Contacts of the helix formed by residues 807 - 821 (chain A) 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 PRO 807 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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784A ILE* 3.5 33.2 - - + -
785A ALA 3.6 5.8 - - - +
786A TYR* 3.5 17.2 - - + +
805A ASN 3.9 2.9 - - - +
806A ILE* 1.3 86.9 - - - +
808A ALA* 1.3 66.4 + - - +
809A LEU* 3.2 5.8 - - + +
810A GLU* 3.1 35.5 + - + +
811A LEU* 3.1 9.0 + - - +
925A ARG* 3.2 35.4 - - - +
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Residues in contact with ALA 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709A LEU* 3.8 3.2 - - + +
712A ILE* 4.6 2.2 - - + -
713A PHE* 4.0 18.6 - - + -
785A ALA* 2.8 31.1 + - + +
786A TYR* 3.9 2.0 - - - +
787A ILE* 3.3 34.8 - - + +
806A ILE 3.6 2.3 + - - -
807A PRO* 1.3 70.6 - - - +
809A LEU* 1.3 63.2 + - - +
811A LEU* 3.3 4.5 + - - +
812A MET* 2.9 25.6 + - - +
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Residues in contact with LEU 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713A PHE* 3.6 32.9 - - + -
784A ILE* 5.8 4.2 - - + +
785A ALA 4.7 0.4 + - - -
807A PRO* 3.2 6.6 + - + +
808A ALA* 1.3 77.7 - - - +
810A GLU* 1.3 60.6 + - + +
812A MET* 3.2 10.6 + - + +
813A ALA* 3.0 26.7 + - - +
874A LEU* 4.7 9.0 - - + -
878A GLU* 4.5 26.2 - - + +
881A ARG* 4.0 31.0 - - + +
882A PHE* 4.0 27.6 - - + +
885A LEU* 5.0 2.7 - - + -
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Residues in contact with GLU 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806A ILE* 3.6 11.5 - - + +
807A PRO* 3.1 20.0 + - + +
809A LEU* 1.3 80.6 - - + +
811A LEU* 1.3 62.7 + - - +
813A ALA* 3.2 5.9 + - - +
814A LEU* 3.1 19.2 + - - +
881A ARG* 2.9 25.8 + - - +
885A LEU* 3.3 30.1 - - + +
922A GLU 5.7 0.4 - - - -
925A ARG* 2.6 54.4 + - - +
926A LEU* 6.0 1.1 - - - -
929A CYS* 4.9 10.9 - - - -
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Residues in contact with LEU 811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753A THR* 4.1 26.9 - - + +
787A ILE* 3.4 35.2 - - + -
803A SER* 3.7 28.5 - - - +
806A ILE* 3.8 40.6 - - + +
807A PRO 3.1 7.0 + - - +
808A ALA 4.0 5.2 - - - +
810A GLU* 1.3 72.7 - - - +
812A MET* 1.3 64.5 + - - +
814A LEU* 3.2 12.6 + - + +
815A TYR* 3.0 39.5 + - - +
929A CYS* 4.8 2.0 - - - -
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Residues in contact with MET 812 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704A PHE* 3.6 34.3 - - + -
709A LEU* 3.7 18.1 - - + +
713A PHE* 4.0 33.4 - - + -
715A ILE* 3.9 16.8 - - - -
808A ALA 2.9 17.4 + - - +
809A LEU* 3.5 9.0 - - + +
811A LEU* 1.3 74.8 - - - +
813A ALA* 1.3 66.5 + - - +
815A TYR* 3.3 2.4 + - - +
816A VAL* 2.9 31.8 + - + +
870A PHE* 5.5 0.4 - - - -
871A LEU* 3.9 18.4 - - + -
874A LEU* 4.7 1.6 - - + -
882A PHE* 3.6 26.7 - - + -
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Residues in contact with ALA 813 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809A LEU 3.0 11.7 + - - +
810A GLU* 3.2 10.7 + - - +
812A MET* 1.3 77.7 - - - +
814A LEU* 1.3 51.8 + - - +
817A ALA* 2.7 37.5 + - - +
882A PHE* 3.4 20.3 - - + -
885A LEU* 3.6 32.1 - - + -
886A VAL* 3.6 14.3 - - + +
889A ALA* 5.5 0.9 - - - -
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Residues in contact with LEU 814 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749A VAL* 4.1 24.5 - - + -
753A THR* 4.2 22.2 - - + -
810A GLU 3.1 9.4 + - - +
811A LEU* 3.4 19.7 - - + +
812A MET 3.1 0.4 - - - -
813A ALA* 1.3 79.8 - - - +
815A TYR* 1.3 59.8 + - + +
817A ALA* 3.3 4.0 + - - +
818A ALA* 2.9 31.1 + - - +
889A ALA* 4.4 12.8 - - + -
929A CYS* 3.4 39.5 - - + +
