Contacts of the helix formed by residues 897 - 910 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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848C SER* 4.1 20.4 + - - +
891C LEU* 5.0 13.6 + - - +
894C ASP* 3.0 14.0 + - - +
896C LYS* 1.3 86.2 - - + +
898C HIS* 1.3 66.5 + - - +
899C PHE 3.3 2.7 - - - -
900C ASP* 3.0 29.6 + - + +
901C PHE* 3.1 41.5 + - + -
847D ARG* 4.6 18.4 - - - +
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Residues in contact with HIS 898 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894C ASP 3.9 1.2 + - - -
895C LEU* 3.1 25.8 + - + +
896C LYS 3.3 0.6 - - - -
897C LYS* 1.3 77.0 - - - +
899C PHE* 1.3 95.1 + + + +
901C PHE* 3.6 3.3 + - - +
902C LEU* 3.1 33.6 + - + +
934C LYS* 3.0 41.3 + - - +
938C ILE* 5.0 0.6 - - + +
994C HIS 4.6 1.6 + - - -
995C ILE* 3.7 48.2 + - + +
998C PRO* 5.2 0.4 - - - +
999C LEU* 4.1 21.1 - - + -
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Residues in contact with PHE 899 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895C LEU 5.2 3.1 - - - -
896C LYS 5.0 6.7 + - - -
897C LYS 3.3 0.6 - - - -
898C HIS* 1.3 95.4 - + + +
900C ASP* 1.3 61.3 + - - +
902C LEU* 3.7 11.1 - - + +
903C ALA* 2.8 33.7 + - - +
994C HIS* 4.0 13.9 - - + -
995C ILE* 3.8 21.5 - - + -
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Residues in contact with ASP 900 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896C LYS 4.5 3.3 - - - +
897C LYS* 3.0 30.1 + - + +
899C PHE* 1.3 80.1 - - - +
901C PHE* 1.3 64.9 + - + +
903C ALA* 3.5 4.9 - - - +
904C GLU* 3.0 25.3 + - - +
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Residues in contact with PHE 901 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888C GLU 5.2 0.2 - - - -
891C LEU 5.2 0.4 - - - -
892C ALA* 3.7 33.0 - - + -
897C LYS* 3.1 50.7 + - + +
898C HIS 3.9 3.8 - - - +
900C ASP* 1.3 80.4 - - + +
902C LEU* 1.3 58.2 + - - +
904C GLU* 3.4 6.2 + - - +
905C PHE* 2.8 31.3 + - - +
927C LEU* 4.1 18.0 - - + +
930C GLN* 3.5 39.0 - - + -
931C VAL* 5.3 6.7 - - + -
934C LYS* 4.1 24.9 - - + -
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Residues in contact with LEU 902 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898C HIS* 3.1 36.7 + - + +
899C PHE* 3.7 11.0 - - + +
901C PHE* 1.3 72.9 - - - +
903C ALA* 1.3 68.5 + - - +
905C PHE* 3.1 8.2 + - + +
906C ASN* 2.8 51.2 + - - +
931C VAL* 6.0 0.9 - - + -
934C LYS* 5.6 0.6 - - - +
998C PRO* 4.1 27.1 - - + +
999C LEU* 4.1 21.5 - - + -
1002C SER* 3.5 22.9 - - - +
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Residues in contact with ALA 903 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899C PHE 2.8 20.7 + - - +
900C ASP* 3.5 6.1 - - - +
902C LEU* 1.3 75.1 - - - +
904C GLU* 1.3 64.2 + - - +
906C ASN* 3.2 7.4 + - - +
907C ALA* 3.0 21.7 + - - +
911C ASP* 5.0 1.4 - - - +
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Residues in contact with GLU 904 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900C ASP 3.0 17.4 + - - +
901C PHE* 3.7 7.2 - - - +
903C ALA* 1.3 76.1 - - - +
905C PHE* 1.3 66.6 + - - +
907C ALA* 3.1 9.1 + - + +
908C LYS* 3.1 24.9 + - + +
927C LEU* 4.0 26.5 - - + +
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Residues in contact with PHE 905 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901C PHE 2.8 21.6 + - - +
902C LEU* 3.1 8.7 + - + +
904C GLU* 1.3 75.3 - - - +
906C ASN* 1.3 64.3 + - - +
908C LYS* 3.1 3.8 + - - +
909C ALA* 3.1 22.4 + - + +
910C ASN* 4.2 2.2 - - - -
917C ILE* 4.7 8.5 - - + -
927C LEU* 3.8 19.0 - - + +
928C VAL* 4.5 13.9 - - + -
931C VAL* 3.4 37.0 - - + -
1002C SER* 3.4 45.5 - - - -
1003C TYR* 4.0 13.5 - + - -
1006C ALA* 3.8 11.7 - - + -
1008C LEU* 3.8 30.1 - - + -
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Residues in contact with ASN 906 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902C LEU* 2.8 45.1 + - - +
903C ALA* 3.6 6.5 - - - +
905C PHE* 1.3 72.7 - - - +
907C ALA* 1.3 57.0 + - - +
910C ASN* 2.6 49.5 + - + +
911C ASP* 2.8 24.3 + - - +
1002C SER* 2.4 32.1 + - - -
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Residues in contact with ALA 907 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903C ALA 3.0 12.5 + - - +
904C GLU* 3.3 13.2 - - + +
905C PHE 3.1 0.2 - - - -
906C ASN* 1.3 79.5 - - - +
908C LYS* 1.3 65.3 + - + +
909C ALA 3.1 0.3 + - - -
910C ASN 3.8 3.1 + - - -
911C ASP* 3.7 20.2 + - + +
913C ASN* 3.9 15.8 - - - +
915C ASN* 5.1 1.7 - - - +
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Residues in contact with LYS 908 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904C GLU* 3.1 14.4 + - + +
905C PHE 3.6 6.5 - - - +
907C ALA* 1.3 78.8 - - + +
909C ALA* 1.3 58.7 + - - +
915C ASN* 3.5 29.8 + - - +
916C GLY 2.9 36.1 + - - +
917C ILE* 4.3 11.9 - - + -
918C GLU* 4.5 5.1 + - - -
921C ASN* 4.9 5.3 - - - +
924C ASP* 3.3 38.3 + - - +
927C LEU* 4.4 17.3 - - + -
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Residues in contact with ALA 909 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905C PHE* 3.1 12.7 + - + +
906C ASN 3.6 0.2 - - - -
908C LYS* 1.3 80.4 - - - +
910C ASN* 1.3 72.5 + - - +
914C SER* 6.6 0.4 - - - -
915C ASN 5.9 0.2 - - - +
916C GLY* 4.5 6.5 - - - +
917C ILE* 3.4 35.9 - - + +
1005C ALA 5.0 0.3 - - - +
1006C ALA* 4.5 19.2 - - + -
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Residues in contact with ASN 910 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905C PHE* 4.2 4.9 - - - -
906C ASN* 2.6 40.3 + - - +
907C ALA 3.8 1.2 + - - -
909C ALA* 1.3 88.3 + - - +
911C ASP* 1.3 70.1 + - - +
912C VAL 3.7 0.5 + - - -
913C ASN 5.5 0.6 + - - -
1002C SER* 3.0 29.1 + - - +
1005C ALA* 3.5 32.1 - - - +
1006C ALA* 4.1 5.1 - - - +
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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
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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