Contacts of the helix formed by residues 807 - 821 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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784I ILE* 3.5 26.9 - - + -
785I ALA 3.6 4.9 - - - +
786I TYR* 3.5 15.2 - - + +
805I ASN 3.9 2.9 - - - +
806I ILE* 1.3 86.4 - - - +
808I ALA* 1.3 67.2 + - - +
809I LEU* 3.2 7.4 - - + +
810I GLU* 3.1 34.2 + - + +
811I LEU* 3.1 8.7 + - - +
925I ARG* 3.2 36.8 - - - +
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Residues in contact with ALA 808 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709I LEU* 3.8 3.3 - - + +
712I ILE* 4.6 2.7 - - + -
713I PHE* 3.9 18.4 - - + -
785I ALA* 2.8 30.2 + - + +
786I TYR* 3.9 2.1 - - - +
787I ILE* 3.3 34.3 - - + +
806I ILE 3.6 1.6 + - - -
807I PRO* 1.3 68.5 - - - +
809I LEU* 1.3 66.3 + - - +
811I LEU* 3.3 4.1 + - - +
812I MET* 2.9 25.5 + - - +
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Residues in contact with LEU 809 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713I PHE* 3.6 32.4 - - + -
785I ALA 4.7 0.6 + - - -
807I PRO* 3.2 6.8 + - + +
808I ALA* 1.3 75.8 - - - +
810I GLU* 1.3 65.0 + - + +
812I MET* 3.2 9.6 + - + +
813I ALA* 3.0 21.1 + - - +
874I LEU* 4.8 9.2 - - + -
878I GLU* 4.5 23.8 - - + +
881I ARG* 4.1 31.6 - - + +
882I PHE* 3.9 28.3 - - + +
885I LEU* 5.0 3.6 - - + -
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Residues in contact with GLU 810 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806I ILE* 3.6 11.9 - - + +
807I PRO* 3.1 18.7 + - - +
809I LEU* 1.3 79.0 - - + +
811I LEU* 1.3 65.9 + - - +
813I ALA* 3.2 5.9 + - - +
814I LEU* 3.1 19.6 + - - +
881I ARG* 2.9 26.1 + - - +
885I LEU* 3.3 30.0 - - + +
922I GLU 5.7 0.4 - - - -
925I ARG* 2.6 55.9 + - - +
926I LEU* 6.0 1.3 - - - -
929I CYS* 4.9 10.1 - - - -
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Residues in contact with LEU 811 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753I THR* 4.1 26.7 - - + +
787I ILE* 3.4 34.8 - - + -
802I LEU* 4.6 0.4 - - + +
803I SER* 3.7 28.5 - - - +
806I ILE* 3.8 39.9 - - + +
807I PRO 3.1 7.4 + - - +
808I ALA 3.3 5.6 + - - +
810I GLU* 1.3 76.8 - - - +
812I MET* 1.3 62.9 + - - +
814I LEU* 3.3 13.7 + - + +
815I TYR* 3.0 39.6 + - - +
929I CYS* 4.8 1.8 - - - -
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Residues in contact with MET 812 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704I PHE* 3.6 33.2 - - + -
709I LEU* 3.7 17.5 - - + +
713I PHE* 4.0 34.8 - - + -
715I ILE* 3.9 16.4 - - - -
808I ALA 2.9 17.4 + - - +
809I LEU* 3.5 8.1 - - + +
810I GLU 3.2 0.2 - - - -
811I LEU* 1.3 74.4 - - - +
813I ALA* 1.3 65.7 + - - +
815I TYR* 3.3 2.9 + - - +
816I VAL* 2.9 32.0 + - + +
870I PHE* 5.4 0.4 - - - -
871I LEU* 3.9 19.7 - - + -
874I LEU* 4.7 1.6 - - + -
882I PHE* 3.6 25.4 - - + -
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Residues in contact with ALA 813 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809I LEU 3.0 10.5 + - - +
810I GLU* 3.4 10.3 - - - +
812I MET* 1.3 78.0 - - - +
814I LEU* 1.3 51.6 + - - +
817I ALA* 2.7 38.4 + - - +
882I PHE* 3.3 23.1 - - + -
885I LEU* 3.6 31.4 - - + -
886I VAL* 3.7 15.1 - - + +
889I ALA* 5.5 0.4 - - - -
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Residues in contact with LEU 814 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749I VAL* 4.1 24.2 - - + -
753I THR* 4.2 21.8 - - + -
810I GLU 3.1 11.5 + - - +
811I LEU* 3.4 20.0 - - + +
812I MET 3.1 0.2 - - - -
813I ALA* 1.3 77.5 - - - +
815I TYR* 1.3 60.4 + - + +
817I ALA* 3.3 4.1 + - - +
818I ALA* 2.8 30.5 + - - +
889I ALA* 4.3 13.5 - - + -
