Contacts of the helix formed by residues 848 - 865 (chain H) 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 SER 848 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847G ARG* 5.7 3.4 + - - -
830H ASN* 4.3 2.9 - - - -
846H ASP 3.9 2.8 + - - -
847H ARG* 1.3 70.5 - - - +
849H VAL* 1.3 56.5 + - - +
850H LEU 3.2 2.8 + - - -
851H GLU* 3.2 21.9 + - - -
852H ASN* 2.8 38.1 + - - -
891H LEU* 4.2 10.3 + - - +
894H ASP* 2.6 35.4 + - - +
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Residues in contact with VAL 849 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830H ASN* 3.2 12.9 + - + +
833H LEU* 4.2 14.1 - - + -
834H VAL* 4.1 13.2 - - + -
840H GLN* 3.4 36.6 - - + +
841H ALA* 3.5 17.9 - - + +
844H TYR* 3.9 8.7 - - + -
846H ASP* 3.6 34.5 - - - +
847H ARG 2.8 6.0 + - - +
848H SER* 1.3 70.2 - - - +
850H LEU* 1.3 63.1 + - - +
852H ASN* 3.8 2.1 - - - +
853H HIS* 3.2 21.8 + - - +
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Residues in contact with LEU 850 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825H HIS* 3.5 21.1 - - + +
826H PRO* 3.6 25.4 - - + -
828H ARG 3.2 25.4 - - - +
829H THR* 4.6 1.1 - - - -
830H ASN* 2.7 37.5 + - - +
833H LEU* 3.6 24.5 - - + -
840H GLN* 4.3 8.5 - - - +
849H VAL* 1.3 70.8 - - - +
851H GLU* 1.3 72.1 + - - +
853H HIS* 2.8 10.3 + - + +
854H HIS* 2.8 39.9 + - + +
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Residues in contact with GLU 851 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830H ASN* 3.2 27.7 + - - -
848H SER* 3.6 16.0 - - - +
850H LEU* 1.3 76.4 - - - +
852H ASN* 1.3 61.7 + - - +
854H HIS* 3.3 12.8 + - + +
855H ALA* 3.3 19.4 + - - +
890H ILE* 3.6 16.5 - - - +
891H LEU* 3.8 17.2 - - + +
893H THR* 3.5 23.8 - - - +
894H ASP* 3.4 37.3 - - + +
895H LEU 4.9 0.2 + - - -
2138H MG 4.0 12.0 - - - -
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Residues in contact with ASN 852 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844G TYR 4.5 4.9 - - - +
845G ASN* 2.9 28.5 + - - +
847G ARG* 5.2 6.5 + - - +
844H TYR* 3.5 33.0 - - + +
847H ARG* 2.9 29.5 + - - +
848H SER* 2.8 26.4 + - - +
849H VAL 3.8 0.2 - - - +
851H GLU* 1.3 73.8 - - - +
853H HIS* 1.3 57.5 + - - +
856H ALA* 3.0 32.4 + - - +
891H LEU* 3.6 16.0 - - - +
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Residues in contact with HIS 853 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823H TYR 4.2 7.2 - - - -
824H ASP* 2.8 37.3 + - - -
826H PRO* 6.0 0.2 - - + -
840H GLN* 3.6 38.7 + - - +
844H TYR* 4.0 19.9 + - + -
849H VAL 3.2 11.4 + - - +
850H LEU* 2.8 13.7 + - + +
852H ASN* 1.3 77.9 - - - +
854H HIS* 1.3 70.6 + + - +
856H ALA* 6.0 0.2 - - - +
857H SER* 2.9 50.4 + - - -
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Residues in contact with HIS 854 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820H MET 3.9 6.3 - - - +
821H HIS 3.2 30.5 - - - +
822H ASP* 3.1 30.0 + - - -
823H TYR* 2.6 34.8 + - - +
824H ASP 4.4 1.1 - - - -
825H HIS* 3.8 22.7 + + - -
850H LEU* 2.8 49.2 + - + +
851H GLU* 3.4 11.9 - - + +
852H ASN 3.3 0.4 - - - -
853H HIS* 1.3 78.7 - + - +
855H ALA* 1.3 57.2 + - - +
857H SER* 3.7 1.0 - - - -
858H ALA* 3.0 31.4 + - - +
890H ILE* 4.2 3.4 - - + -
2138H MG 4.4 3.7 - - - -
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Residues in contact with ALA 855 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845G ASN* 3.4 20.4 - - - +
851H GLU 3.3 11.6 + - - +
854H HIS* 1.3 77.5 - - - +
856H ALA* 1.3 66.3 + - - +
858H ALA* 3.4 1.5 + - - +
859H TRP* 3.0 32.1 + - + -
887H ILE* 4.5 15.9 - - + +
890H ILE* 3.9 30.4 - - + +
891H LEU* 5.3 1.8 - - + -
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Residues in contact with ALA 856 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842G VAL* 3.5 15.8 - - - +
843G LEU* 3.1 34.4 - - + +
845G ASN* 3.1 9.3 + - - +
844H TYR* 3.5 9.4 - - - +
852H ASN 3.0 18.4 + - - +
853H HIS* 4.2 1.6 - - - +
855H ALA* 1.3 77.8 - - - +
