Contacts of the helix formed by residues 897 - 911 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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847A ARG* 6.0 3.2 - - - +
848B SER* 4.7 10.5 - - - +
891B LEU* 5.0 8.1 - - + +
894B ASP* 3.1 20.2 + - - +
896B LYS* 1.3 80.8 - - + +
898B HIS* 1.3 63.9 + - - +
899B PHE 3.4 2.7 - - - -
900B ASP* 3.1 26.7 + - - +
901B PHE* 3.0 57.9 + - + -
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Residues in contact with HIS 898 (chain B).
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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894B ASP 3.9 1.0 + - - -
895B LEU* 3.1 25.4 + - + +
896B LYS 3.4 0.8 - - - -
897B LYS* 1.3 76.0 - - - +
899B PHE* 1.3 90.1 + + + +
901B PHE* 3.4 2.6 + - - +
902B LEU* 2.9 41.5 + - + +
934B LYS* 2.9 37.4 + - - +
994B HIS 4.4 1.2 + - - -
995B ILE* 3.4 50.7 + - + +
999B LEU* 3.9 23.6 - - + -
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Residues in contact with PHE 899 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895B LEU 5.5 2.7 - - - -
896B LYS 5.2 4.2 + - - -
897B LYS 3.4 0.6 - - - -
898B HIS* 1.3 94.3 - + + +
900B ASP* 1.3 64.0 + - - +
902B LEU* 3.8 11.4 - - + +
903B ALA* 2.9 30.7 + - - +
994B HIS* 3.7 30.1 - - + -
995B ILE* 5.2 5.2 - - + -
998B PRO* 5.7 1.3 - - + -
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Residues in contact with ASP 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896B LYS 4.8 2.5 - - - +
897B LYS* 3.1 33.6 + - + +
899B PHE* 1.3 79.6 - - - +
901B PHE* 1.3 58.1 + - + +
903B ALA* 3.3 4.8 + - - +
904B GLU* 2.8 35.7 + - - +
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Residues in contact with PHE 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891B LEU 5.3 0.4 - - - -
892B ALA* 3.7 34.1 - - + -
897B LYS* 3.0 63.2 + - + -
898B HIS 3.8 5.2 - - - +
900B ASP* 1.3 72.9 - - + +
902B LEU* 1.3 66.9 + - - +
904B GLU* 3.7 15.0 - - - +
905B PHE* 2.9 27.1 + - - +
927B LEU* 4.1 13.5 - - + +
930B GLN* 3.5 37.9 - - + -
931B VAL* 4.8 6.7 - - + +
934B LYS* 4.0 26.5 - - + -
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Residues in contact with LEU 902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898B HIS* 2.9 38.6 + - + +
899B PHE* 3.8 12.1 - - + +
900B ASP 3.3 0.2 - - - -
901B PHE* 1.3 78.9 - - - +
903B ALA* 1.3 57.2 + - - +
905B PHE* 3.2 8.1 + - + +
906B ASN* 2.9 43.8 + - - +
931B VAL* 5.5 1.6 - - + -
934B LYS* 5.5 0.8 - - - +
998B PRO* 3.8 32.3 - - + +
999B LEU* 3.9 23.6 - - + +
1002B SER* 3.4 28.3 - - - +
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Residues in contact with ALA 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899B PHE 2.9 19.0 + - - +
900B ASP* 3.6 5.2 - - - +
902B LEU* 1.3 71.4 - - - +
904B GLU* 1.3 63.4 + - - +
905B PHE 2.9 6.4 + - - -
906B ASN* 3.2 9.5 + - - +
907B ALA* 3.1 22.5 + - - +
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Residues in contact with GLU 904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900B ASP* 2.8 24.4 + - - +
901B PHE* 3.9 17.6 - - - +
903B ALA* 1.3 73.2 - - - +
905B PHE* 1.3 59.7 + - - +
907B ALA* 3.8 7.5 - - - +
908B LYS* 3.8 15.3 + - + +
927B LEU* 3.2 30.7 - - + +
930B GLN* 5.4 0.2 - - - +
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Residues in contact with PHE 905 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901B PHE 2.9 18.8 + - - +
902B LEU* 3.3 4.9 - - + +
904B GLU* 1.3 76.2 - - - +
906B ASN* 1.3 58.8 + - - +
907B ALA 2.9 5.4 + - - -
908B LYS* 3.1 3.5 + - - +
909B ALA* 2.8 41.0 + - + +
910B ASN* 4.0 6.7 - - - -
917B ILE* 4.6 6.3 - - + -
927B LEU* 3.3 20.6 - - + -
928B VAL* 4.5 14.8 - - + -
931B VAL* 3.6 38.8 - - + -
1002B SER* 3.5 41.3 - - - -
1003B TYR* 4.2 6.7 - + - -
1006B ALA* 3.9 17.9 - - + -
1008B LEU* 4.0 13.2 - - + -
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Residues in contact with ASN 906 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902B LEU* 2.9 33.7 + - - +
903B ALA* 3.8 7.6 - - - +
905B PHE* 1.3 74.9 - - - +
907B ALA* 1.3 57.5 + - - +
910B ASN* 2.9 40.4 + - + +
911B ASP* 2.7 31.7 + - - +
1002B SER* 2.6 30.6 + - - -
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Residues in contact with ALA 907 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903B ALA 3.1 15.2 + - - +
904B GLU* 3.8 9.4 - - - +
905B PHE 2.9 0.4 + - - -
906B ASN* 1.3 81.4 - - - +
908B LYS* 1.3 66.6 + - + +
909B ALA 3.2 0.5 + - - -
911B ASP* 3.9 22.0 + - - +
914B SER* 4.5 7.3 + - - -
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Residues in contact with LYS 908 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904B GLU* 3.8 11.8 + - + +
905B PHE 3.1 5.4 + - - +
907B ALA* 1.3 81.5 - - + +
909B ALA* 1.3 57.7 + - - +
914B SER* 5.2 3.5 - - - -
916B GLY* 2.9 31.5 - - - +
917B ILE* 3.6 6.8 + - + +
918B GLU* 3.6 16.4 + - - +
921B ASN* 3.8 9.1 - - - +
923B ASN* 5.6 3.5 - - - +
924B ASP* 2.8 39.6 + - - +
927B LEU* 4.5 11.4 - - + -
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Residues in contact with ALA 909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905B PHE* 2.8 35.8 + - + +
908B LYS* 1.3 81.4 - - - +
910B ASN* 1.3 67.5 + - - +
911B ASP 3.9 0.9 - - - -
914B SER* 6.3 0.4 - - - -
916B GLY* 4.2 14.4 - - - -
917B ILE* 3.3 28.5 - - + -
1006B ALA* 4.3 12.9 - - + +
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Residues in contact with ASN 910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905B PHE* 4.0 11.1 - - - -
906B ASN* 2.9 33.4 + - - +
909B ALA* 1.3 85.9 - - - +
911B ASP* 1.3 73.1 + - - +
1002B SER* 2.9 27.3 + - - +
1005B ALA* 3.0 19.4 - - + +
1006B ALA* 3.0 22.8 + - - +
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Residues in contact with ASP 911 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906B ASN* 2.7 35.7 + - - +
907B ALA* 3.9 11.5 + - - +
909B ALA 3.9 0.8 - - - -
910B ASN* 1.3 89.4 - - - +
912B VAL* 1.3 81.0 + - + +
914B SER* 3.1 22.2 + - - +
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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