929I CYS* 3.4 41.7 - - + +
932I CYS* 4.4 4.5 - - + -
933I ILE* 3.8 19.2 - - + +
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Residues in contact with TYR 815 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700I MET* 4.0 2.4 - - - +
703I LEU* 5.9 3.4 - - + -
704I PHE* 3.9 18.6 - + + -
707I THR* 4.0 14.4 - - - -
709I LEU* 3.8 19.7 - - + -
746I LEU* 3.6 21.8 - - + +
749I VAL* 3.9 15.9 - - + -
750I TRP* 3.7 22.9 - + + -
753I THR* 3.0 27.4 + - - -
754I THR* 4.1 9.5 + - - -
787I ILE* 3.5 32.1 - - + +
811I LEU* 3.0 24.2 + - + +
812I MET 3.8 3.6 - - - +
814I LEU* 1.3 80.3 - - + +
816I VAL* 1.3 63.4 + - - +
818I ALA* 3.3 6.0 + - - +
819I ALA* 3.1 18.2 + - - +
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Residues in contact with VAL 816 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700I MET* 4.9 2.2 - - - -
704I PHE* 4.0 19.3 - - + -
724I PHE* 4.2 20.2 - - + -
812I MET* 2.9 23.5 + - + +
813I ALA 3.8 2.9 - - - +
815I TYR* 1.3 73.0 - - - +
817I ALA* 1.3 67.2 + - - +
819I ALA* 3.0 16.1 + - - +
820I MET* 3.0 46.3 + - + +
870I PHE* 4.9 9.2 - - + -
882I PHE* 3.7 26.0 - - + -
886I VAL* 4.6 4.3 - - + -
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Residues in contact with ALA 817 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813I ALA 2.7 22.9 + - - +
814I LEU 3.5 4.0 - - - +
816I VAL* 1.3 73.0 - - - +
818I ALA* 1.3 52.3 + - - +
820I MET* 3.1 3.8 + - - +
821I HIS* 2.7 39.5 + - - +
886I VAL* 3.7 24.1 - - + +
889I ALA* 3.5 29.8 - - + -
890I ILE* 3.9 5.8 - - + +
933I ILE* 4.3 3.1 - - + -
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Residues in contact with ALA 818 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742I ALA* 4.0 10.5 - - - +
745I VAL* 4.2 8.3 - - + -
746I LEU* 3.9 14.1 - - - +
749I VAL* 3.8 23.8 - - + -
814I LEU 2.8 17.6 + - - +
815I TYR 3.5 6.5 - - - +
817I ALA* 1.3 78.1 - - - +
819I ALA* 1.3 60.0 + - - +
821I HIS* 2.9 27.7 + - - -
933I ILE* 4.2 13.1 - - + +
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Residues in contact with ALA 819 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696I LEU* 3.7 26.8 - - + +
700I MET* 3.8 24.2 - - + -
724I PHE* 4.3 12.6 - - + -
727I LEU* 3.8 5.4 - - + +
731I TYR* 2.9 24.1 + - - -
742I ALA* 3.9 3.1 - - - +
746I LEU* 5.0 2.4 - - + +
815I TYR 3.1 12.2 + - - +
816I VAL 3.0 10.3 + - - +
818I ALA* 1.3 76.7 - - - +
820I MET* 1.3 59.1 + - - +
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Residues in contact with MET 820 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723I TYR* 3.2 32.5 - - + +
727I LEU* 3.8 12.8 - - + -
731I TYR* 3.4 3.4 - - - -
816I VAL* 3.0 40.4 - - + +
817I ALA 3.8 4.0 - - - +
819I ALA* 1.3 78.9 - - - +
821I HIS* 1.3 62.1 + - - +
822I ASP 3.3 2.9 - - - -
823I TYR* 3.1 19.3 + - - +
854I HIS* 3.8 7.4 - - - +
858I ALA* 3.6 28.0 - - + +
859I TRP* 4.5 22.2 - - + -
862I TYR* 6.2 0.2 - - + -
886I VAL* 3.8 20.4 - - + -
890I ILE* 3.9 12.9 - - + +
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Residues in contact with HIS 821 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731I TYR* 4.5 0.8 + - - -
741I HIS* 3.6 6.3 - + - -
742I ALA* 4.4 5.4 - - - -
745I VAL* 3.5 28.3 - - + -
817I ALA 2.7 21.7 + - - +
818I ALA* 2.9 22.4 + - - +
819I ALA 3.6 0.2 - - - -
820I MET* 1.3 72.4 - - - +
822I ASP* 1.3 78.1 + - + +
854I HIS* 3.0 22.8 - - - +
890I ILE* 4.0 23.1 - - + +
893I THR* 4.2 15.5 + - + +
933I ILE* 4.6 7.0 - - + -
937I ASP* 2.8 19.6 + - + -
2139I MG 2.0 31.6 - - - -
2140I MG 4.0 2.7 - - - -
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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