Contacts of the helix formed by residues 875 - 892 (chain C) 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 ASP 875 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873C HIS 4.1 1.2 + - - -
874C LEU* 1.3 73.3 - - - +
876C HIS* 1.3 67.3 + - + +
877C VAL* 3.7 19.8 - - + +
878C GLU* 2.8 43.6 + - - +
879C PHE* 3.0 10.4 + - - +
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Residues in contact with HIS 876 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874C LEU 3.7 1.2 + - - -
875C ASP* 1.3 72.9 - - - +
877C VAL* 1.3 63.7 + - + +
879C PHE* 4.0 6.1 - - - +
880C LYS* 3.0 29.8 + - + +
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Residues in contact with VAL 877 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875C ASP* 2.9 20.0 + - + +
876C HIS* 1.3 82.0 - - + +
878C GLU* 1.3 64.7 + - + +
880C LYS* 3.4 5.2 - - - +
881C ARG* 3.2 20.4 + - - +
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Residues in contact with GLU 878 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713C PHE* 4.8 8.5 - - - -
809C LEU* 4.5 19.4 - - + +
873C HIS 4.6 1.2 - - - +
874C LEU* 3.2 33.0 - - + +
875C ASP* 2.8 38.6 + - - +
877C VAL* 1.3 74.3 - - + +
879C PHE* 1.3 57.9 + - - +
881C ARG* 3.1 8.3 + - - +
882C PHE* 2.8 29.5 + - - +
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Residues in contact with PHE 879 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859C TRP* 3.8 24.7 - + - -
862C TYR* 3.9 19.1 - + - -
863C LEU* 4.9 9.4 - - + -
869C ASN* 5.4 1.3 - - - -
871C LEU* 3.7 43.1 - - + -
874C LEU* 4.2 14.2 - - + +
875C ASP 3.0 14.8 + - - +
876C HIS* 4.1 7.0 - - - +
878C GLU* 1.3 76.6 - - - +
880C LYS* 1.3 70.1 + - + +
882C PHE* 3.6 6.8 - + - +
883C ARG* 3.0 37.6 + - + +
837D ASN* 6.0 3.1 - - - -
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Residues in contact with LYS 880 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876C HIS* 3.0 21.5 + - + +
877C VAL* 3.4 6.7 - - - +
879C PHE* 1.3 83.1 - - + +
881C ARG* 1.3 64.1 - - - +
883C ARG* 3.5 5.6 + - - +
884C PHE* 3.2 18.8 + - - +
834D VAL* 3.6 37.0 + - - +
835D ALA* 4.0 14.9 + - - +
837D ASN* 4.8 7.5 + - - +
846D ASP* 5.7 1.6 - - - -
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Residues in contact with ARG 881 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809C LEU* 4.0 17.8 - - + +
810C GLU* 2.9 32.1 + - - -
877C VAL* 3.2 7.7 + - + +
878C GLU* 3.1 9.7 + - - +
880C LYS* 1.3 78.7 - - - +
882C PHE* 1.3 65.7 + - - +
884C PHE* 3.1 15.1 + - + +
885C LEU* 2.9 51.7 + - + +
922C GLU* 3.5 45.5 + - - +
926C LEU* 6.2 1.2 - - - +
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Residues in contact with PHE 882 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809C LEU* 3.9 26.6 - - + +
812C MET* 3.6 22.0 - - + -
813C ALA* 3.4 30.1 - - + -
816C VAL* 3.7 30.5 - - + -
859C TRP* 4.0 15.5 - + - -
870C PHE* 5.7 0.2 - + - -
871C LEU* 3.6 31.0 - - + -
874C LEU* 4.8 3.6 - - + -
878C GLU 2.8 19.6 + - - +
879C PHE* 3.6 10.3 - + - +
881C ARG* 1.3 74.3 - - - +
883C ARG* 1.3 65.8 + - - +
885C LEU* 3.3 7.3 + - - +
886C VAL* 2.9 44.4 + - + +
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Residues in contact with ARG 883 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859C TRP* 3.7 53.1 - - + +
863C LEU* 5.4 4.5 - - - +
879C PHE* 3.0 32.1 + - + +
880C LYS* 3.7 6.1 - - - +
882C PHE* 1.3 75.9 - - - +
884C PHE* 1.3 63.6 + - - +
886C VAL* 3.3 2.4 + - - +
887C ILE* 3.0 34.9 + - + +
837D ASN* 5.2 10.5 + - - -
841D ALA 4.1 1.0 + - - -
842D VAL* 3.7 44.4 + - - +
845D ASN* 4.2 8.1 + - - +
846D ASP* 2.4 38.8 + - - -
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Residues in contact with PHE 884 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880C LYS 3.2 10.6 + - - +
881C ARG* 3.1 19.0 + - + +
883C ARG* 1.3 78.2 - - - +
885C LEU* 1.3 88.6 + - + +
887C ILE* 3.1 10.7 + - + +
