Contacts of the helix formed by residues 921 - 938 (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 ASN 921 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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908A LYS* 6.0 1.0 - - - +
918A GLU* 2.9 31.6 + - + +
919A TRP 3.2 0.2 - - - -
920A SER* 1.3 78.2 + - - +
922A GLU* 1.3 56.2 + - - +
923A ASN* 2.9 24.5 + - - +
924A ASP* 2.8 42.9 + - + +
925A ARG* 3.1 14.0 + - - +
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Residues in contact with GLU 922 (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 GLU* 4.9 0.9 - - - +
881A ARG* 3.2 47.3 + - - +
920A SER 3.8 4.6 + - - -
921A ASN* 1.3 71.6 + - - +
923A ASN* 1.3 73.2 + - - +
925A ARG* 3.4 22.3 + - - +
926A LEU* 3.1 23.6 + - - +
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Residues in contact with ASN 923 (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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921A ASN* 2.9 13.9 + - - +
922A GLU* 1.3 84.5 + - - +
924A ASP* 1.3 68.8 + - - +
926A LEU* 3.9 11.0 - - - +
927A LEU* 3.2 24.1 + - - +
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Residues in contact with ASP 924 (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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908A LYS* 3.8 32.0 + - - +
916A GLY 3.8 5.2 - - - +
917A ILE* 3.6 15.0 - - + +
918A GLU* 2.8 43.5 + - - +
921A ASN* 2.8 26.2 + - - +
923A ASN* 1.3 76.0 - - - +
925A ARG* 1.3 66.0 + - - +
927A LEU* 3.3 8.6 + - - +
928A VAL* 3.0 29.5 + - - +
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Residues in contact with ARG 925 (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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786A TYR* 5.6 2.4 + - - -
805A ASN 3.9 8.6 + - - +
806A ILE* 4.3 7.8 - - + +
807A PRO* 3.5 24.3 - - - +
810A GLU* 3.0 42.0 + - - +
919A TRP* 2.8 34.9 + - + +
920A SER* 3.2 29.5 + - - +
921A ASN 3.1 8.0 + - - +
922A GLU* 3.6 35.7 - - - +
924A ASP* 1.3 76.3 - - - +
926A LEU* 1.3 57.6 + - - +
928A VAL* 3.1 10.4 + - - +
929A CYS* 2.8 33.4 + - - -
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Residues in contact with LEU 926 (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 GLU* 4.8 1.1 + - - -
881A ARG* 6.3 0.4 - - - +
884A PHE* 4.4 14.6 - - + -
885A LEU* 4.0 26.2 - - + +
888A GLU* 3.9 44.9 - - + +
889A ALA* 5.2 1.6 - - + +
922A GLU 3.1 13.6 + - - +
923A ASN* 3.9 11.4 - - - +
924A ASP 3.4 0.2 - - - -
925A ARG* 1.3 79.5 - - - +
927A LEU* 1.3 52.2 + - - +
929A CYS* 3.0 12.8 + - + +
930A GLN* 2.7 54.8 + - + +
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Residues in contact with LEU 927 (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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901A PHE* 4.4 12.8 - - + +
904A GLU* 4.0 29.2 - - + +
905A PHE* 3.9 33.7 - - + +
908A LYS* 4.0 24.9 - - + -
917A ILE* 5.5 2.0 - - + -
923A ASN 3.2 17.4 + - - +
924A ASP* 3.5 6.7 - - - +
926A LEU* 1.3 78.7 - - - +
928A VAL* 1.3 62.6 + - + +
930A GLN* 3.2 16.2 + - - +
931A VAL* 3.0 35.4 + - + +
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Residues in contact with VAL 928 (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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802A LEU* 4.5 13.2 - - + -
806A ILE* 4.5 5.2 - - + -
905A PHE* 4.4 9.9 - - + -
917A ILE* 4.1 33.2 - - + -
919A TRP* 4.1 21.1 - - + -
924A ASP 3.0 23.0 + - - +
925A ARG* 3.3 8.5 - - - +
927A LEU* 1.3 75.1 - - + +
929A CYS* 1.3 65.4 + - - +
931A VAL* 3.1 9.8 + - - +
932A CYS* 2.9 20.8 + - + +
1003A TYR* 4.6 3.1 - - + +
1008A LEU* 3.9 22.7 - - + -
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Residues in contact with CYS 929 (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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753A THR* 6.1 0.2 - - - -
806A ILE* 4.0 33.4 - - - -
810A GLU* 4.4 15.5 - - - -
811A LEU* 4.4 1.1 - - - -
814A LEU* 3.6 32.9 - - + +
889A ALA* 5.9 2.0 - - + -
925A ARG 2.8 18.5 + - - -
926A LEU* 3.3 15.0 - - + +
928A VAL* 1.3 78.0 - - - +
930A GLN* 1.3 61.8 + - + +
932A CYS* 3.0 9.7 + - - +
933A ILE* 2.9 19.6 + - - +
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Residues in contact with GLN 930 (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* 3.2 45.0 + - - +
889A ALA* 4.5 3.1 - - - +
892A ALA* 3.8 15.2 - - + +
901A PHE* 3.6 34.6 - - + -
926A LEU* 2.7 35.9 + - + +
927A LEU* 3.5 22.8 - - - +
928A VAL 3.2 0.2 - - - -
929A CYS* 1.3 71.9 - - + +
931A VAL* 1.3 57.8 + - - +
