Contacts of the helix formed by residues 875 - 892 (chain A) in PDB entry 1SO2
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 ASP 875 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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873A HIS 3.8 2.2 + - - -
874A LEU* 1.3 76.4 - - - +
876A HIS* 1.3 52.7 + - - +
877A VAL* 2.6 20.6 + - - +
878A GLU* 2.6 58.9 + - - +
879A PHE* 2.8 32.0 + - - +
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Residues in contact with HIS 876 (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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875A ASP* 1.3 73.6 + - - +
877A VAL* 1.3 63.0 + - + +
879A PHE* 3.5 6.8 + - - +
880A LYS* 3.1 42.0 + - + +
835B ALA 5.8 1.6 + - - -
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Residues in contact with VAL 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A ASP* 2.6 16.1 + - - +
876A HIS* 1.3 78.7 - - + +
878A GLU* 1.3 66.7 + - + +
880A LYS* 3.5 6.3 + - - +
881A ARG* 3.1 26.2 + - + +
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Residues in contact with GLU 878 (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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713A PHE* 5.4 6.0 - - - -
809A LEU* 4.4 19.9 - - + +
873A HIS 4.5 2.1 - - - +
874A LEU* 3.6 24.3 - - + +
875A ASP* 2.6 47.9 + - - +
877A VAL* 1.3 72.2 - - + +
879A PHE* 1.3 67.2 + - - +
881A ARG* 3.3 6.6 + - - +
882A PHE* 3.0 24.1 + - - +
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Residues in contact with PHE 879 (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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859A TRP* 3.9 28.3 - + - -
862A TYR* 4.2 17.3 - + - -
863A LEU* 4.8 12.8 - - + -
869A ASN* 5.6 0.7 - - - -
871A LEU* 4.1 38.4 - - + -
874A LEU* 4.1 15.7 - - + +
875A ASP 2.8 17.8 + - - +
876A HIS* 3.9 7.2 - - - +
878A GLU* 1.3 78.1 - - - +
880A LYS* 1.3 65.5 + - - +
882A PHE* 3.2 3.3 + + - +
883A ARG* 3.0 32.6 + - + +
837B ASN* 5.6 8.1 - - - -
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Residues in contact with LYS 880 (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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876A HIS* 3.1 34.1 + - + +
877A VAL* 3.8 7.6 - - - +
878A GLU 3.3 0.2 - - - -
879A PHE* 1.3 83.8 - - + +
881A ARG* 1.3 61.6 + - - +
883A ARG* 3.5 6.1 + - + +
884A PHE* 3.2 21.5 + - - +
834B VAL* 5.3 13.7 - - + -
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Residues in contact with ARG 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A LEU* 4.3 15.6 - - + +
810A GLU* 3.4 29.5 + - - +
877A VAL* 3.1 21.1 + - + +
878A GLU* 3.3 6.3 + - - +
880A LYS* 1.3 74.9 - - - +
882A PHE* 1.3 60.6 + - - +
884A PHE* 3.3 20.5 + - + +
885A LEU* 2.9 61.3 + - + +
922A GLU* 3.2 46.8 + - - +
926A LEU* 6.3 0.2 - - - +
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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
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809A LEU* 3.8 22.4 - - + -
812A MET* 3.5 27.1 - - + -
813A ALA* 3.4 27.8 - - + -
816A VAL* 3.7 33.4 - - + -
859A TRP* 3.9 15.3 - + - -
870A PHE* 5.7 0.2 - + - -
871A LEU* 3.4 31.2 - - + -
874A LEU* 4.3 7.2 - - + -
878A GLU 3.0 17.5 + - - +
879A PHE* 3.2 10.1 + + - +
881A ARG* 1.3 74.5 - - - +
883A ARG* 1.3 67.0 + - - +
885A LEU* 3.3 8.3 + - - +
886A VAL* 3.0 40.4 + - + +
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Residues in contact with ARG 883 (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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859A TRP* 3.4 61.9 + - + +
863A LEU* 5.3 3.3 - - - +
879A PHE* 3.0 27.6 + - + +
880A LYS* 3.8 7.6 - - + +
882A PHE* 1.3 77.6 - - - +
884A PHE* 1.3 63.9 + - - +
886A VAL* 3.5 1.6 + - - +
887A ILE* 3.0 43.7 + - + +
834B VAL* 5.7 1.0 + - - +
837B ASN* 4.4 11.6 + - - -
841B ALA 4.1 1.4 + - - -
842B VAL* 3.7 34.0 + - - +
845B ASN* 4.1 5.7 + - - +
846B ASP* 2.9 40.0 + - - +
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Residues in contact with PHE 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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880A LYS 3.2 11.9 + - - +
881A ARG* 3.4 23.8 - - - +
883A ARG* 1.3 82.8 - - - +
885A LEU* 1.3 77.7 + - + +