932A CYS* 4.3 7.9 - - + -
933A ILE* 3.8 19.2 - - + +
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Residues in contact with TYR 815 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700A MET* 4.0 1.7 - - - +
703A LEU* 5.9 3.6 - - + -
704A PHE* 3.9 18.6 - + + -
707A THR* 4.0 13.9 - - - -
709A LEU* 3.8 19.5 - - + -
746A LEU* 3.6 22.9 - - + +
749A VAL* 3.9 16.2 - - + -
750A TRP* 3.7 23.9 - + + -
753A THR* 3.0 28.3 + - - -
754A THR* 4.1 9.0 + - - -
787A ILE* 3.5 32.6 - - + +
811A LEU* 3.0 24.5 + - + +
812A MET 3.7 3.8 - - - +
814A LEU* 1.3 81.9 - - + +
816A VAL* 1.3 62.2 + - - +
818A ALA* 3.3 6.2 + - - +
819A ALA* 3.1 19.1 + - - +
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Residues in contact with VAL 816 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700A MET* 5.0 2.5 - - - -
704A PHE* 4.0 19.7 - - + -
724A PHE* 4.2 20.2 - - + -
812A MET* 2.9 22.6 + - + +
813A ALA 3.8 2.7 - - - +
815A TYR* 1.3 72.3 - - - +
817A ALA* 1.3 67.8 + - - +
819A ALA* 3.0 15.1 + - - +
820A MET* 3.0 49.0 + - + +
859A TRP* 5.9 0.2 - - + -
870A PHE* 4.9 8.3 - - + -
882A PHE* 3.7 27.6 - - + -
886A VAL* 4.5 3.8 - - + -
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Residues in contact with ALA 817 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813A ALA 2.7 23.0 + - - +
814A LEU 3.5 4.3 - - - +
816A VAL* 1.3 72.5 - - - +
818A ALA* 1.3 53.0 + - - +
820A MET* 3.2 4.0 + - - +
821A HIS* 2.7 39.8 + - - +
886A VAL* 3.7 24.9 - - + +
889A ALA* 3.5 29.6 - - + -
890A ILE* 3.8 5.0 - - + +
933A ILE* 4.4 3.1 - - + -
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Residues in contact with ALA 818 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742A ALA* 4.1 9.3 - - - +
745A VAL* 4.2 9.0 - - + -
746A LEU* 3.9 15.0 - - - +
749A VAL* 3.8 23.6 - - + -
814A LEU 2.9 18.2 + - - +
815A TYR 3.5 5.8 - - - +
817A ALA* 1.3 77.6 - - - +
819A ALA* 1.3 59.8 + - - +
821A HIS* 2.9 29.0 + - - -
933A ILE* 4.2 12.0 - - + +
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Residues in contact with ALA 819 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696A LEU* 3.7 28.4 - - + +
700A MET* 3.8 29.2 - - + -
724A PHE* 4.2 13.2 - - + -
727A LEU* 3.8 5.9 - - + +
731A TYR* 2.8 24.3 + - - -
742A ALA* 3.9 3.6 - - - +
746A LEU* 5.0 2.2 - - + +
815A TYR 3.1 6.0 + - - +
816A VAL 3.0 9.5 + - - +
818A ALA* 1.3 77.1 - - - +
820A MET* 1.3 58.5 - - - +
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Residues in contact with MET 820 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723A TYR* 3.3 33.0 - - + +
727A LEU* 3.7 15.5 - - + -
731A TYR* 3.4 3.4 - - - -
816A VAL* 3.0 39.3 - - + +
817A ALA 3.7 4.3 - - - +
819A ALA* 1.3 79.0 - - - +
821A HIS* 1.3 63.0 + - - +
822A ASP 3.3 2.7 - - - -
823A TYR* 3.1 18.5 + - - +
854A HIS* 3.8 7.3 - - - +
858A ALA* 3.7 24.2 - - + +
859A TRP* 4.5 21.5 - - + -
862A TYR* 6.2 0.4 - - + -
870A PHE* 6.3 0.2 - - + -
886A VAL* 3.8 22.4 - - + -
890A ILE* 3.9 12.0 - - + +
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Residues in contact with HIS 821 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731A TYR* 4.5 0.6 + - - -
741A HIS* 3.6 6.1 - + - -
742A ALA* 4.4 5.4 - - - -
745A VAL* 3.5 29.1 - - + +
817A ALA 2.7 21.0 + - - +
818A ALA* 2.9 23.2 + - - -
820A MET* 1.3 71.2 - - - +
822A ASP* 1.3 76.7 + - + +
823A TYR 3.5 0.2 - - - -
854A HIS* 3.0 23.4 - - - +
890A ILE* 4.0 22.3 - - + +
893A THR* 4.2 15.1 + - + +
933A ILE* 4.6 7.4 - - + -
937A ASP* 2.8 19.1 + - + -
2123A MG 2.0 31.9 - - - -
2124A MG 4.0 4.0 - - - -
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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