Contacts of the helix formed by residues 805 - 820 (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 SER 805 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747B HIS* 3.2 31.4 - - - +
748B CYS 6.2 0.2 - - - -
749B THR* 4.7 0.3 + - - -
764B VAL* 4.9 4.9 - - - -
765B SER 3.9 16.8 - - - -
766B THR* 2.8 27.6 + - - -
768B ASN* 5.7 0.2 - - - +
772B THR* 4.5 3.5 + - - -
800B GLY 4.4 0.6 + - - -
801B LYS* 3.4 8.7 + - - +
803B THR* 4.1 3.5 + - - +
804B ARG* 1.3 76.7 - - - +
806B THR* 1.3 63.9 + - - +
807B LEU 3.1 0.2 - - - -
808B VAL* 3.2 8.9 + - - +
809B SER* 3.1 21.8 + - - -
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Residues in contact with THR 806 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B THR* 5.3 0.5 + - - +
768B ASN* 5.7 1.1 - - + +
771B LYS* 4.3 4.5 - - + +
772B THR* 4.1 28.9 - - - +
775B PHE* 3.6 37.1 - - + -
803B THR* 3.0 20.3 + - - +
804B ARG* 4.5 2.4 + - - -
805B SER* 1.3 78.2 + - - +
807B LEU* 1.3 70.4 + - - +
808B VAL 3.1 0.2 - - - -
809B SER* 3.7 9.2 - - - +
810B VAL* 2.9 34.0 + - - +
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Residues in contact with LEU 807 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B LEU* 4.7 0.3 - - - +
646B THR* 6.2 2.9 - - + -
652B GLU* 4.0 11.2 - - - +
653B THR 5.7 4.5 - - - +
654B VAL* 5.6 2.3 - - - +
666B ILE* 3.9 27.6 - - + +
804B ARG* 3.3 57.9 - - - +
805B SER 3.1 0.4 - - - -
806B THR* 1.3 82.8 + - - +
808B VAL* 1.3 63.5 + - + +
810B VAL* 4.8 1.3 - - - +
811B ALA* 3.7 18.7 + - - +
835B ILE* 3.7 33.2 - - + +
836B THR* 4.3 7.0 - - + -
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Residues in contact with VAL 808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B LEU* 5.8 0.7 - - + -
607B LEU* 4.5 9.9 - - + -
747B HIS* 4.1 13.0 - - + -
748B CYS* 4.9 3.1 - - - +
749B THR* 4.3 11.0 - - - +
804B ARG 5.3 0.7 - - - +
805B SER 3.2 8.6 + - - +
807B LEU* 1.3 82.6 - - + +
809B SER* 1.3 65.2 + - - +
810B VAL 3.3 0.4 - - - -
811B ALA* 3.3 5.0 + - - +
812B VAL* 3.0 33.7 + - + +
825B CYS* 4.0 30.3 - - - +
827B LEU* 3.8 36.8 - - + -
835B ILE* 6.4 0.4 - - + -
836B THR* 5.6 1.1 - - + -
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Residues in contact with SER 809 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749B THR* 2.7 33.5 + - - -
762B LEU* 4.3 3.7 - - - +
764B VAL* 3.4 13.9 - - - +
772B THR* 3.7 25.6 + - - +
776B VAL* 4.2 4.7 - - - +
805B SER 3.1 16.9 + - - -
806B THR* 3.4 5.1 + - - -
808B VAL* 1.3 77.4 - - - +
810B VAL* 1.3 58.0 + - - +
812B VAL* 3.8 1.2 - - - +
813B ALA* 2.8 30.7 + - - +
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Residues in contact with VAL 810 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B THR* 5.0 6.3 - - + +
654B VAL* 3.5 24.0 - - + -
775B PHE* 4.1 33.0 - - + +
776B VAL* 4.4 6.5 - - + +
779B MET* 3.3 41.3 - - + +
806B THR* 2.9 23.3 + - - +
807B LEU* 4.8 1.1 - - - +
809B SER* 1.3 73.7 - - - +
811B ALA* 1.3 60.9 + - - +
813B ALA* 3.3 5.1 + - - -
814B LEU* 2.9 25.8 + - - +
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Residues in contact with ALA 811 (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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605B LEU* 3.5 18.8 - - + +
607B LEU* 3.8 24.2 - - + -
635B LEU* 4.6 1.4 - - - +
654B VAL* 4.9 3.0 - - + +
655B PHE* 4.2 21.7 - - + -
666B ILE* 5.6 0.2 - - + -
669B ALA* 5.0 0.2 - - + -
807B LEU 3.7 14.7 + - - +
808B VAL 3.3 7.2 + - - +
810B VAL* 1.3 78.5 - - - +
812B VAL* 1.3 63.8 + - - +
814B LEU* 3.2 9.6 + - - +
815B ALA 3.0 17.2 + - - -
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Residues in contact with VAL 812 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B LEU* 4.1 13.9 - - + -
749B THR* 4.0 15.5 - - + +
751B ALA* 3.5 16.4 - - + +
808B VAL* 3.0 24.4 + - + +
809B SER 3.8 3.1 - - - +
811B ALA* 1.3 73.8 - - - +
813B ALA* 1.3 66.7 + - - +
815B ALA* 3.0 4.5 + - - +
816B ALA* 3.0 20.4 + - - +
