Contacts of the helix formed by residues 878 - 895 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876A ASP 4.8 3.1 - - - +
877A MET* 1.3 74.2 - - - +
879A GLU* 1.3 59.8 + - - +
880A GLU* 2.8 11.3 + - - -
881A ALA* 3.0 14.5 + - - +
882A PHE* 2.9 18.7 + - - +
55B THR* 4.8 6.7 - - + -
448B GLU* 5.8 4.0 - - + -
451B THR* 4.7 14.4 - - + +
455B LEU* 3.7 34.5 - - + -
457B GLU* 2.3 32.8 + - - +
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Residues in contact with GLU 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A MET 3.7 1.6 + - - -
878A THR* 1.3 70.5 - - - +
880A GLU* 1.3 58.4 + - - +
882A PHE* 3.9 10.7 - - - -
883A GLN* 3.1 45.9 + - + +
932A THR* 3.8 26.0 - - - +
933A LYS* 4.3 25.6 + - + +
55B THR* 5.3 1.4 + - - -
447B GLU* 6.0 3.1 - - + -
448B GLU* 3.4 32.6 + - + +
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Residues in contact with GLU 880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A THR* 2.8 3.4 + - - +
879A GLU* 1.3 78.9 - - - +
881A ALA* 1.3 57.5 + - - +
882A PHE 2.9 0.4 - - - -
883A GLN* 2.7 37.9 + - - +
884A LYS* 3.0 16.1 + - - +
327B LYS* 3.4 41.0 - - + -
448B GLU* 5.9 0.8 - - - -
457B GLU* 3.1 31.8 - - + +
458B GLU* 3.7 20.5 - - - +
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Residues in contact with ALA 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU* 6.3 1.6 - - - -
877A MET* 4.2 18.2 - - + -
878A THR* 3.0 27.4 + - - +
880A GLU* 1.3 74.8 - - - +
882A PHE* 1.3 60.5 + - - +
884A LYS* 3.2 28.7 - - + +
885A HIS* 3.2 22.6 + - + +
457B GLU* 3.8 7.1 + - - +
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Residues in contact with PHE 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810A LEU* 3.8 20.4 - - + +
814A ILE* 4.1 23.3 - - + -
874A ILE* 5.1 3.1 - - + -
877A MET* 3.9 19.6 - - - -
878A THR 2.9 13.4 + - - +
879A GLU* 3.8 16.4 - - - +
880A GLU 2.8 1.8 + - - -
881A ALA* 1.3 73.7 - - - +
883A GLN* 1.3 74.8 + - - +
885A HIS* 3.4 6.3 + - - +
886A ILE* 3.3 29.6 + - + +
931A LEU 3.6 9.2 - - - -
932A THR* 3.5 36.1 - - - -
933A LYS* 3.7 31.0 - - + -
936A ILE* 4.3 8.5 - - + -
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Residues in contact with GLN 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A GLU* 3.1 37.5 + - + +
880A GLU* 2.7 27.6 + - - +
882A PHE* 1.3 80.0 - - - +
884A LYS* 1.3 53.0 + - - +
886A ILE* 3.2 22.9 + - - +
887A GLN* 2.9 35.3 + - - +
929A LYS* 4.8 7.7 + - - +
931A LEU 4.4 7.6 - - - +
932A THR* 5.5 0.2 - - - +
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Residues in contact with LYS 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A GLU* 3.4 51.5 - - + +
134A HIS* 4.4 19.1 - - + +
880A GLU* 3.0 13.0 + - - +
881A ALA* 3.2 23.6 - - - +
883A GLN* 1.3 76.4 - - - +
885A HIS* 1.3 56.6 + - - +
887A GLN* 3.2 9.6 + - - +
888A ALA 2.9 23.7 + - - -
415B LYS* 4.9 6.8 - - - +
457B GLU* 3.4 47.6 + - - +
458B GLU* 3.9 16.6 - - + +
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Residues in contact with HIS 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A SER* 5.5 3.4 - - - -
133A GLU* 4.1 25.4 + - + +
810A LEU* 4.3 5.4 - - + +
813A GLN* 3.1 47.4 + - + +
814A ILE* 3.8 38.3 + - + +
817A GLU* 6.4 1.6 - - + -
818A PRO* 6.0 1.8 - - + -
877A MET* 3.6 30.9 - - + +
881A ALA* 3.2 22.6 + - - +
882A PHE* 3.7 7.0 - - - +
883A GLN 3.3 0.6 - - - -
884A LYS* 1.3 77.4 - - + +
886A ILE* 1.3 64.9 + - - +
889A LEU* 3.2 19.2 + - - +
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Residues in contact with ILE 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810A LEU* 4.2 20.2 - - + -
882A PHE* 3.3 20.9 + - + +
883A GLN* 3.2 24.5 + - - +
885A HIS* 1.3 76.9 - - - +
887A GLN* 1.3 59.8 + - - +
889A LEU 3.4 0.7 + - - -
890A ALA* 2.9 26.7 + - - +
928A LEU* 3.6 40.8 - - + +
929A LYS* 4.1 33.7 - - + +
931A LEU* 3.8 23.6 - - + +
