Contacts of the helix formed by residues 738 - 753 (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 ASN 738 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731F TYR* 3.6 10.8 - - - -
732F ARG 3.7 18.2 - - - +
733F ASP* 5.2 2.0 - - - +
734F ILE 3.0 24.7 + - - +
735F PRO 3.6 8.9 + - - -
736F TYR* 2.7 26.7 + - - +
737F HIS* 1.3 75.3 - - - +
739F ARG* 1.3 71.3 + - + +
740F ILE* 2.9 41.0 + - - +
741F HIS* 2.8 17.3 + - - +
742F ALA 3.1 8.5 + - - -
951F TRP* 5.2 2.6 - - - -
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Residues in contact with ARG 739 (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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692F SER 4.6 4.0 - - - -
693F GLY* 2.8 40.3 + - - -
695F ILE* 5.3 5.4 - - + +
696F LEU* 4.5 9.2 - - + +
728F GLU* 3.2 18.4 + - + +
729F ASN* 3.3 38.6 + - - +
731F TYR* 3.1 48.4 + - + +
732F ARG 5.2 0.8 + - - -
733F ASP* 5.7 1.8 - - - +
738F ASN* 1.3 73.9 - - + +
740F ILE* 1.3 63.2 + - + +
742F ALA* 3.4 6.0 - - - +
743F THR* 2.8 32.3 + - - -
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Residues in contact with ILE 740 (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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681F ILE* 4.3 18.9 - - + +
682F PHE* 4.4 16.4 - - + -
685F VAL* 3.8 30.5 - - + -
692F SER* 5.7 0.7 - - - +
695F ILE* 3.9 17.9 - - + -
738F ASN* 2.8 19.0 + - - +
739F ARG* 1.3 82.1 - - + +
741F HIS* 1.3 62.2 + - - +
743F THR* 3.3 8.0 + - - -
744F ASP* 3.0 21.0 + - - +
951F TRP* 3.7 18.6 - - + -
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Residues in contact with HIS 741 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736F TYR* 3.2 48.9 + + - +
737F HIS* 4.1 15.0 + - - -
738F ASN* 2.8 14.5 + - - +
740F ILE* 1.3 68.9 - - - +
742F ALA* 1.3 67.7 + - - +
744F ASP* 3.0 9.1 + - - +
745F VAL* 3.0 35.7 + - + +
821F HIS* 3.2 6.6 + + - -
822F ASP* 3.1 12.6 - - + -
937F ASP* 3.0 23.1 + - - -
939F ASN* 5.9 0.4 - - - -
951F TRP* 3.9 16.9 - - + -
2133F MG 1.9 33.4 - - - -
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Residues in contact with ALA 742 (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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696F LEU* 4.2 12.8 - - + -
731F TYR* 3.6 39.5 - - + +
738F ASN 3.1 2.4 + - - +
739F ARG* 3.4 11.2 - - - +
741F HIS* 1.3 80.6 - - - +
743F THR* 1.3 64.1 + - - +
745F VAL* 3.1 4.7 + - - +
746F LEU* 2.9 22.7 + - - +
818F ALA 4.3 5.1 - - - +
819F ALA 4.3 2.9 - - - +
821F HIS* 4.3 12.8 - - + -
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Residues in contact with THR 743 (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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679F PHE* 5.3 4.0 - - + -
681F ILE* 4.7 10.8 - - + -
695F ILE* 3.7 25.4 - - + +
696F LEU* 3.3 31.9 + - + +
699F VAL* 3.7 28.8 - - + +
739F ARG 2.8 18.4 + - - -
740F ILE* 3.5 6.5 - - - -
741F HIS 3.2 0.2 - - - -
742F ALA* 1.3 75.7 - - - +
744F ASP* 1.3 61.0 + - - +
746F LEU* 3.4 3.4 + - - +
747F HIS* 3.0 22.2 + - + +
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Residues in contact with ASP 744 (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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679F PHE* 5.6 0.4 - - - -
681F ILE* 3.0 31.5 - - + +
740F ILE 3.0 12.0 + - - +
741F HIS* 3.0 14.0 + - - +
743F THR* 1.3 75.0 - - - +
745F VAL* 1.3 64.9 + - + +
747F HIS* 3.3 11.7 + - - +
748F ALA* 3.0 21.1 + - - +
939F ASN* 3.1 28.3 + - - +
943F LYS* 3.2 17.4 + - - -
951F TRP* 3.5 23.8 + - + -
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Residues in contact with VAL 745 (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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741F HIS* 3.0 41.0 + - + +
742F ALA 3.6 5.4 - - - +
744F ASP* 1.3 72.0 - - + +
746F LEU* 1.3 67.2 + - - +
748F ALA* 3.1 2.8 + - - +
749F VAL* 3.0 22.2 + - - +
818F ALA* 4.2 13.2 - - + -
821F HIS* 3.6 22.4 - - + +
933F ILE* 4.6 9.4 - - + +
936F ALA* 3.5 37.2 - - + +
937F ASP* 3.8 8.1 - - + +
939F ASN* 4.9 0.9 - - - +
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Residues in contact with LEU 746 (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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696F LEU* 4.2 11.2 - - + -
