Contacts of the strand formed by residues 900 - 909 (chain A) in PDB entry 3FCS
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 900 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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785A GLU* 3.4 22.4 + - - +
786A LEU 3.4 13.5 - - - +
787A HIS* 3.1 51.2 + - + +
822A GLY* 4.2 12.3 - - - +
895A MET* 3.6 3.8 - - - -
898A GLY* 3.9 9.9 + - - +
899A GLN* 1.3 89.2 + - - +
901A ALA* 1.3 65.8 + - - +
592B GLY* 4.2 11.3 + - - -
593B SER 4.0 8.5 + - - -
594B TYR* 3.1 58.7 - - + +
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Residues in contact with ALA 901 (chain A).
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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785A GLU* 3.5 1.8 - - - +
786A LEU* 2.7 44.6 + - + +
821A GLN 3.4 17.9 - - - +
822A GLY* 4.2 3.6 - - - +
824A LEU* 4.5 13.4 - - + +
892A LEU* 4.1 24.9 - - + -
895A MET* 4.0 4.9 - - + +
900A ARG* 1.3 79.9 - - - +
902A MET* 1.3 59.1 + - - +
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Residues in contact with MET 902 (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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783A THR* 3.2 34.1 - - + -
784A TYR 3.3 11.9 - - - +
785A GLU* 4.0 12.6 - - + +
819A GLN 3.9 0.6 - - - +
820A PRO* 3.5 1.2 - - - +
821A GLN* 2.8 66.0 + - + +
824A LEU* 5.4 0.2 - - - -
901A ALA* 1.3 75.5 - - - +
903A VAL* 1.3 64.1 + - - +
904A THR* 3.4 13.7 - - - +
594B TYR* 5.4 1.6 - - - -
602B PRO* 3.7 30.5 - - + +
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Residues in contact with VAL 903 (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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782A HIS 4.0 1.7 - - - +
783A THR* 3.4 1.7 - - - -
784A TYR* 2.9 35.1 + - + +
799A LEU* 4.5 9.2 - - + -
801A ILE* 4.1 21.9 - - + +
818A ILE* 3.7 29.4 - - + -
819A GLN 3.6 3.1 - - - -
820A PRO* 3.9 13.0 - - + -
824A LEU* 3.4 32.5 - - + -
826A CYS* 4.0 10.3 - - - -
890A CYS* 4.4 2.9 - - - -
902A MET* 1.3 74.8 - - - +
904A THR* 1.3 68.2 + - - +
905A VAL* 4.7 1.1 - - + +
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Residues in contact with THR 904 (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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781A GLU* 3.4 30.1 - - + +
782A HIS 3.8 0.2 - - - -
783A THR* 3.0 27.3 + - - +
817A ASP 4.0 0.2 - - - +
818A ILE* 3.6 2.3 - - - -
819A GLN* 2.8 49.6 + - + +
821A GLN* 5.5 2.2 + - - -
902A MET* 3.4 22.0 - - - +
903A VAL* 1.3 71.4 - - - +
905A VAL* 1.3 66.2 + - - +
906A LEU* 3.9 3.6 + - + +
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Residues in contact with VAL 905 (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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780A VAL 4.0 0.7 - - - +
781A GLU* 3.2 6.1 - - - +
782A HIS* 2.9 42.2 + - + +
784A TYR* 6.1 0.7 - - + -
801A ILE* 4.5 18.6 - - + -
803A LEU* 3.6 43.1 - - + -
815A ILE* 4.2 12.8 - - + -
817A ASP 3.8 2.9 - - - +
818A ILE* 4.2 18.6 - - + -
888A VAL* 5.3 0.4 - - + -
903A VAL* 4.7 1.1 - - + +
904A THR* 1.3 76.4 - - - +
906A LEU* 1.3 69.7 + - - +
907A ALA* 5.1 3.6 - - + -
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Residues in contact with LEU 906 (chain A).
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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779A LYS* 4.4 15.3 - - + +
780A VAL 4.1 1.6 - - - +
781A GLU* 3.6 34.5 - - + +
815A ILE* 3.6 6.2 - - - +
816A LEU* 2.9 48.1 + - + -
817A ASP* 2.8 25.3 + - + +
839A TRP* 4.0 19.5 - - - -
904A THR* 3.9 3.3 + - + +
905A VAL* 1.3 72.6 - - - +
907A ALA* 1.3 73.6 + - - +
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Residues in contact with ALA 907 (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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779A LYS* 3.4 5.4 - - - +
780A VAL* 2.8 39.8 + - + +
813A LEU* 4.6 20.9 - - + -
814A TYR 3.2 21.5 - - - +
815A ILE* 3.9 8.1 - - + -
816A LEU* 4.1 3.5 - - - +
905A VAL* 5.1 4.3 - - + -
906A LEU* 1.3 81.7 - - - +
908A PHE* 1.3 63.9 + - - +
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Residues in contact with PHE 908 (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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776A TRP* 3.9 33.7 - + + -
777A GLY 3.7 20.0 - - - +
778A PRO 3.3 16.6 - - - +
779A LYS* 3.9 5.8 - - + -
780A VAL* 4.4 2.5 - - - +
813A LEU* 3.7 2.6 - - - -
814A TYR* 2.9 65.4 + + + +
816A LEU* 3.6 29.2 - - + -
837A VAL* 5.8 1.8 - - + -
907A ALA* 1.3 80.1 - - - +
909A LEU* 1.3 86.3 + - - +
910A TRP* 4.2 21.8 - + - -
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Residues in contact with LEU 909 (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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759A LEU* 4.3 2.9 - - + -
761A VAL* 4.6 2.5 - - + -
777A GLY* 3.5 13.9 + - - -
778A PRO* 3.3 34.5 + - + +
780A VAL* 4.8 6.1 - - + -
812A LEU* 3.5 12.8 - - + +
813A LEU* 3.3 30.1 - - + -
908A PHE* 1.3 92.3 - - - +
910A TRP* 1.3 60.1 + - - +
911A LEU* 3.6 1.7 + - + -
914A LEU* 3.5 32.3 - - + -
924A LEU* 3.7 13.7 - - + -
955A LEU* 3.6 27.6 - - + -
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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
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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