823B VAL* 3.3 34.5 - - + +
824B ARG 4.5 0.7 - - - -
825B CYS* 3.7 30.3 - - + +
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Residues in contact with ALA 813 (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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751B ALA* 3.9 5.1 - - - +
760B MET* 3.6 22.8 - - + +
762B LEU* 4.4 3.4 - - + -
776B VAL* 3.8 32.5 - - + -
779B MET* 3.9 8.3 - - + -
809B SER 2.8 18.7 + - - +
810B VAL 3.5 4.9 - - - +
812B VAL* 1.3 76.9 - - - +
814B LEU* 1.3 63.2 + - - +
816B ALA 3.2 1.0 + - - -
817B TYR* 2.9 23.6 + - - +
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Residues in contact with LEU 814 (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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635B LEU* 4.1 16.2 - - + -
639B ASP* 3.8 30.5 - - + +
640B ILE* 4.0 12.1 - - + -
641B PRO* 3.8 17.5 - - + -
654B VAL* 5.6 1.6 - - + -
655B PHE* 3.2 38.1 - - + -
779B MET* 3.5 17.9 - - + +
810B VAL* 2.9 14.0 + - + +
811B ALA* 3.2 9.4 + - - +
813B ALA* 1.3 77.2 - - - +
815B ALA* 1.3 56.6 + - - +
817B TYR* 3.2 11.1 + - + +
818B LYS* 2.9 29.8 + - + +
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Residues in contact with ALA 815 (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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605B LEU* 3.9 5.4 - - + -
635B LEU* 3.6 23.1 - - + +
671B VAL* 3.8 18.8 - - + -
811B ALA 3.0 10.7 + - - +
812B VAL 3.0 8.5 + - - +
814B LEU* 1.3 78.0 - - - +
816B ALA* 1.3 56.5 + - - +
818B LYS* 3.9 1.1 - - - +
819B THR* 2.9 36.8 + - - +
823B VAL* 3.8 20.9 - - + -
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Residues in contact with ALA 816 (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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751B ALA* 3.7 25.6 - - + +
753B PRO* 3.7 17.6 - - + +
760B MET* 4.2 4.7 - - + -
812B VAL 3.0 12.3 + - - +
813B ALA 3.7 6.7 - - - +
815B ALA* 1.3 73.6 - - - +
817B TYR* 1.3 62.1 + - - +
820B GLY* 2.8 30.8 + - - -
821B HIS 3.4 22.0 - - - +
823B VAL* 3.7 3.8 - - + +
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Residues in contact with TYR 817 (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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95A LYS* 6.0 10.3 - - + +
639B ASP 4.6 4.9 - - - -
641B PRO* 3.6 44.3 - - + +
753B PRO* 5.1 2.0 - - - -
758B GLY* 6.5 1.3 - - - -
760B MET* 4.0 9.5 - - + +
780B LEU* 3.7 23.8 - - + -
813B ALA 2.9 13.4 + - - +
814B LEU* 3.5 13.5 - - + +
816B ALA* 1.3 79.0 - - - +
818B LYS* 1.3 71.7 + - + +
820B GLY* 3.8 5.4 + - - -
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Residues in contact with LYS 818 (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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632B VAL* 5.3 3.6 + - - +
633B CYS* 4.1 24.3 - - - +
635B LEU* 3.8 27.1 - - + -
639B ASP* 5.3 11.7 - - + +
814B LEU* 2.9 19.3 + - + +
815B ALA 3.9 1.8 - - - +
817B TYR* 1.3 89.1 - - + +
819B THR* 1.3 72.3 + - + +
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Residues in contact with THR 819 (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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603B LEU* 3.9 24.0 - - + -
632B VAL* 4.3 16.2 - - + -
633B CYS* 4.5 4.9 - - - -
671B VAL* 4.5 7.4 - - + -
815B ALA* 2.9 22.7 + - - +
818B LYS* 1.3 92.3 - - + +
820B GLY* 1.3 60.0 + - - +
821B HIS* 2.9 40.3 + - - +
823B VAL* 4.0 2.9 - - + +
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Residues in contact with GLY 820 (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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95A LYS* 6.3 2.9 - - - -
601B ASN* 4.7 3.1 + - - -
753B PRO* 3.5 18.0 - - - +
816B ALA 2.8 19.3 + - - -
817B TYR 3.8 4.4 + - - -
818B LYS 3.5 1.6 - - - -
819B THR* 1.3 74.0 - - - +
821B HIS* 1.3 62.2 + - - +
822B PRO* 4.6 1.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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