699F VAL* 4.0 20.6 - - + -
700F MET* 2.9 52.5 - - + +
703F LEU* 3.7 15.7 - - + -
742F ALA 2.9 12.6 + - - +
743F THR 3.5 7.9 - - - +
745F VAL* 1.3 76.9 - - - +
747F HIS* 1.3 62.9 + - - +
749F VAL* 3.0 18.3 - - + +
750F TRP* 3.0 7.3 + - - +
815F TYR* 3.8 28.0 - - + +
818F ALA* 3.7 13.8 - - + +
819F ALA* 4.8 3.4 - - + +
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Residues in contact with HIS 747 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674F MET* 2.9 59.7 + - + -
676F ASN 3.4 17.0 - - - -
677F TRP* 3.8 17.0 + + - -
679F PHE* 3.4 26.1 - + + +
703F LEU* 4.5 4.0 - - - -
743F THR 3.0 14.1 + - - +
744F ASP* 3.5 16.4 + - - +
745F VAL 3.2 0.2 - - - -
746F LEU* 1.3 78.4 - - - +
748F ALA* 1.3 60.3 + - - +
750F TRP* 3.4 14.7 + + - +
751F TYR* 2.9 34.2 + - + +
943F LYS* 5.2 4.2 + - - -
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Residues in contact with ALA 748 (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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677F TRP* 4.2 23.6 - - + -
744F ASP 3.0 13.0 + - - +
745F VAL 3.1 3.6 + - - +
747F HIS* 1.3 79.8 + - - +
749F VAL* 1.3 61.8 + - - +
751F TYR* 3.1 2.0 + - - +
752F LEU* 2.7 36.0 + - + +
936F ALA* 3.3 30.5 - - + +
939F ASN* 4.3 7.2 - - - +
943F LYS* 5.7 1.3 - - - -
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Residues in contact with VAL 749 (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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745F VAL 3.0 10.7 + - - +
746F LEU* 3.0 25.4 - - + +
748F ALA* 1.3 73.5 - - - +
750F TRP* 1.3 59.9 + - - +
753F THR* 2.8 31.8 + - - +
814F LEU* 4.1 18.2 - - + +
815F TYR* 3.9 17.9 - - + -
818F ALA* 3.9 11.4 - - + -
932F CYS* 4.2 10.1 - - - -
933F ILE* 3.8 33.2 - - + +
936F ALA* 3.5 21.3 - - + -
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Residues in contact with TRP 750 (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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671F ILE* 5.2 3.6 - - + -
674F MET* 3.5 34.8 - - + -
675F SER* 4.6 1.6 - - - -
703F LEU* 3.4 40.7 - - + +
706F ASP* 3.3 25.9 + - - -
707F THR* 3.7 23.4 - - + +
746F LEU 3.0 18.8 + - - +
747F HIS* 3.5 21.8 - + - +
749F VAL* 1.3 80.1 - - - +
751F TYR* 1.3 76.9 + + - +
753F THR* 3.6 0.7 + - - -
754F THR* 3.1 31.8 + - - -
755F ARG* 3.0 38.8 - - - -
791F SER* 3.6 8.5 - - - -
815F TYR* 3.8 22.7 - + + -
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Residues in contact with TYR 751 (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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674F MET 4.3 12.8 - - - -
675F SER 4.0 14.9 + - - -
676F ASN* 4.4 0.7 - - - -
677F TRP* 3.5 61.9 + + + +
747F HIS* 2.9 21.2 + - + +
748F ALA* 3.5 4.7 - - - +
750F TRP* 1.3 86.1 - + + +
752F LEU* 1.3 66.2 + - + +
753F THR 3.1 1.0 + - - -
754F THR 3.1 10.6 + - - -
755F ARG* 3.1 59.8 + - + +
1010F PRO* 4.4 14.6 - - + +
1060F GLN* 4.4 6.6 + - - -
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Residues in contact with LEU 752 (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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677F TRP* 4.1 23.6 - - + -
748F ALA 2.7 26.9 + - - +
749F VAL 4.1 0.4 - - - +
751F TYR* 1.3 73.6 - - + +
753F THR* 1.3 57.9 + - - +
754F THR 3.4 1.0 + - - -
755F ARG 4.9 2.1 - - - +
757F VAL* 5.0 2.1 - - - +
802F LEU* 3.7 14.6 - - - +
932F CYS* 3.8 36.6 - - - +
935F LEU* 4.2 21.1 - - + -
936F ALA* 4.7 4.9 - - + +
1003F TYR* 4.3 9.0 + - + +
1008F LEU 4.4 1.7 - - - +
1009F LEU* 4.1 15.0 - - + -
1010F PRO* 3.7 38.8 - - + +
1061F LEU* 4.2 4.9 - - + -
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Residues in contact with THR 753 (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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749F VAL 2.8 20.2 + - - +
750F TRP 3.6 0.9 + - - -
752F LEU* 1.3 76.7 - - - +
754F THR* 1.3 61.0 + - - +
802F LEU* 3.6 26.7 - - + -
803F SER* 3.2 24.0 + - - -
806F ILE* 5.4 1.6 - - + -
811F LEU* 4.0 15.7 - - + -
814F LEU* 4.0 15.0 - - + -
815F TYR* 2.8 29.6 + - - -
932F CYS* 3.7 25.1 - - - -
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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