Contacts of the helix formed by residues 840 - 850 (chain D) in PDB entry 1S77
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 840 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549D MET* 4.7 5.2 - - - +
839D CYS* 1.3 72.0 - - - +
841D VAL* 1.3 52.6 + - - +
842D LEU* 3.7 7.1 + - - +
843D ALA* 3.1 32.8 + - + +
844D ASP* 2.7 46.0 + - - +
864D LEU* 5.2 0.9 - - - +
867D LYS* 3.8 31.2 + - - -
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Residues in contact with VAL 841 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549D MET* 3.5 47.3 - - + +
730D PRO* 3.9 17.9 - - + -
782D PHE* 3.7 15.5 - - + -
786D GLN* 3.5 23.3 - - - +
836D TYR* 4.2 13.2 - - + -
839D CYS* 3.5 10.4 + - + +
840D ASP* 1.3 72.4 + - - +
842D LEU* 1.3 65.0 + - + +
844D ASP* 3.5 8.9 - - - +
845D PHE* 2.9 27.9 + - - +
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Residues in contact with LEU 842 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549D MET* 3.3 30.7 - - + +
550D LEU* 3.5 32.1 - - + -
695D ALA* 4.4 9.4 - - + -
698D TRP* 3.4 26.0 - - + -
699D LEU* 4.6 11.4 - - + -
782D PHE* 3.5 21.1 - - + -
840D ASP* 3.2 7.0 + - - +
841D VAL* 1.3 77.8 - - - +
843D ALA* 1.3 62.0 + - - +
845D PHE* 3.2 5.5 + - - +
846D TYR* 2.9 24.8 + - - +
864D LEU* 3.9 13.0 - - + -
865D PRO* 3.7 17.7 - - + -
867D LYS* 5.4 3.1 - - - +
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Residues in contact with ALA 843 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840D ASP* 3.1 33.5 + - + +
842D LEU* 1.3 79.9 - - - +
844D ASP* 1.3 60.2 + - - +
846D TYR* 3.5 3.2 + - - +
847D ASP* 2.9 36.7 + - - +
864D LEU* 3.9 24.6 - - + +
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Residues in contact with ASP 844 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728D VAL 5.9 3.8 - - - +
839D CYS* 3.9 10.3 - - - +
840D ASP* 2.7 47.1 + - - +
841D VAL* 3.4 9.3 + - - +
843D ALA* 1.3 71.3 - - - +
845D PHE* 1.3 68.1 + - - +
847D ASP* 3.1 13.7 + - - +
848D GLN* 3.1 25.6 + - + +
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Residues in contact with PHE 845 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698D TRP* 3.3 26.5 - + - -
699D LEU* 3.3 27.8 - - + -
702D ALA* 4.0 11.9 - - + -
725D VAL* 3.2 35.9 - - + -
726D HIS 3.5 13.0 - - - -
727D TRP* 3.7 24.7 - + + -
778D ILE* 4.1 7.9 - - + -
782D PHE* 4.4 10.8 - + + -
841D VAL 2.9 20.4 + - - +
842D LEU* 3.3 5.4 - - - +
844D ASP* 1.3 77.8 - - - +
846D TYR* 1.3 52.1 + - - +
848D GLN* 2.7 34.0 + - - +
849D PHE* 3.1 28.0 - + - -
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Residues in contact with TYR 846 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698D TRP* 3.7 18.4 - + + -
842D LEU 2.9 16.7 + - - +
843D ALA* 3.7 8.5 - - - +
845D PHE* 1.3 71.6 - - - +
847D ASP* 1.3 66.3 + - - +
848D GLN 2.8 6.9 + - - -
849D PHE* 3.1 32.8 + + - -
850D ALA* 2.8 59.0 + - + +
854D HIS* 4.8 4.7 - + - -
859D ASP* 4.6 11.3 + - - -
861D MET* 3.8 25.0 - - + +
862D PRO 5.7 0.4 - - - -
864D LEU* 4.7 8.7 - - + -
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Residues in contact with ASP 847 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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843D ALA* 2.9 26.4 + - - +
844D ASP* 3.1 14.4 + - - +
846D TYR* 1.3 86.6 - - - +
848D GLN* 1.3 58.7 + - - +
850D ALA* 4.7 2.0 - - - -
851D ASP* 3.0 21.6 - - - +
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Residues in contact with GLN 848 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726D HIS* 3.6 46.2 + - - +
727D TRP* 4.4 6.5 - - - -
728D VAL* 4.0 21.5 - - + +
844D ASP* 3.1 16.2 + - + +
845D PHE* 2.7 17.3 + - - +
847D ASP* 1.3 83.0 - - - +
849D PHE* 1.3 56.8 + - - +
851D ASP* 4.5 1.4 - - - +
852D GLN* 4.1 27.4 + - - +
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Residues in contact with PHE 849 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698D TRP* 3.8 5.6 - + - -
702D ALA* 3.7 15.0 - - + -
706D LEU* 3.4 36.8 - - + -
726D HIS 5.5 2.5 - - - +
845D PHE* 3.1 52.0 - + + -
846D TYR* 3.3 49.4 - + - -
848D GLN* 1.3 76.5 - - + +
850D ALA* 1.3 67.4 + - - +
851D ASP 3.2 3.8 + - - -
852D GLN 3.2 7.1 - - - +
853D LEU* 2.6 27.4 - - + +
854D HIS* 3.6 9.8 - + - +
861D MET* 3.4 25.1 - - + -
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Residues in contact with ALA 850 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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846D TYR* 2.8 51.0 + - + +
847D ASP* 4.7 2.2 - - - -
848D GLN 3.8 0.2 - - - -
849D PHE* 1.3 80.4 - - - +
851D ASP* 1.3 61.3 + - - +
854D HIS* 3.0 37.6 + - - +
855D GLU* 5.9 0.3 - - - +
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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