Contacts of the helix formed by residues 848 - 865 (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 SER 848 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830C ASN* 4.2 4.3 - - - +
846C ASP 4.0 2.2 + - - -
847C ARG* 1.3 69.5 - - - +
849C VAL* 1.3 66.6 + - - +
850C LEU 3.0 3.8 + - - -
851C GLU* 3.1 27.7 + - - -
852C ASN* 2.9 27.4 + - - -
891C LEU* 4.3 9.3 + - - +
894C ASP* 2.9 25.2 + - - +
897C LYS* 4.1 19.2 + - - -
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Residues in contact with VAL 849 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830C ASN* 3.7 14.2 + - + +
833C LEU* 4.2 16.8 - - + -
834C VAL* 4.4 8.7 - - + -
840C GLN* 3.3 39.7 - - + +
841C ALA* 3.7 28.0 - - + +
844C TYR* 3.8 12.4 - - + -
846C ASP* 3.8 24.5 - - - +
847C ARG 2.5 10.9 + - - +
848C SER* 1.3 73.5 - - - +
850C LEU* 1.3 61.0 + - - +
852C ASN 3.6 0.2 + - - -
853C HIS* 3.3 19.2 + - - +
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Residues in contact with LEU 850 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C 666 6.4 0.9 - - + -
824C ASP 5.6 0.2 - - - +
825C HIS* 3.6 17.9 - - - +
826C PRO* 3.5 28.0 - - + -
828C ARG 3.3 25.4 - - - +
829C THR* 4.3 1.3 - - - -
830C ASN* 2.9 34.6 + - - +
833C LEU* 3.8 19.5 - - + -
840C GLN* 5.4 6.5 - - - +
848C SER 3.0 0.4 + - - -
849C VAL* 1.3 72.6 - - - +
851C GLU* 1.3 77.9 + - - +
853C HIS* 3.0 9.2 + - + +
854C HIS* 3.0 39.5 + - + +
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Residues in contact with GLU 851 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C MG 4.1 12.8 - - - -
830C ASN* 3.2 17.0 + - - -
848C SER* 3.1 8.5 + - - +
850C LEU* 1.3 89.3 - - - +
852C ASN* 1.3 64.0 + - - +
854C HIS* 3.1 22.8 + - + +
855C ALA* 3.2 11.6 + - - +
890C ILE* 3.8 13.1 - - - +
891C LEU* 3.6 21.7 - - + +
893C THR* 3.7 22.1 - - - +
894C ASP* 2.9 49.3 - - + +
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Residues in contact with ASN 852 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844C TYR* 3.4 36.6 - - + +
847C ARG* 2.9 33.7 + - - +
848C SER* 2.9 15.6 + - - +
851C GLU* 1.3 77.3 - - - +
853C HIS* 1.3 57.6 + - - +
856C ALA* 3.0 32.9 + - - +
891C LEU* 3.5 19.5 - - - +
844D TYR* 4.9 1.8 - - - +
845D ASN* 3.3 22.0 + - - +
847D ARG* 4.8 6.3 + - - +
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Residues in contact with HIS 853 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823C TYR 4.3 3.1 - - - -
824C ASP* 2.6 47.1 + - + +
826C PRO* 6.0 0.2 - - + -
840C GLN* 3.2 38.5 + - - +
844C TYR* 4.1 14.8 + - + -
849C VAL 3.3 8.4 + - - +
850C LEU* 3.0 15.0 + - + +
852C ASN* 1.3 77.8 - - - +
854C HIS* 1.3 68.9 + + - +
856C ALA* 4.4 1.0 - - - +
857C SER* 2.7 52.7 + - - -
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Residues in contact with HIS 854 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C MG 4.1 3.3 - - - -
820C MET 3.7 14.3 - - - +
821C HIS 2.8 29.4 - - - +
822C ASP* 3.3 27.2 + - - -
823C TYR* 2.6 32.1 + - - +
824C ASP 4.3 2.0 - - - -
825C HIS* 3.6 25.9 - + - -
850C LEU* 3.0 42.1 + - + +
851C GLU* 3.1 12.5 + - + +
853C HIS* 1.3 79.3 - + - +
855C ALA* 1.3 57.2 + - - +
857C SER* 4.0 0.7 - - - -
858C ALA* 3.0 32.6 + - - +
890C ILE* 4.2 3.8 - - + -
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Residues in contact with ALA 855 (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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851C GLU 3.2 10.9 + - - +
854C HIS* 1.3 76.9 - - - +
856C ALA* 1.3 68.5 + - - +
858C ALA* 3.2 2.5 + - - +
859C TRP* 3.0 31.5 + - + +
887C ILE* 4.5 15.5 - - + -
890C ILE* 4.0 28.4 - - + +
891C LEU* 5.7 2.0 - - + -
845D ASN* 3.1 23.6 - - - +
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Residues in contact with ALA 856 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844C TYR* 3.4 8.3 - - - +
852C ASN 3.0 17.5 + - - +
853C HIS* 4.1 2.5 - - - +
855C ALA* 1.3 78.1 - - - +
857C SER* 1.3 58.2 + - - +
859C TRP* 3.5 0.6 + - - -
860C ASN* 2.9 31.0 + - - +