887A ILE* 3.5 8.8 + - + +
888A GLU* 2.9 66.0 + - + +
926A LEU* 4.4 11.4 - - + -
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Residues in contact with LEU 885 (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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809A LEU* 4.7 5.6 - - + +
810A GLU* 3.8 30.1 - - + +
813A ALA* 3.5 23.3 - - + -
881A ARG* 2.9 54.0 + - + +
882A PHE* 3.6 4.5 - - - +
884A PHE* 1.3 89.5 - - + +
886A VAL* 1.3 66.4 + - - +
888A GLU* 3.0 6.9 + - - +
889A ALA* 2.9 24.5 + - - +
926A LEU* 4.0 27.8 - - + +
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Residues in contact with VAL 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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813A ALA* 3.7 20.0 - - - +
816A VAL* 4.2 3.6 - - + -
817A ALA* 4.0 14.4 - - - +
820A MET* 3.7 23.3 - - - -
859A TRP* 3.6 22.0 - - + +
882A PHE* 3.0 43.7 + - + +
883A ARG 3.8 3.8 - - - +
885A LEU* 1.3 72.3 - - - +
887A ILE* 1.3 64.7 + - - +
889A ALA* 3.2 3.7 + - - +
890A ILE* 2.9 33.0 + - + +
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Residues in contact with ILE 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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855A ALA* 4.8 4.5 - - + -
859A TRP* 3.9 13.9 - - + +
883A ARG* 3.0 48.6 + - + +
884A PHE* 3.6 8.3 - - + +
886A VAL* 1.3 77.4 - - - +
888A GLU* 1.3 62.4 + - - +
890A ILE* 3.2 5.8 + - - +
891A LEU* 2.8 47.8 + - + +
845B ASN* 3.6 52.0 - - + +
846B ASP* 4.7 2.0 - - - +
847B ARG* 4.9 3.1 - - + +
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Residues in contact with GLU 888 (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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884A PHE* 2.9 55.4 + - + +
885A LEU 3.0 4.9 + - - +
887A ILE* 1.3 78.0 - - - +
889A ALA* 1.3 60.6 + - - +
891A LEU* 4.2 2.8 - - - +
892A ALA* 3.3 13.9 + - - +
926A LEU* 3.9 25.4 - - + +
930A GLN* 3.2 31.4 + - - +
847B ARG* 3.2 31.3 + - - -
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Residues in contact with ALA 889 (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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814A LEU* 4.3 16.4 - - + -
817A ALA* 3.6 23.8 - - + -
885A LEU 2.9 11.8 + - - +
886A VAL* 3.7 2.0 - - - +
888A GLU* 1.3 73.6 - - - +
890A ILE* 1.3 68.7 + - - +
892A ALA* 3.1 19.5 + - - +
893A THR* 3.6 11.1 - - - +
926A LEU* 5.2 1.5 - - + +
929A CYS* 5.9 1.8 - - + -
930A GLN* 4.5 8.0 - - + +
933A ILE* 3.8 17.7 - - + +
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Residues in contact with ILE 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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817A ALA* 3.6 26.7 - - + +
820A MET* 4.1 19.1 - - + -
821A HIS* 4.0 24.9 - - - +
851A GLU* 3.6 27.4 - - - +
854A HIS* 4.3 0.2 - - + -
855A ALA* 3.9 28.7 - - + +
859A TRP* 5.4 0.2 - - - +
886A VAL* 2.9 37.7 + - + +
887A ILE 3.8 3.4 - - - +
889A ALA* 1.3 75.3 - - - +
891A LEU* 1.3 58.5 + - - +
893A THR* 2.5 32.0 + - - +
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Residues in contact with LEU 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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848A SER* 4.2 10.3 - - - -
851A GLU* 3.6 32.8 - - + +
852A ASN* 3.7 27.4 - - - +
855A ALA* 5.5 1.1 - - + -
887A ILE* 2.8 35.6 + - + +
888A GLU 4.4 2.7 - - - +
890A ILE* 1.3 67.7 - - + +
892A ALA* 1.3 60.1 + - - +
893A THR 3.0 7.0 + - - -
894A ASP* 3.2 12.5 + - - +
897A LYS* 3.3 23.5 + - - +
901A PHE* 5.3 0.4 - - - -
845B ASN* 5.1 2.0 - - - +
847B ARG* 3.1 49.1 - - - +
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Residues in contact with ALA 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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888A GLU 3.3 15.3 + - - +
889A ALA* 3.1 13.1 + - - +
891A LEU* 1.3 76.8 - - - +
893A THR* 1.3 61.3 + - - +
894A ASP 3.3 4.5 + - - +
901A PHE* 3.7 33.8 - - + -
930A GLN* 3.8 28.7 - - + +
933A ILE* 4.7 0.4 - - + -
934A LYS* 3.3 23.1 + - + +
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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
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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