Contacts of the strand formed by residues 900 - 909 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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785C GLU* 3.9 15.8 + - - +
786C LEU 3.5 7.6 - - - +
787C HIS* 3.3 52.1 + - - +
822C GLY* 4.1 12.8 - - - +
895C MET* 3.5 6.5 - - - -
898C GLY 3.7 10.6 + - - +
899C GLN* 1.3 88.7 + - - +
901C ALA* 1.3 61.8 + - - +
592D GLY* 4.0 12.7 + - - -
593D SER 4.1 7.5 + - - -
594D TYR* 3.2 66.5 - - + +
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Residues in contact with ALA 901 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785C GLU* 3.4 4.0 - - - +
786C LEU* 2.7 46.4 + - + +
821C GLN 3.5 14.6 - - - +
822C GLY 4.3 9.9 - - - +
824C LEU* 4.7 13.2 - - + -
892C LEU* 4.3 12.1 - - + -
895C MET* 3.6 11.6 - - + +
900C ARG* 1.3 77.4 - - - +
902C MET* 1.3 60.1 + - - +
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Residues in contact with MET 902 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783C THR* 4.2 9.2 - - + -
784C TYR 3.5 12.6 - - - +
785C GLU* 4.2 10.8 - - + +
819C GLN 3.9 1.5 - - - +
820C PRO* 3.4 1.6 - - - +
821C GLN* 2.7 74.4 + - + +
901C ALA* 1.3 75.6 - - - +
903C VAL* 1.3 67.3 + - - +
904C THR* 4.2 12.1 - - - +
594D TYR* 5.2 4.7 - - - +
602D PRO* 3.7 34.8 - - + -
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Residues in contact with VAL 903 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782C HIS 4.0 1.2 - - - +
783C THR* 3.4 2.1 - - - +
784C TYR* 2.9 38.2 + - + +
799C LEU* 4.3 13.5 - - + -
801C ILE* 4.3 22.2 - - + +
818C ILE* 3.5 30.3 - - + -
819C GLN 3.7 3.4 - - - -
820C PRO* 4.0 11.9 - - + -
824C LEU* 3.4 33.4 - - + -
826C CYS* 4.4 6.7 - - - -
888C VAL* 6.2 0.2 - - + -
890C CYS* 4.6 0.2 - - - -
902C MET* 1.3 75.6 - - - +
904C THR* 1.3 65.4 + - - +
905C VAL* 4.1 4.4 - - + +
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Residues in contact with THR 904 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781C GLU* 3.2 27.4 - - + +
782C HIS 3.7 2.9 - - - +
783C THR* 3.1 30.7 + - - +
817C ASP 3.6 3.3 - - - +
819C GLN* 2.8 45.7 + - + +
902C MET* 4.2 10.0 - - - +
903C VAL* 1.3 71.7 - - - +
905C VAL* 1.3 67.3 + - - +
906C LEU* 4.0 2.3 + - + +
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Residues in contact with VAL 905 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781C GLU* 3.1 8.8 - - - +
782C HIS* 3.0 40.4 + - + +
784C TYR* 6.1 1.6 - - + -
801C ILE* 5.1 10.5 - - + -
803C LEU* 3.4 41.5 - - + -
815C ILE* 3.9 19.1 - - + -
817C ASP 3.5 2.9 - - - -
818C ILE* 3.8 29.8 - - + +
888C VAL* 5.4 0.9 - - + -
903C VAL* 4.5 6.5 - - + -
904C THR* 1.3 73.7 - - - +
906C LEU* 1.3 65.6 + - - +
907C ALA* 5.4 1.3 - - + -
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Residues in contact with LEU 906 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779C LYS* 4.0 33.9 - - + +
780C VAL 4.0 0.4 - - - +
781C GLU* 3.8 25.4 - - + +
815C ILE* 3.6 5.9 - - - +
816C LEU* 2.7 56.0 + - + -
817C ASP* 2.9 22.8 + - + +
904C THR* 5.2 2.0 - - + +
905C VAL* 1.3 75.8 - - - +
907C ALA* 1.3 63.7 + - - +
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Residues in contact with ALA 907 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779C LYS* 3.7 5.9 - - - +
780C VAL* 2.8 36.2 + - - +
813C LEU* 4.0 24.0 - - + -
814C TYR 3.0 26.7 - - - +
815C ILE* 3.8 5.2 - - + -
816C LEU* 4.1 6.3 - - - +
905C VAL* 5.4 2.5 - - + -
906C LEU* 1.3 80.9 - - - +
908C PHE* 1.3 64.0 + - - +
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Residues in contact with PHE 908 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777C GLY* 3.9 19.3 - - - +
778C PRO 3.3 14.6 - - - +
779C LYS* 4.4 11.4 - - + -
780C VAL* 4.6 1.8 - - - +
813C LEU* 3.2 15.2 - - - +
814C TYR* 3.1 44.9 + + + -
816C LEU* 3.0 48.9 - - + -
907C ALA* 1.3 77.7 - - - +
909C LEU* 1.3 69.2 + - - +
910C TRP* 4.0 4.0 - + + -
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Residues in contact with LEU 909 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777C GLY* 3.4 18.0 + - - -
778C PRO* 3.5 33.0 + - + +
780C VAL* 4.8 7.2 - - + -
812C LEU* 3.4 23.3 - - + +
813C LEU* 3.6 8.1 - - + -
814C TYR* 5.7 0.2 - - - -
908C PHE* 1.3 76.8 - - - +
910C TRP* 1.3 61.3 + - - +
911C LEU* 3.1 8.5 + - - +
914C LEU* 4.0 23.8 - - + -
924C LEU* 3.3 34.3 - - + -
955C LEU* 3.5 31.6 - - + -
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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