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Residues in contact with GLN 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A GLU* 5.7 3.0 + - - -
157A HIS* 6.2 1.6 - - - +
883A GLN 2.9 13.9 + - - +
884A LYS* 3.2 13.2 + - - +
886A ILE* 1.3 75.0 - - + +
888A ALA* 1.3 63.7 + - - +
890A ALA* 3.3 12.1 - - - +
891A ILE* 3.0 55.8 + - + +
929A LYS* 4.9 12.1 + - - +
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Residues in contact with ALA 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A SER 3.8 1.1 - - - +
133A GLU 3.8 8.7 + - - +
135A ALA* 3.6 32.8 - - - +
813A GLN* 3.5 27.4 - - - +
884A LYS 2.9 14.2 + - - +
885A HIS* 3.8 1.1 - - - +
886A ILE 3.3 0.6 - - - -
887A GLN* 1.3 71.9 - - - +
889A LEU* 1.3 67.1 + - - +
891A ILE* 3.0 7.2 + - - +
892A ARG* 2.9 24.2 + - - +
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Residues in contact with LEU 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A MET* 3.9 18.4 - - + -
809A GLU* 3.6 45.3 - - + +
810A LEU* 3.7 9.9 - - + +
813A GLN* 4.1 19.7 + - + +
885A HIS 3.2 10.9 + - - +
886A ILE* 3.7 7.9 - - - +
888A ALA* 1.3 75.1 - - - +
890A ALA* 1.3 55.4 + - - +
892A ARG* 3.0 16.5 + - + +
893A ARG* 2.8 56.5 + - + +
928A LEU* 3.8 9.6 - - + -
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Residues in contact with ALA 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886A ILE 2.9 14.9 + - - +
887A GLN* 3.3 23.6 - - - +
889A LEU* 1.3 74.8 - - - +
891A ILE* 1.3 65.0 + - + +
893A ARG* 3.2 1.9 + - - +
894A LEU* 3.0 34.6 + - + +
925A VAL* 4.1 28.5 - - + -
928A LEU* 4.1 4.8 - - + +
929A LYS* 4.9 10.3 - - + +
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Residues in contact with ILE 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ASP* 4.5 17.1 - - + +
85A LYS* 4.8 9.6 - - + -
134A HIS* 4.9 2.2 - - - +
135A ALA* 3.6 18.2 - - + -
154A SER* 3.7 33.7 - - - +
157A HIS* 5.8 2.5 - - + +
887A GLN* 3.0 49.8 + - + +
888A ALA* 3.0 7.8 + - - +
890A ALA* 1.3 75.4 - - + +
892A ARG* 1.3 64.1 + - - +
894A LEU* 3.7 3.6 - - - -
895A ASP* 3.0 23.7 + - - +
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Residues in contact with ARG 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LYS* 4.8 13.8 + - - +
132A SER* 3.7 15.2 + - - +
135A ALA* 3.4 31.8 + - + +
136A GLY 2.7 29.1 + - - +
137A SER* 5.0 2.4 - - - -
813A GLN* 3.0 26.9 + - - -
888A ALA* 2.9 14.6 + - - +
889A LEU* 3.4 19.1 - - + +
891A ILE* 1.3 79.7 - - - +
893A ARG* 1.3 64.5 + - + +
895A ASP* 3.5 16.5 - - - +
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Residues in contact with ARG 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806A MET* 3.7 15.0 - - + +
809A GLU* 3.0 33.2 + - - -
889A LEU* 2.8 35.5 + - + +
890A ALA 3.9 2.5 - - - +
892A ARG* 1.3 81.9 - - + +
894A LEU* 1.3 59.6 + - - +
895A ASP 3.6 2.4 + - - +
906A LYS* 4.4 4.7 + - - -
920A ARG* 3.6 15.4 - - - +
921A ASP* 3.0 52.4 + - - +
924A GLU* 2.7 32.6 + - - +
925A VAL* 3.9 17.9 - - + +
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Residues in contact with LEU 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ASP* 4.1 4.2 - - - +
890A ALA* 3.0 23.5 + - + +
891A ILE* 3.7 3.4 - - - +
893A ARG* 1.3 75.5 - - - +
895A ASP* 1.3 64.8 + - - +
896A LYS* 3.1 20.8 + - - +
921A ASP* 4.0 16.8 - - + +
922A ASN* 3.9 24.5 - - - +
925A VAL* 3.9 35.9 - - + -
929A LYS* 5.5 3.8 - - - +
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Residues in contact with ASP 895 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASP* 3.3 27.3 - - + +
85A LYS* 3.3 31.8 + - - +
891A ILE* 3.0 12.2 + - - +
892A ARG* 3.5 16.7 - - - +
893A ARG 3.3 5.1 - - - +
894A LEU* 1.3 75.2 - - - +
896A LYS* 1.3 68.8 + - - +
897A PRO* 3.7 6.4 - - - +
898A LYS* 3.7 17.6 + - - -
906A LYS* 5.2 4.7 + - - +
2001A DIO 3.4 13.5 - - - +
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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