Contacts of the strand formed by residues 856 - 868 (chain B) in PDB entry 1FO4
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 ILE 856 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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848B VAL* 3.7 22.0 - - + -
849B GLY 3.7 2.5 - - - +
850B PHE* 4.1 2.7 - - + -
854B GLY 3.7 10.1 - - - +
855B THR* 1.3 80.5 - - - +
857B VAL* 1.3 66.6 + - - +
858B ALA 4.0 6.5 - - - +
859B LEU* 4.9 0.4 - - + -
889B TYR* 5.7 0.2 - - + -
890B LYS 4.5 3.8 - - - +
891B ILE* 4.0 33.2 - - + -
892B PRO* 3.6 16.2 - - - +
926B TRP* 3.8 20.2 - - + -
927B MET* 4.1 4.3 - - + -
930B VAL* 3.7 33.2 - - + -
945B ASN* 2.8 31.1 + - + +
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Residues in contact with VAL 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722B GLY* 3.4 23.7 - - - +
725B GLU* 4.8 9.0 - - + +
726B ALA* 3.5 23.3 - - + +
849B GLY* 2.8 19.0 + - - +
850B PHE* 3.9 1.6 - - - +
851B MET* 3.9 22.9 - - + -
855B THR* 4.1 9.9 - - + +
856B ILE* 1.3 80.0 - - - +
858B ALA* 1.3 61.3 + - - +
892B PRO* 4.4 8.6 - - + +
893B ASN* 2.8 40.1 + - - +
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Residues in contact with ALA 858 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719B LEU* 4.4 3.8 - - + +
722B GLY* 3.8 3.4 - - - -
723B PHE* 3.7 52.0 - - + +
847B LYS 4.4 0.4 - - - -
848B VAL* 3.2 10.7 - - - +
849B GLY* 2.7 31.8 + - - +
856B ILE* 3.9 2.4 - - - +
857B VAL* 1.3 81.4 - - - +
859B LEU* 1.3 62.0 + - - +
893B ASN* 3.3 7.4 - - + +
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Residues in contact with LEU 859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719B LEU* 3.4 7.3 - - - +
723B PHE* 4.7 0.4 - - - -
847B LYS 3.4 12.6 - - - +
848B VAL* 4.0 12.6 - - + -
856B ILE* 4.9 0.2 - - + -
858B ALA* 1.3 76.2 - - - +
860B GLU* 1.3 69.9 + - - +
861B VAL* 3.5 19.7 - - + -
885B MET* 3.8 26.7 - - + +
891B ILE* 3.8 27.4 - - + -
893B ASN 3.0 6.5 + - - -
894B ILE* 3.3 6.9 - - + -
895B ARG 3.0 24.8 + - - -
926B TRP* 3.4 47.6 - - + +
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Residues in contact with GLU 860 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719B LEU* 2.9 37.7 - - + +
723B PHE* 3.2 20.7 - - + -
845B ARG 4.5 0.4 - - - -
846B TYR* 3.1 4.9 - - - -
847B LYS* 2.8 64.0 + - + +
859B LEU* 1.3 72.8 - - - +
861B VAL* 1.3 63.8 + - - +
862B ASP* 5.6 3.4 - - - +
895B ARG* 3.4 22.4 + - + +
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Residues in contact with VAL 861 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844B ALA* 4.3 4.5 - - + -
845B ARG 3.4 7.4 - - - +
846B TYR* 3.9 9.2 - - + -
859B LEU* 3.5 27.6 - - + -
860B GLU* 1.3 80.4 - - - +
862B ASP* 1.3 68.4 + - - +
863B HIS* 3.3 34.9 + - + +
885B MET* 3.9 13.5 - - + +
895B ARG 3.0 7.8 + - - +
896B GLY* 3.3 3.1 - - - -
897B THR 2.9 25.5 + - - +
922B ILE* 4.1 17.5 - - + -
926B TRP* 4.3 7.9 - - + +
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Residues in contact with ASP 862 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711B GLU* 5.3 0.2 - - - +
844B ALA* 3.4 5.9 - - - -
845B ARG* 2.8 44.1 + - + +