933A ILE* 3.1 13.3 - - - +
934A LYS* 3.0 31.5 + - - +
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Residues in contact with VAL 931 (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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901A PHE* 4.8 10.5 - - + +
902A LEU* 5.9 0.9 - - - -
905A PHE* 3.7 42.0 - - + -
927A LEU* 3.0 22.3 + - + +
928A VAL* 3.4 8.7 - - - +
930A GLN* 1.3 74.5 - - + +
932A CYS* 1.3 57.6 + - - +
934A LYS* 3.2 10.9 + - + +
935A LEU* 2.9 28.5 + - + +
999A LEU* 4.4 19.4 - - + +
1003A TYR* 3.3 30.1 - - + -
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Residues in contact with CYS 932 (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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749A VAL* 4.1 12.1 - - - -
752A LEU* 4.0 19.4 - - - +
753A THR* 3.9 25.8 - - + -
802A LEU* 5.8 0.2 - - + -
814A LEU* 4.3 4.0 - - + -
928A VAL* 2.9 14.0 + - + +
929A CYS* 3.0 14.6 + - - +
931A VAL* 1.3 78.8 - - - +
933A ILE* 1.3 56.9 + - - +
935A LEU* 3.3 4.5 + - - +
936A ALA* 3.0 27.0 + - - +
1003A TYR* 3.6 28.5 - - - +
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Residues in contact with ILE 933 (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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745A VAL* 4.2 15.0 - - + -
749A VAL* 3.8 10.1 - - + -
814A LEU* 3.7 15.7 - - + -
817A ALA* 4.1 16.2 - - + +
818A ALA* 4.0 28.7 - - + +
821A HIS* 4.7 3.8 - - + -
889A ALA* 3.8 31.0 - - + +
892A ALA* 4.7 1.3 - - + -
893A THR* 4.2 17.7 - - + -
929A CYS 2.9 11.0 + - - +
930A GLN* 3.1 20.4 - - - +
932A CYS* 1.3 74.0 - - - +
934A LYS* 1.3 59.8 + - - +
936A ALA 3.7 0.2 - - - -
937A ASP* 2.8 33.5 + - + +
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Residues in contact with LYS 934 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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892A ALA* 3.3 29.9 + - + +
893A THR* 4.6 5.5 + - - +
895A LEU* 3.8 16.2 - - - +
898A HIS* 2.7 57.5 + - - +
901A PHE* 4.2 21.5 - - + -
902A LEU 5.6 0.4 - - - +
930A GLN 3.0 17.3 + - - +
931A VAL* 3.2 14.6 + - + +
933A ILE* 1.3 80.6 - - + +
935A LEU* 1.3 63.3 + - - +
937A ASP* 3.5 6.4 + - - +
938A ILE* 3.4 24.7 + - - +
999A LEU* 4.1 15.7 - - + +
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Residues in contact with LEU 935 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677A TRP* 4.9 2.9 - - + -
752A LEU* 3.8 19.7 - - + -
931A VAL 2.9 15.5 + - - +
932A CYS* 3.7 6.3 - - - +
934A LYS* 1.3 74.9 - - - +
936A ALA* 1.3 67.8 + - - +
938A ILE* 3.2 6.4 + - - +
939A ASN* 3.1 26.8 + - + -
942A ALA* 5.9 1.6 - - + -
999A LEU* 3.9 17.0 - - + +
1000A CYS* 4.2 31.0 - - - +
1003A TYR* 3.9 39.7 - - + -
1009A LEU* 4.7 6.5 - - + -
1061A LEU* 4.5 14.6 - - + -
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Residues in contact with ALA 936 (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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741A HIS* 5.2 0.3 - - - -
745A VAL* 3.6 16.5 - - + +
748A ALA* 3.5 30.7 - - + -
749A VAL* 3.5 20.9 - - + +
752A LEU* 5.1 1.3 - - + -
932A CYS 3.0 17.4 + - - +
933A ILE 3.3 2.7 + - - +
935A LEU* 1.3 80.6 - - - +
937A ASP* 1.3 60.9 + - - +
939A ASN* 3.1 27.0 + - - +
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Residues in contact with ASP 937 (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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471A MG 2.0 32.2 - - - -
736A TYR* 3.8 5.7 + - - -
741A HIS* 3.0 26.5 + - - -
745A VAL* 3.7 10.4 - - + +
821A HIS* 2.7 18.8 + - - +
893A THR* 4.1 23.4 - - + +
895A LEU* 5.7 3.3 - - - +
933A ILE 2.8 20.9 + - - +
934A LYS* 3.7 8.7 - - - +
935A LEU 3.3 0.2 - - - -
936A ALA* 1.3 73.0 - - - +
938A ILE* 1.3 67.8 + - + +
939A ASN 4.0 0.3 + - - -
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Residues in contact with ILE 938 (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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461A 666 3.5 27.7 - - + +
895A LEU* 4.8 16.8 - - + -
898A HIS* 5.1 0.7 - - + +
934A LYS* 3.4 14.3 + - - +
935A LEU* 3.2 4.9 + - + +
936A ALA 3.2 0.6 - - - -
937A ASP* 1.3 88.1 - - - +
939A ASN* 1.3 60.8 + - - +
940A GLY 3.3 4.3 + - - -
941A PRO* 3.7 6.2 - - - +
991A PHE* 4.0 18.8 - - + -
995A ILE* 3.5 30.7 - - + -
996A VAL* 4.0 26.6 - - + +
999A LEU* 3.9 20.6 - - + -
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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
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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