Contacts of the helix formed by residues 897 - 910 (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 LYS 897 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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848A SER* 2.8 30.8 + - - +
891A LEU* 3.3 34.7 + - - +
894A ASP* 3.0 19.2 + - + +
896A LYS* 1.3 81.2 - - + +
898A HIS* 1.3 65.2 + - - +
899A PHE 3.3 2.9 - - - -
900A ASP* 3.1 20.6 + - + +
901A PHE* 3.0 47.9 + - + -
847B ARG* 4.9 9.1 - - - +
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Residues in contact with HIS 898 (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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894A ASP 3.8 0.6 + - - -
895A LEU* 2.9 25.5 + - + +
896A LYS 3.3 0.6 - - - -
897A LYS* 1.3 78.5 - - - +
899A PHE* 1.3 90.7 + + + +
901A PHE* 3.5 2.6 + - - +
902A LEU* 3.2 33.9 + - + +
934A LYS* 2.7 42.9 + - - +
994A HIS 4.4 2.0 + - - -
995A ILE* 3.5 51.9 + - + +
998A PRO* 5.3 0.2 - - - +
999A LEU* 4.1 17.3 - - + -
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Residues in contact with PHE 899 (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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895A LEU 5.3 2.0 - - - -
896A LYS 4.8 6.2 + - - -
897A LYS 3.3 1.0 - - - -
898A HIS* 1.3 93.8 - + + +
900A ASP* 1.3 67.6 + - - +
902A LEU* 4.0 13.9 - - + +
903A ALA* 3.1 23.9 + - - +
994A HIS* 4.1 26.2 - - + -
995A ILE* 5.3 5.8 - - + -
998A PRO* 6.3 0.2 - - + -
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Residues in contact with ASP 900 (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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896A LYS 4.8 2.1 - - - +
897A LYS* 3.1 29.3 + - + +
899A PHE* 1.3 78.8 - - - +
901A PHE* 1.3 66.6 + - + +
903A ALA* 3.2 7.7 + - - +
904A GLU* 3.0 35.7 + - - +
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Residues in contact with PHE 901 (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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892A ALA* 3.7 40.8 - - + -
897A LYS* 3.0 53.1 + - + +
898A HIS 3.8 3.8 - - - +
900A ASP* 1.3 79.5 - - + +
902A LEU* 1.3 63.1 + - - +
904A GLU* 3.3 17.0 + - - +
905A PHE* 3.0 24.0 + - - +
927A LEU* 4.4 14.6 - - + +
930A GLN* 3.6 37.0 - - + -
931A VAL* 4.8 5.9 - - + +
934A LYS* 4.2 18.2 - - + -
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Residues in contact with LEU 902 (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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898A HIS* 3.2 34.4 + - + +
899A PHE* 4.0 13.9 - - + +
901A PHE* 1.3 75.2 - - - +
903A ALA* 1.3 61.5 + - - +
905A PHE* 3.4 6.3 + - + +
906A ASN* 2.8 47.5 + - - +
931A VAL* 5.9 1.1 - - - -
934A LYS* 5.6 0.8 - - - +
998A PRO* 4.2 27.8 - - + +
999A LEU* 4.4 17.7 - - + +
1002A SER* 3.0 37.0 - - - +
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Residues in contact with ALA 903 (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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899A PHE 3.1 16.5 + - - +
900A ASP* 3.4 7.2 - - - +
902A LEU* 1.3 80.9 - - - +
904A GLU* 1.3 58.7 + - + +
906A ASN* 3.4 6.7 - - - +
907A ALA* 2.8 32.3 + - - +
911A ASP* 4.8 0.7 - - - +
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Residues in contact with GLU 904 (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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900A ASP* 3.0 28.0 + - - +
901A PHE* 3.6 18.2 + - - +
903A ALA* 1.3 79.0 - - + +
905A PHE* 1.3 63.8 + - - +
907A ALA* 3.0 9.4 + - - +
908A LYS* 2.9 24.8 + - - +
927A LEU* 4.0 23.6 - - + +
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Residues in contact with PHE 905 (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 3.0 16.3 + - - +
902A LEU* 3.8 5.8 - - + +
904A GLU* 1.3 75.2 - - - +
906A ASN* 1.3 65.3 + - - +
908A LYS* 3.0 12.5 + - - +
909A ALA* 3.1 12.9 + - + +
910A ASN* 4.0 9.1 + - - -
917A ILE* 4.5 11.0 - - + -
927A LEU* 3.9 21.4 - - + +
928A VAL* 4.4 16.4 - - + -
931A VAL* 3.7 35.0 - - + -
999A LEU* 6.3 0.4 - - + -
1002A SER* 3.7 32.1 - - - -
1003A TYR* 3.8 15.0 - + - -
1006A ALA* 3.7 22.4 - - + -
1008A LEU* 3.9 22.0 - - + -
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Residues in contact with ASN 906 (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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902A LEU* 2.8 35.3 + - - +
903A ALA* 3.4 6.6 - - - +
905A PHE* 1.3 73.1 - - - +
907A ALA* 1.3 58.7 + - - +
910A ASN* 2.7 45.7 + - - +
911A ASP* 2.8 41.6 + - - +
1002A SER* 3.0 24.6 + - - -
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Residues in contact with ALA 907 (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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903A ALA 2.8 17.9 + - - +
904A GLU* 3.0 11.4 + - - +
906A ASN* 1.3 72.2 - - - +
908A LYS* 1.3 59.6 + - + +
911A ASP* 3.3 19.6 + - - +
914A SER* 2.9 24.3 - - - -
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Residues in contact with LYS 908 (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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904A GLU* 2.9 13.6 + - + +
905A PHE 3.0 9.6 + - - +
907A ALA* 1.3 80.3 - - + +
909A ALA* 1.3 58.8 + - - +
914A SER* 3.8 2.6 - - - -
915A ASN* 4.9 11.1 - - - +
916A GLY* 3.0 35.6 + - - +
917A ILE* 4.0 13.2 - - + -
918A GLU* 4.7 9.1 + - - -
921A ASN* 6.0 1.2 - - - +
924A ASP* 3.8 33.6 + - - +
927A LEU* 4.0 18.2 - - + -
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Residues in contact with ALA 909 (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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905A PHE* 3.1 10.4 + - + +
906A ASN 3.4 0.2 + - - -
908A LYS* 1.3 79.1 - - - +
910A ASN* 1.3 65.6 - - - +
914A SER* 3.8 8.0 + - - -
916A GLY* 4.0 8.1 - - - -
917A ILE* 3.7 30.3 - - + +
1005A ALA 5.3 0.3 - - - +
1006A ALA* 4.2 24.2 - - + +
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Residues in contact with ASN 910 (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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905A PHE* 4.0 9.9 + - - -
906A ASN* 2.7 38.3 + - - +
909A ALA* 1.3 79.0 - - - +
911A ASP* 1.3 68.1 + - - +
912A VAL* 3.7 1.9 + - - +
1002A SER* 3.0 26.9 + - - +
1005A ALA* 3.1 37.9 - - + +
1006A ALA* 3.2 9.3 + - - -
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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