860B GLU* 5.7 3.3 - - - +
861B VAL* 1.3 76.7 + - - +
863B HIS* 1.3 61.1 + - - +
864B TYR* 3.8 27.6 + - + +
895B ARG* 3.8 15.3 + - - +
897B THR* 2.6 33.1 + - - +
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Residues in contact with HIS 863 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842B PHE* 3.9 16.4 - + + -
843B LEU 3.8 3.6 - - - -
844B ALA* 4.7 0.2 - - - +
861B VAL* 3.3 32.7 + - + +
862B ASP* 1.3 73.7 - - - +
864B TYR* 1.3 67.7 + - - +
878B MET* 3.7 21.1 - - - -
881B ALA* 5.0 0.9 - - + -
882B LEU* 3.7 19.9 - - + +
885B MET* 4.3 16.5 - - + +
897B THR* 2.8 29.8 + - - +
898B GLY* 3.2 1.6 - - - -
899B ARG* 2.8 25.1 + - - +
919B ALA* 4.4 16.3 + - + +
922B ILE* 3.4 32.8 - - + +
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Residues in contact with TYR 864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698B ILE* 3.6 23.0 - - + +
702B ILE* 3.9 34.7 - - + +
707B PHE* 4.2 11.0 - + - -
842B PHE* 3.5 5.1 - - - -
843B LEU* 3.0 42.6 + - + +
845B ARG* 4.4 24.9 + - - -
862B ASP* 3.8 36.1 + - + +
863B HIS* 1.3 76.6 - - - +
865B SER* 1.3 61.0 + - - +
878B MET* 4.3 1.1 - - - -
899B ARG* 3.4 31.9 - - + -
901B CYS* 4.1 3.1 - - - -
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Residues in contact with SER 865 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698B ILE* 4.2 1.8 - - - -
840B HIS* 4.1 17.5 - - - -
841B PRO 3.4 4.5 - - - -
842B PHE* 3.6 28.3 - - - -
864B TYR* 1.3 74.8 - - - +
866B ASN* 1.3 60.2 + - - +
867B ALA* 3.3 1.4 + - - +
874B SER 5.3 0.3 + - - -
877B ILE* 6.1 0.7 - - - -
878B MET* 3.6 5.7 - - - +
899B ARG 3.1 5.9 + - - -
900B LEU* 3.6 27.5 - - - +
901B CYS* 2.8 31.9 + - - +
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Residues in contact with ASN 866 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696B ILE 3.1 24.5 + - - -
697B THR* 4.1 1.6 - - - +
698B ILE* 3.7 29.4 - - + +
840B HIS* 3.3 8.9 - - - -
841B PRO* 3.1 29.1 + - + +
865B SER* 1.3 70.8 - - - +
867B ALA* 1.3 56.7 + - - +
868B GLY* 3.5 2.6 + - - -
901B CYS* 4.1 2.7 - - - -
903B THR* 2.6 29.9 + - - +
905B LEU* 3.4 17.5 - - - +
908B ASN* 2.8 26.2 + - - -
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Residues in contact with ALA 867 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708B TYR* 3.6 24.5 - - + -
840B HIS* 3.7 9.0 - - + +
865B SER* 3.3 2.9 + - - +
866B ASN* 1.3 73.8 - - - +
868B GLY* 1.3 61.1 + - - +
874B SER* 3.5 22.0 - - - +
900B LEU* 4.6 2.7 - - + -
901B CYS 2.9 23.4 + - - +
907B SER* 3.6 0.2 - - - -
908B ASN* 2.9 13.6 + - - -
4019B CA 2.7 22.4 - - - -
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Residues in contact with GLY 868 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708B TYR* 2.7 25.1 + - - -
866B ASN* 3.5 3.1 + - - -
867B ALA* 1.3 79.7 - - - +
869B ASN* 1.3 51.7 + - - -
870B SER 3.3 4.4 + - - -
901B CYS 3.7 0.6 + - - -
903B THR* 3.0 35.0 + - - +
905B LEU* 3.3 14.4 - - - -
906B SER 3.6 10.3 - - - -
907B SER* 3.9 0.2 - - - -
908B ASN* 5.1 0.7 - - - -
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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