Contacts of the helix formed by residues 897 - 910 (chain F) in PDB entry 1SOJ
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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891F LEU 5.8 0.7 - - - +
894F ASP* 3.1 13.8 + - + +
895F LEU 3.0 0.4 - - - -
896F LYS* 1.3 78.4 - - + +
898F HIS* 1.3 64.8 + - - +
899F PHE 3.4 2.0 - - - -
900F ASP* 3.1 18.3 + - + +
901F PHE* 3.0 46.1 + - + -
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Residues in contact with HIS 898 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894F ASP 3.8 1.0 + - - -
895F LEU* 2.9 35.5 + - + +
896F LYS 3.2 0.6 - - - -
897F LYS* 1.3 77.7 - - - +
899F PHE* 1.3 94.7 + + + +
901F PHE 3.4 0.3 + - - -
902F LEU* 3.1 32.8 + - + +
934F LYS* 3.1 42.8 + - - +
938F ILE* 4.7 0.7 - - + -
994F HIS 4.3 1.8 + - - -
995F ILE* 3.5 43.9 + - + -
999F LEU* 4.2 19.1 - - + -
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Residues in contact with PHE 899 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895F LEU 5.5 2.7 - - - -
896F LYS 4.8 3.6 + - - -
897F LYS 3.4 0.6 - - - -
898F HIS* 1.3 93.0 - + + +
900F ASP* 1.3 65.8 + - - +
902F LEU* 3.6 14.9 - - + +
903F ALA* 2.9 29.5 + - - +
994F HIS* 3.4 33.7 - - + -
995F ILE* 4.8 7.2 - - + -
998F PRO* 5.3 1.6 - - + -
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Residues in contact with ASP 900 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896F LYS 4.2 4.6 - - - +
897F LYS* 3.1 25.8 + - + +
899F PHE* 1.3 79.0 + - - +
901F PHE* 1.3 66.8 + - + +
903F ALA* 3.3 6.3 + - - +
904F GLU* 3.0 26.6 + - - +
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Residues in contact with PHE 901 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891F LEU 4.7 2.7 - - - -
892F ALA* 3.5 42.6 - - + -
897F LYS* 3.0 43.0 + - + -
898F HIS 3.9 4.9 - - - +
900F ASP* 1.3 77.8 - - + +
902F LEU* 1.3 58.3 + - - +
904F GLU* 3.5 10.9 + - - +
905F PHE* 2.8 32.1 + - - +
927F LEU* 4.3 18.8 - - + +
930F GLN* 3.8 32.1 - - + -
931F VAL* 4.7 8.0 - - + +
934F LYS* 3.9 17.3 - - + +
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Residues in contact with LEU 902 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898F HIS* 3.1 32.0 + - + +
899F PHE* 3.6 17.3 - - + +
900F ASP 3.2 0.2 - - - -
901F PHE* 1.3 78.6 - - - +
903F ALA* 1.3 62.7 + - - +
905F PHE* 3.3 6.7 + - + +
906F ASN* 2.9 36.6 + - - +
931F VAL* 6.0 1.1 - - + -
934F LYS* 5.1 0.6 - - - +
998F PRO* 4.0 32.3 - - + +
999F LEU* 4.0 21.8 - - + -
1002F SER* 3.5 33.9 - - - +
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Residues in contact with ALA 903 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899F PHE 2.9 19.2 + - - +
900F ASP* 3.5 7.0 - - - +
902F LEU* 1.3 76.6 - - - +
904F GLU* 1.3 64.1 + - - +
906F ASN* 3.0 9.1 + - - +
907F ALA* 2.9 22.6 + - - +
911F ASP* 5.1 0.7 - - - +
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Residues in contact with GLU 904 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900F ASP 3.0 15.0 + - - +
901F PHE* 3.9 10.9 - - - +
903F ALA* 1.3 78.9 - - - +
905F PHE* 1.3 63.4 + - - +
907F ALA* 3.2 17.9 + - + +
908F LYS* 3.3 25.2 + - - +
927F LEU* 3.9 28.0 - - + +
1073I LYS* 5.5 3.3 - - - +
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Residues in contact with PHE 905 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901F PHE 2.8 20.2 + - - +
902F LEU* 3.6 5.8 - - + +
903F ALA 3.2 0.2 - - - -
904F GLU* 1.3 76.4 - - - +
906F ASN* 1.3 62.1 + - - +
908F LYS* 3.3 2.8 + - + +
909F ALA* 3.0 40.1 + - + +
910F ASN* 4.8 0.4 - - - -
917F ILE* 5.0 3.8 - - + -
927F LEU* 3.7 21.0 - - + +
928F VAL* 4.3 15.0 - - + -
931F VAL* 3.5 35.0 - - + -
1002F SER* 3.3 45.3 - - - -
1003F TYR* 4.0 9.6 - + - -
1006F ALA* 3.6 19.7 - - + -
1008F LEU* 3.9 18.4 - - + -
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Residues in contact with ASN 906 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902F LEU* 2.9 36.0 + - - +
903F ALA* 3.0 9.1 + - - +
905F PHE* 1.3 77.4 - - - +
907F ALA* 1.3 63.6 + - - +
910F ASN* 2.9 53.4 + - - +
911F ASP* 3.5 19.0 - - - +
1002F SER* 2.5 30.1 + - - -
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Residues in contact with ALA 907 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903F ALA 2.9 12.9 + - - +
904F GLU* 3.2 14.8 + - + +
906F ASN* 1.3 76.4 - - - +
908F LYS* 1.3 64.7 + - + +
911F ASP* 3.6 16.1 + - - +
913F ASN 5.1 0.3 - - - -
914F SER* 3.6 17.0 - - - -
915F ASN* 4.1 1.7 + - - +
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Residues in contact with LYS 908 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904F GLU* 3.3 20.6 + - - +
905F PHE* 3.3 5.5 + - + +
906F ASN 3.2 0.6 - - - -
907F ALA* 1.3 78.9 - - + +
909F ALA* 1.3 63.1 + - - +
914F SER* 3.5 0.5 - - - -
915F ASN* 3.2 16.3 + - + +
916F GLY 3.1 33.7 + - - +
917F ILE* 4.8 7.9 - - + -
924F ASP* 3.2 32.4 + - - +
927F LEU* 4.1 17.9 - - + -
1070I LYS 3.5 16.7 + - - -
1071I ILE* 3.5 16.0 + - - +
1073I LYS* 3.3 23.8 + - - -
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Residues in contact with ALA 909 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905F PHE* 3.0 33.0 + - + +
908F LYS* 1.3 79.0 - - - +
910F ASN* 1.3 63.8 + - - +
914F SER* 3.7 7.5 + - - -
916F GLY* 3.7 14.9 - - - +
917F ILE* 4.5 9.0 - - + -
1006F ALA* 3.7 30.2 - - + -
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Residues in contact with ASN 910 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906F ASN* 2.9 44.7 + - - +
909F ALA* 1.3 78.5 - - - +
911F ASP* 1.3 67.4 + - - +
914F SER* 3.7 3.1 - - - -
1002F SER* 3.8 9.7 + - - +
1005F ALA* 2.9 20.6 - - + +
1006F ALA* 2.6 42.3 + - - +
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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