Contacts of the strand formed by residues 808 - 814 (chain A) in PDB entry 6S1M
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 ARG 808 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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803A LEU* 4.0 0.2 - - - +
804A ILE* 3.1 26.7 + - + +
805A SER* 3.3 33.0 + - - +
806A LYS 3.2 4.8 - - - +
807A LYS* 1.3 82.6 + - + +
809A TYR* 1.3 66.0 + - - +
827A LYS 3.3 5.8 - - - -
828A GLY* 3.1 33.5 + - - -
829A LEU* 3.7 21.8 - - + +
830A GLU* 3.1 26.8 + - - -
833A ARG* 4.3 22.0 - - - +
968A ARG* 4.7 5.7 - - - +
5T T 4.7 13.9 + - - +
6T T 3.6 37.7 + - - -
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Residues in contact with TYR 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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753A TYR* 4.2 22.9 - + - -
760A MET* 3.4 30.5 - - + +
798A TYR* 4.3 12.6 - + - -
801A TYR* 3.2 27.6 - + + +
802A LEU 3.2 14.4 - - - +
803A LEU* 3.8 13.5 - - + +
804A ILE* 4.6 2.2 - - - +
807A LYS* 4.8 3.4 - - - -
808A ARG* 1.3 83.4 - - - +
810A ALA* 1.3 67.6 + - - +
825A ASP* 5.8 0.7 - - + -
826A CYS* 3.7 1.0 - - - -
827A LYS* 2.9 77.1 + - + +
829A LEU* 4.0 8.9 - - - +
24P G 5.2 1.8 - - - -
25P DOC 3.5 17.0 + - - -
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Residues in contact with ALA 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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798A TYR* 5.0 0.4 - - - -
801A TYR* 3.1 10.7 - - - -
802A LEU* 2.9 42.9 + - + +
809A TYR* 1.3 80.7 - - - +
811A GLY* 1.3 60.5 + - - +
824A MET* 6.3 0.2 - - - -
825A ASP* 3.0 15.3 - - - +
826A CYS* 4.6 1.3 - - - -
829A LEU* 4.2 8.5 - - + -
848A LEU* 3.8 29.4 - - + -
852A LEU* 5.0 3.6 - - + -
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Residues in contact with GLY 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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798A TYR* 3.6 20.4 - - - -
800A PRO 3.7 11.9 - - - -
801A TYR* 4.5 0.7 - - - -
810A ALA* 1.3 77.0 - - - +
812A LEU* 1.3 61.8 + - - -
824A MET* 3.3 10.6 - - - +
825A ASP 2.8 29.9 + - - +
852A LEU* 5.1 8.8 - - - +
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Residues in contact with LEU 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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797A VAL 3.4 2.4 - - - +
798A TYR* 3.3 27.6 - - - -
799A PHE 3.4 17.0 + - - +
800A PRO* 3.6 19.7 + - + -
811A GLY* 1.3 75.2 - - - +
813A LEU* 1.3 59.5 + - - +
814A PHE* 3.8 7.6 - - + -
821A HIS* 4.6 17.3 - - + -
823A ARG 3.4 20.9 - - - +
824A MET* 3.7 21.1 - - + -
852A LEU* 3.6 33.4 - - + +
853A ILE* 4.3 17.7 - - + -
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Residues in contact with LEU 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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796A LYS* 3.7 48.2 - - + -
797A VAL 4.3 0.7 - - - +
798A TYR* 4.6 3.4 - - + -
812A LEU* 1.3 72.6 - - - +
814A PHE* 1.3 63.9 + - - +
821A HIS* 3.5 6.4 - - - +
822A ASP* 2.9 42.8 + - + +
823A ARG* 3.0 60.5 + - + +
825A ASP* 3.6 22.4 - - - +
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Residues in contact with PHE 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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768A VAL* 3.6 22.9 - - + -
772A MET* 3.8 16.6 - - + +
794A PHE* 5.7 0.2 - - - -
795A GLU 4.8 0.3 - - - +
796A LYS* 3.8 10.7 - - - +
797A VAL* 3.4 37.2 + - + +
799A PHE* 3.7 43.5 - + + -
812A LEU* 3.8 9.4 - - + -
813A LEU* 1.3 81.8 - - - +
815A SER* 1.3 60.7 + - - +
816A SER 4.2 6.1 - - - +
817A ARG* 3.3 27.1 - - - -
820A ALA 3.1 27.4 - - - -
821A HIS* 4.6 10.1 - - + +
822A ASP* 4.2 1.3 - - - -
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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