Contacts of the strand formed by residues 779 - 788 (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 LYS 779 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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755C PHE 5.2 1.6 - - - +
756C PRO* 3.6 15.0 - - + +
777C GLY 3.9 1.0 - - - -
778C PRO* 1.3 73.4 - - - +
780C VAL* 1.3 70.3 + - - +
781C GLU* 3.1 32.3 + - + -
906C LEU* 4.0 21.9 - - + +
907C ALA 3.7 6.5 - - - +
908C PHE* 4.4 10.8 - - + -
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Residues in contact with VAL 780 (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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755C PHE 3.8 7.9 - - - +
756C PRO* 4.6 9.9 - - + +
778C PRO* 3.7 11.4 + - + +
779C LYS* 1.3 81.9 - - - +
781C GLU* 1.3 66.6 + - - +
782C HIS* 4.3 11.2 - - + +
813C LEU* 5.2 9.4 - - + -
907C ALA* 2.8 39.2 + - - +
908C PHE* 5.3 0.2 - - - -
909C LEU* 4.8 19.1 - - + -
924C LEU* 5.2 5.4 - - + -
953C THR* 3.7 34.8 - - + +
955C LEU* 5.2 4.9 - - + -
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Residues in contact with GLU 781 (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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753C ASN 4.2 0.3 - - - +
754C SER* 3.3 3.1 - - - -
755C PHE* 2.8 62.0 + - + +
779C LYS* 3.1 29.8 + - - -
780C VAL* 1.3 77.9 - - - +
782C HIS* 1.3 64.7 + - - +
783C THR* 4.2 2.8 + - - -
904C THR* 3.2 24.6 - - + +
905C VAL 3.1 17.5 - - - +
906C LEU* 3.8 15.8 - - + +
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Residues in contact with HIS 782 (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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753C ASN 3.8 3.6 - - - -
754C SER* 4.0 1.3 - - - -
780C VAL* 4.3 10.1 - - + +
781C GLU* 1.3 81.5 - - - +
783C THR* 1.3 60.9 + - - +
784C TYR* 4.1 10.2 + - + -
803C LEU* 5.5 5.4 - - + -
813C LEU* 5.8 8.0 - - + +
903C VAL 4.0 1.2 - - - +
904C THR* 3.7 0.3 - - - -
905C VAL* 3.0 39.7 + - + +
924C LEU* 4.3 11.7 + - + +
925C GLN 5.0 0.4 - - - -
926C SER* 2.8 34.3 + - - +
951C VAL* 3.2 33.1 - - + +
953C THR* 2.7 33.6 + - - -
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Residues in contact with THR 783 (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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752C GLY* 3.3 3.1 - - - -
753C ASN 3.1 29.4 + - - -
755C PHE* 4.0 25.2 - - + -
781C GLU* 4.2 1.9 + - - -
782C HIS* 1.3 71.1 - - - +
784C TYR* 1.3 69.1 + - - +
902C MET* 4.2 15.9 - - - -
903C VAL 3.4 5.4 - - - +
904C THR* 3.1 35.6 + - - +
951C VAL* 5.4 0.4 - - - +
602D PRO* 4.5 16.4 - - + +
603D THR* 4.0 5.6 - - + +
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Residues in contact with TYR 784 (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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750C LEU* 4.6 9.2 - - + -
751C ARG 3.4 14.6 - - - -
752C GLY* 4.0 2.5 - - - -
782C HIS* 4.8 11.4 - - + -
783C THR* 1.3 78.5 - - - +
785C GLU* 1.3 61.6 + - - +
799C LEU* 5.3 4.9 - - + -
801C ILE* 3.7 43.3 - - + -
803C LEU* 5.7 0.7 - - + -
902C MET* 3.5 4.0 - - - +
903C VAL* 2.9 36.1 + - + +
905C VAL* 6.1 1.8 - - + -
926C SER* 3.2 43.2 + - - -
927C HIS* 3.6 1.6 + - - -
928C ALA* 3.9 20.6 - - + -
949C ALA* 4.0 20.9 - - + -
950C GLN* 3.6 2.3 - - - -
951C VAL* 3.3 26.0 + - + -
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Residues in contact with GLU 785 (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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749C GLU 3.8 0.5 - - - +
750C LEU* 3.2 9.0 - - - +
751C ARG* 3.0 34.7 + - + +
783C THR* 5.5 0.2 - - + -
784C TYR* 1.3 76.6 - - - +
786C LEU* 1.3 69.9 + - - +
787C HIS* 5.6 0.2 - - + -
900C ARG* 3.9 21.3 + - - +
901C ALA 3.4 13.2 - - - +
902C MET* 4.2 9.0 - - + +
592D GLY* 4.1 7.1 - - - +
594D TYR* 3.4 25.5 + - - -
602D PRO* 3.5 23.8 - - + +
603D THR* 3.5 33.3 + - + +
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Residues in contact with LEU 786 (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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748C VAL* 3.5 17.5 - - + -
749C GLU 3.3 13.2 - - - +
750C LEU* 3.3 32.1 - - + -
785C GLU* 1.3 79.6 - - - +
787C HIS* 1.3 63.6 + - - +
797C LEU* 3.6 37.2 - - + -
799C LEU* 4.6 21.3 - - + -
824C LEU* 5.9 4.0 - - + -
892C LEU* 6.1 1.6 - - + -
895C MET* 4.1 13.0 - - + -
900C ARG* 3.5 3.1 - - - +
901C ALA* 2.7 40.4 + - + +
930C PHE* 4.2 9.0 - - + -
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Residues in contact with HIS 787 (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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748C VAL* 4.3 2.9 - - - +
749C GLU* 2.8 52.8 + - + +
785C GLU* 5.6 0.7 - - + -
786C LEU* 1.3 77.2 - - - +
788C ASN* 1.3 74.4 + - - +
789C ASN* 3.2 39.5 + - + +
895C MET* 4.4 0.2 - - - -
898C GLY* 4.0 15.0 - - - -
899C GLN 3.8 11.7 + - - -
900C ARG* 3.3 46.9 + - - +
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Residues in contact with ASN 788 (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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746C ALA* 4.1 9.5 - - - +
747C GLN 4.0 5.0 + - - +
748C VAL* 4.3 8.3 - - + +
787C HIS* 1.3 69.4 + - - +
789C ASN* 1.3 61.0 + - - +
790C GLY 3.8 9.9 + - - +
792C GLY 3.6 23.1 + - - +
794C VAL* 3.8 10.9 - - + +
895C MET* 2.8 48.1 + - + +
896C ALA* 2.9 22.5 + - - +
897C ARG* 3.8 1.5 - - - +
898C GLY* 2.9 27.9 + - - -
899C GLN 3.2 8.2 + - - +
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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