857H SER* 1.3 56.4 + - - +
859H TRP* 4.7 1.3 - - - -
860H ASN* 3.0 29.5 + - - +
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Residues in contact with SER 857 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823H TYR* 3.5 28.0 - - - -
824H ASP* 4.9 0.7 - - - +
853H HIS* 2.9 44.2 + - - -
854H HIS 3.7 0.2 - - - -
856H ALA* 1.3 76.4 - - - +
858H ALA* 1.3 60.3 + - - +
860H ASN* 3.3 7.7 + - - +
861H LEU* 2.9 28.8 + - - +
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Residues in contact with ALA 858 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723H TYR* 2.9 20.5 + - - +
727H LEU* 4.0 6.1 - - + -
820H MET* 3.6 39.7 - - + -
823H TYR* 4.0 7.8 - - + -
854H HIS 3.0 18.3 + - - +
855H ALA 4.0 1.6 - - - +
857H SER* 1.3 75.8 - - - +
859H TRP* 1.3 59.1 + - - +
861H LEU* 3.2 6.2 + - - +
862H TYR* 2.9 23.6 + - - +
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Residues in contact with TRP 859 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842G VAL* 4.1 17.0 - - + -
845G ASN* 4.9 0.7 - - - -
820H MET* 4.4 14.5 - - + -
855H ALA* 3.0 31.8 + - - +
856H ALA* 4.1 0.4 - - - +
858H ALA* 1.3 75.1 - - - +
860H ASN* 1.3 65.4 + - - +
862H TYR* 3.0 30.6 + + + +
863H LEU* 3.0 32.3 + - + +
871H LEU* 4.6 2.2 - - + -
879H PHE* 3.8 26.0 - + - -
882H PHE* 3.8 27.6 - + - -
883H ARG* 3.6 44.6 - - + +
886H VAL* 3.6 31.3 - - + +
887H ILE* 4.0 21.4 - - + +
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Residues in contact with ASN 860 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865F ARG* 4.7 10.5 + - - +
842G VAL* 4.0 13.6 - - + +
856H ALA 3.0 20.0 + - - +
857H SER* 3.6 7.4 + - - +
859H TRP* 1.3 77.2 - - - +
861H LEU* 1.3 57.6 + - - +
863H LEU* 3.3 5.2 + - - +
864H SER* 2.7 37.2 + - - -
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Residues in contact with LEU 861 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723H TYR* 3.4 27.4 - - + +
726H ALA* 4.0 9.0 - - + +
727H LEU* 3.9 25.4 - - + +
823H TYR* 3.7 23.8 - - + +
857H SER 2.9 14.5 + - - +
858H ALA* 3.2 9.2 - - - +
860H ASN* 1.3 79.1 - - - +
862H TYR* 1.3 61.1 + - - +
864H SER* 2.8 29.6 + - - +
868H TYR* 3.2 34.5 - - + +
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Residues in contact with TYR 862 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723H TYR* 3.5 25.3 - + + +
820H MET* 5.9 1.8 - - + -
858H ALA 2.9 13.9 + - - +
859H TRP* 3.0 27.3 + + + +
861H LEU* 1.3 78.2 - - - +
863H LEU* 1.3 77.3 + - + +
864H SER 3.4 0.3 + - - -
865H ARG 3.8 4.2 - - - +
868H TYR* 3.2 38.8 - - - +
869H ASN* 2.4 41.2 + - + +
870H PHE* 3.6 23.6 - + - -
871H LEU* 3.1 30.5 + - + +
879H PHE* 4.1 18.3 - + - -
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Residues in contact with LEU 863 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866F PRO* 3.4 24.0 - - + +
837G ASN* 4.7 20.9 - - + +
842G VAL* 3.9 32.1 - - + -
859H TRP* 3.0 25.7 + - + +
860H ASN* 3.7 4.0 - - - +
862H TYR* 1.3 96.4 - - + +
864H SER* 1.3 63.5 + - - +
865H ARG* 3.4 3.7 + - - -
879H PHE* 4.6 15.5 - - + -
883H ARG* 5.9 2.9 - - - +
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Residues in contact with SER 864 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864F SER 2.9 14.9 - - - +
865F ARG* 3.5 39.3 + - - +
866F PRO* 3.6 3.4 - - - +
860H ASN* 2.7 24.9 + - - -
861H LEU* 2.8 26.0 + - - +
863H LEU* 1.3 78.2 - - - +
865H ARG* 1.3 74.0 + - - +
868H TYR* 4.3 3.4 - - - -
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Residues in contact with ARG 865 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860F ASN* 4.9 9.9 + - - +
864F SER* 3.4 26.6 + - - +
865F ARG* 5.5 5.4 - - - +
862H TYR 3.8 5.0 - - - +
863H LEU 4.6 3.1 - - - -
864H SER* 1.3 93.0 - - - +
866H PRO* 1.3 71.9 - - + +
867H GLU* 3.0 38.5 + - - +
868H TYR* 3.2 44.0 + - + +
869H ASN* 4.1 1.6 + - - +
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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