU* 3.9 6.6 - - + +
929B LYS* 4.6 9.4 - - - +
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Residues in contact with ILE 891 (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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84B ASP* 3.9 28.0 - - + +
85B LYS* 4.6 8.7 - - - -
134B HIS 5.8 0.2 - - - -
135B ALA* 4.0 15.3 - - + -
154B SER* 3.0 32.8 - - - +
155B HIS* 6.1 1.6 - - + -
156B GLU* 4.6 5.2 - - - +
157B HIS* 5.8 1.6 - - + +
887B GLN* 3.0 50.6 + - + +
888B ALA* 4.0 3.4 - - - +
889B LEU 3.4 0.2 - - - -
890B ALA* 1.3 75.0 - - + +
892B ARG* 1.3 64.0 + - - +
894B LEU* 3.3 4.4 + - - -
895B ASP* 2.9 24.9 + - + +
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Residues in contact with ARG 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LYS* 4.9 12.8 - - - +
131B LEU 4.3 0.2 + - - -
132B SER* 4.0 12.3 + - - +
135B ALA* 3.5 24.8 + - + +
136B GLY 3.1 26.9 + - - +
137B SER* 5.5 1.0 - - - -
813B GLN* 2.6 38.9 + - - +
888B ALA* 3.2 20.9 + - - +
889B LEU* 3.1 16.0 + - + +
891B ILE* 1.3 77.8 - - - +
893B ARG* 1.3 66.8 + - + +
894B LEU 3.5 0.2 + - - -
895B ASP* 3.5 16.1 + - - +
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Residues in contact with ARG 893 (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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806B MET* 3.5 14.2 - - + +
809B GLU* 2.7 40.7 + - - -
889B LEU* 3.0 33.4 + - + +
890B ALA 3.1 0.2 + - - -
892B ARG* 1.3 81.1 - - - +
894B LEU* 1.3 60.3 + - - +
895B ASP 3.4 3.6 + - - +
906B LYS* 5.0 0.9 + - - -
920B ARG* 3.9 12.5 - - - +
921B ASP* 3.1 51.2 + - - +
924B GLU* 2.6 32.8 + - - +
925B VAL* 3.8 20.8 - - + +
928B LEU* 6.4 0.2 - - + -
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Residues in contact with LEU 894 (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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84B ASP* 4.0 4.3 - - - +
890B ALA* 3.0 19.8 + - + +
891B ILE* 3.6 4.3 - - - +
893B ARG* 1.3 74.7 - - - +
895B ASP* 1.3 65.7 + - - +
896B LYS* 3.1 31.7 + - - +
921B ASP* 3.8 26.5 - - + +
922B ASN* 3.4 30.3 - - - +
925B VAL* 3.9 25.6 - - + -
929B LYS* 5.6 2.2 - - - +
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Residues in contact with ASP 895 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASP* 3.0 27.0 - - - +
85B LYS* 3.4 37.5 + - - +
891B ILE* 2.9 11.9 + - + +
892B ARG 3.6 15.6 - - - +
893B ARG 3.4 4.9 - - - +
894B LEU* 1.3 76.8 - - - +
896B LYS* 1.3 73.2 + - - +
897B PRO* 3.8 4.2 - - - +
898B LYS* 3.2 20.8 + - - -
906B LYS* 5.5 4.5 - - - +
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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