842D VAL* 3.6 17.6 - - - +
843D LEU* 3.2 32.1 - - + +
845D ASN* 3.2 7.5 + - - +
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Residues in contact with SER 857 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823C TYR* 3.6 28.4 - - - -
853C HIS* 2.7 51.8 + - - -
856C ALA* 1.3 75.0 - - - +
858C ALA* 1.3 64.5 + - - +
860C ASN* 3.7 10.1 + - - +
861C LEU* 3.0 22.5 + - - +
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Residues in contact with ALA 858 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723C TYR* 2.5 24.6 + - - +
727C LEU* 4.2 6.1 - - + -
820C MET* 3.5 42.0 - - + +
823C TYR* 4.2 7.1 - - + -
854C HIS 3.0 19.3 + - - +
855C ALA 3.7 2.7 - - - +
857C SER* 1.3 76.2 - - - +
859C TRP* 1.3 58.6 + - - +
861C LEU* 3.2 5.4 - - - +
862C TYR 3.0 16.1 + - - -
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Residues in contact with TRP 859 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816C VAL* 5.4 1.3 - - + -
820C MET* 4.2 17.4 - - + -
855C ALA* 3.0 28.6 + - + +
856C ALA* 4.0 2.0 - - - +
858C ALA* 1.3 72.4 - - - +
860C ASN* 1.3 67.8 + - - +
861C LEU 3.0 1.6 - - - -
862C TYR* 3.0 44.0 + + + +
863C LEU* 2.9 32.7 + - + +
871C LEU* 4.1 7.0 - - + -
879C PHE* 4.2 13.5 - + - -
882C PHE* 4.1 20.9 - + - -
883C ARG* 3.6 54.5 + - + +
886C VAL* 3.8 36.4 - - + +
887C ILE* 4.2 17.1 - - + +
842D VAL* 4.3 5.8 - - + -
845D ASN* 5.0 0.9 - - - +
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Residues in contact with ASN 860 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856C ALA 2.9 20.7 + - - +
857C SER* 3.7 10.0 + - - +
859C TRP* 1.3 75.5 - - - +
861C LEU* 1.3 64.0 + - - +
863C LEU* 3.8 5.0 - - - +
864C SER* 3.0 31.1 + - - -
842D VAL* 3.8 13.7 - - + +
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Residues in contact with LEU 861 (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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723C TYR* 3.6 20.4 - - + +
726C ALA* 3.8 15.9 - - + +
727C LEU* 3.8 30.3 - - + +
823C TYR* 4.0 18.8 - - + +
857C SER 3.0 13.9 + - - +
858C ALA 3.2 9.2 - - - +
859C TRP 3.0 0.4 - - - -
860C ASN* 1.3 80.3 - - - +
862C TYR* 1.3 66.8 + - - +
864C SER* 2.7 28.2 + - - +
868C TYR* 3.2 26.0 - - + +
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Residues in contact with TYR 862 (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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723C TYR* 3.3 27.3 - + + -
858C ALA 3.0 6.1 + - - +
859C TRP* 3.0 32.9 + + + +
861C LEU* 1.3 80.5 - - - +
863C LEU* 1.3 74.8 + - + +
864C SER 3.2 0.2 + - - -
865C ARG 3.5 16.1 - - - +
868C TYR* 3.3 29.8 - - - +
869C ASN* 3.0 30.1 + - + -
870C PHE* 3.4 26.0 - + - -
871C LEU* 3.1 30.9 + - + +
879C PHE* 3.9 20.0 - + - -
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Residues in contact with LEU 863 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859C TRP* 2.9 23.5 + - + +
860C ASN* 4.1 3.4 - - - +
862C TYR* 1.3 96.1 - - + +
864C SER* 1.3 64.2 + - - +
865C ARG* 3.3 3.6 + - - +
879C PHE* 4.5 13.7 - - + -
883C ARG* 4.8 8.5 - - - +
837D ASN* 4.5 25.1 - - + +
842D VAL* 3.9 32.3 - - + -
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Residues in contact with SER 864 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860C ASN* 3.0 22.0 + - - -
861C LEU* 2.7 26.7 + - - +
863C LEU* 1.3 78.2 - - - +
865C ARG* 1.3 75.6 + - - +
866C PRO* 4.5 2.3 - - - +
868C TYR* 3.8 6.6 - - - -
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Residues in contact with ARG 865 (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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691A LYS* 6.3 0.6 - - - +
694A ARG* 5.0 12.6 - - - +
861C LEU 3.9 0.6 + - - -
862C TYR 3.5 13.9 + - - +
863C LEU 3.3 2.2 - - - -
864C SER* 1.3 94.5 + - - +
866C PRO* 1.3 66.5 - - + +
867C GLU* 3.2 39.6 + - + +
868C TYR* 3.3 38.3 + - + +
869C ASN* 4.2 2.6 + - - +
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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