888C GLU* 2.9 59.1 + - + +
926C LEU* 4.3 11.4 - - + -
847D ARG* 6.5 0.4 - - - -
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Residues in contact with LEU 885 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809C LEU* 5.0 3.6 - - + -
810C GLU* 3.3 41.5 - - + +
813C ALA* 3.6 17.0 - - + +
881C ARG* 2.9 49.6 + - + +
882C PHE* 3.6 6.1 - - - +
884C PHE* 1.3 101.2 - - + +
886C VAL* 1.3 63.3 + - - +
888C GLU* 3.3 5.4 + - - +
889C ALA* 3.0 23.6 + - - +
926C LEU* 4.9 18.3 - - + +
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Residues in contact with VAL 886 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813C ALA* 3.7 21.3 - - - +
816C VAL* 4.6 2.7 - - + -
817C ALA* 4.0 17.9 - - - -
820C MET* 3.8 23.3 - - + -
859C TRP* 3.7 21.8 - - + +
882C PHE* 2.9 47.6 + - + +
883C ARG 3.7 4.7 - - - +
885C LEU* 1.3 74.8 - - - +
887C ILE* 1.3 63.5 + - - +
889C ALA* 3.4 2.3 + - - +
890C ILE* 3.0 26.4 + - + +
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Residues in contact with ILE 887 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855C ALA* 4.5 5.6 - - + -
859C TRP* 4.1 15.0 - - + +
883C ARG* 3.0 36.9 + - + +
884C PHE* 3.5 9.4 - - + +
886C VAL* 1.3 74.2 - - - +
888C GLU* 1.3 70.6 + - - +
890C ILE* 3.1 5.3 + - - +
891C LEU* 2.8 43.0 + - + +
845D ASN* 3.4 57.2 - - + +
846D ASP* 5.0 0.9 - - + +
847D ARG* 4.4 9.0 - - - +
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Residues in contact with GLU 888 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884C PHE* 2.9 57.9 + - + +
885C LEU 3.7 6.7 - - - +
887C ILE* 1.3 78.0 - - - +
889C ALA* 1.3 62.2 + - - +
891C LEU* 3.7 4.4 + - - +
892C ALA* 3.2 14.2 + - - +
926C LEU* 4.0 20.2 - - + +
930C GLN* 3.2 32.8 + - - +
847D ARG* 3.0 29.3 + - - -
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Residues in contact with ALA 889 (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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813C ALA 5.5 0.2 - - - -
814C LEU* 4.4 16.2 - - + -
817C ALA* 3.5 25.6 - - + -
885C LEU 3.0 15.6 + - - +
887C ILE 3.1 0.2 - - - -
888C GLU* 1.3 77.3 - - - +
890C ILE* 1.3 64.4 + - - +
892C ALA* 3.2 16.6 + - - +
893C THR* 3.7 4.5 + - - +
926C LEU* 5.3 1.1 - - + +
929C CYS* 5.9 1.8 - - + -
930C GLN* 4.6 6.9 - - + +
933C ILE* 3.8 24.6 - - + +
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Residues in contact with ILE 890 (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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817C ALA* 3.9 18.6 - - + +
820C MET* 3.9 33.7 - - + +
821C HIS* 4.0 24.7 - - + +
851C GLU* 3.9 25.0 - - - +
854C HIS* 4.3 0.2 - - + -
855C ALA* 3.9 29.6 - - + +
886C VAL* 3.0 23.9 + - + +
887C ILE 3.8 2.7 - - - +
889C ALA* 1.3 76.6 - - - +
891C LEU* 1.3 61.1 + - - +
893C THR* 2.5 31.6 + - - +
933C ILE* 5.0 0.4 - - - -
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Residues in contact with LEU 891 (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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848C SER* 4.5 8.3 + - - +
851C GLU* 3.6 14.4 - - + +
852C ASN* 3.5 50.0 - - - +
855C ALA* 5.2 1.3 - - + -
887C ILE* 2.8 32.2 + - + +
888C GLU* 4.4 2.5 - - - +
890C ILE* 1.3 73.6 - - + +
892C ALA* 1.3 59.4 + - - +
893C THR 3.0 1.8 + - - -
894C ASP* 3.4 18.4 + - - +
897C LYS* 5.8 0.7 - - - +
901C PHE* 4.9 3.4 - - - -
845D ASN* 4.9 1.8 - - - +
847D ARG* 2.9 52.3 - - + +
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Residues in contact with ALA 892 (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 3.2 17.9 + - - +
889C ALA 3.2 7.8 + - - +
890C ILE 3.1 1.4 - - - -
891C LEU* 1.3 78.1 - - - +
893C THR* 1.3 57.7 + - - +
894C ASP 3.1 6.9 + - - +
901C PHE* 3.6 33.2 - - + -
930C GLN* 3.8 23.1 - - + +
933C ILE* 4.8 0.4 - - + -
934C LYS* 3.5 30.8 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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