Contacts of the helix formed by residues 805 - 820 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747A HIS* 3.3 29.1 + - - -
748A CYS 6.3 0.2 - - - -
749A THR* 4.7 0.9 + - - -
764A VAL* 4.8 4.3 - - - -
765A SER 3.9 8.1 - - - -
766A THR* 2.7 37.2 + - - -
768A ASN* 5.6 0.2 - - - +
772A THR* 4.3 4.3 + - - -
800A GLY 4.4 1.0 + - - -
801A LYS* 3.6 8.1 + - - -
802A GLU 5.0 0.2 - - - -
803A THR* 3.1 4.0 + - - +
804A ARG* 1.3 77.5 - - - +
806A THR* 1.3 64.1 + - - +
808A VAL* 3.2 15.6 + - - +
809A SER* 3.2 14.6 + - - -
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Residues in contact with THR 806 (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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646A THR* 5.1 0.9 + - - +
768A ASN* 5.6 0.4 - - + +
771A LYS* 4.3 6.1 - - + +
772A THR* 4.1 31.2 - - + +
775A PHE* 3.6 36.1 - - + -
803A THR* 3.1 19.3 + - - +
804A ARG* 3.1 1.9 + - - -
805A SER* 1.3 77.3 - - - +
807A LEU* 1.3 71.6 + - - +
808A VAL 3.1 0.2 - - - -
809A SER* 3.7 8.5 - - - -
810A VAL* 3.0 34.5 + - - +
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Residues in contact with LEU 807 (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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607A LEU* 4.5 1.0 - - - +
646A THR* 6.0 3.8 - - + -
652A GLU* 4.0 12.3 - - - +
653A THR 5.8 3.4 - - - +
654A VAL* 5.8 0.7 - - - +
666A ILE* 3.9 27.8 - - + +
804A ARG* 3.3 56.8 - - - +
805A SER 3.1 0.6 - - - -
806A THR* 1.3 83.2 + - - +
808A VAL* 1.3 64.2 + - + +
810A VAL* 5.1 0.7 - - - +
811A ALA* 3.8 16.1 + - - +
835A ILE* 3.9 33.2 - - + +
836A THR* 4.4 8.3 - - + -
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Residues in contact with VAL 808 (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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605A LEU* 5.6 1.1 - - + -
607A LEU* 4.6 8.7 - - + -
747A HIS* 4.1 14.8 - - + +
748A CYS* 4.8 2.5 - - - +
749A THR* 4.3 11.0 - - - +
804A ARG 5.4 0.7 - - - +
805A SER 3.2 7.9 + - - +
806A THR 3.1 0.2 - - - -
807A LEU* 1.3 82.1 - - + +
809A SER* 1.3 60.7 + - - +
810A VAL 3.4 0.4 - - - -
811A ALA* 3.3 5.3 + - - +
812A VAL* 2.9 44.0 + - + +
825A CYS* 4.0 28.0 - - - +
827A LEU* 3.9 36.1 - - + -
836A THR* 5.7 1.3 - - + -
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Residues in contact with SER 809 (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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749A THR* 2.8 31.6 + - - -
762A LEU* 4.3 5.1 - - - +
764A VAL* 3.3 17.2 - - - +
772A THR* 3.9 22.5 + - - +
776A VAL* 4.4 5.2 - - - -
805A SER 3.2 12.8 + - - -
806A THR* 3.4 7.8 + - - -
808A VAL* 1.3 78.9 - - - +
810A VAL* 1.3 57.5 + - - +
812A VAL* 3.4 2.1 + - - +
813A ALA* 2.8 29.7 + - - +
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Residues in contact with VAL 810 (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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646A THR* 5.0 6.3 - - + +
654A VAL* 3.5 22.9 - - + -
775A PHE* 3.9 34.8 - - + +
776A VAL* 4.2 6.1 - - + +
779A MET* 3.2 40.7 - - + +
806A THR* 3.0 22.3 + - - +
807A LEU 5.1 0.7 - - - +
809A SER* 1.3 72.8 - - - +
811A ALA* 1.3 61.5 + - - +
813A ALA* 3.3 5.3 + - - -
814A LEU* 2.9 24.8 + - - +
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Residues in contact with ALA 811 (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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605A LEU* 3.4 17.1 - - + +
607A LEU* 3.9 22.4 - - + -
635A LEU* 4.7 1.6 - - - +
654A VAL* 4.9 4.6 - - + +
655A PHE* 4.3 24.1 - - + -
666A ILE* 5.7 0.4 - - + -
669A ALA* 5.2 0.2 - - + -
807A LEU 3.8 13.9 + - - +
808A VAL 3.3 8.8 + - - +
810A VAL* 1.3 77.8 - - - +
812A VAL* 1.3 63.9 + - - +
814A LEU* 3.3 5.7 + - - +
815A ALA 3.1 17.0 + - - -
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Residues in contact with VAL 812 (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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605A LEU* 4.0 13.7 - - + -
749A THR* 3.9 15.3 - - + +
751A ALA* 3.6 14.1 - - + +
808A VAL* 2.9 27.4 + - + +
809A SER 3.9 3.1 - - - +
811A ALA* 1.3 72.2 - - - +
813A ALA* 1.3 65.2 + - - +
815A ALA* 3.2 2.6 + - - +
816A ALA* 3.0 21.3 + - - +
823A VAL* 3.2 37.2 - - + +
824A ARG 4.4 0.7 - - - -
825A CYS* 3.6 31.2 - - + +
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Residues in contact with ALA 813 (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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751A ALA* 3.9 4.5 - - - +
760A MET* 3.3 26.9 - - + +
762A LEU* 4.3 3.1 - - + -
776A VAL* 3.7 33.0 - - + -
779A MET* 4.0 6.7 - - + -
809A SER 2.8 18.1 + - - +
810A VAL 3.5 5.4 - - - +
812A VAL* 1.3 76.6 - - - +
814A LEU* 1.3 63.7 + - - +
816A ALA 3.3 1.0 + - - -
817A TYR* 2.9 19.4 + - - +
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Residues in contact with LEU 814 (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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635A LEU* 4.3 17.9 - - + -
639A ASP* 3.8 17.5 - - + +
640A ILE* 4.0 14.6 - - + -
641A PRO* 3.6 31.2 - - + -
654A VAL* 5.7 0.9 - - + -
655A PHE* 3.3 33.7 - - + -
779A MET* 3.4 21.3 - - + +
810A VAL 2.9 9.3 + - - +
811A ALA* 3.6 8.5 - - - +
812A VAL 3.2 0.2 - - - -
813A ALA* 1.3 76.7 - - - +
815A ALA* 1.3 57.5 + - - +
817A TYR* 3.2 12.1 + - + +
818A LYS* 2.9 29.3 + - + +
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Residues in contact with ALA 815 (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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605A LEU* 3.7 26.5 - - + -
635A LEU* 3.6 18.8 - - + +
671A VAL* 3.8 12.6 - - + -
811A ALA 3.1 5.3 + - - -
812A VAL 3.4 9.0 - - - +
814A LEU* 1.3 76.9 - - - +
816A ALA* 1.3 56.8 + - - +
818A LYS* 3.4 1.2 + - - -
819A THR* 2.9 35.0 + - - +
823A VAL* 3.8 15.5 - - + -
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Residues in contact with ALA 816 (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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751A ALA* 3.7 17.9 - - + +
753A PRO* 3.5 31.8 - - + +
760A MET* 4.2 4.9 - - + -
812A VAL 3.0 12.3 + - - +
813A ALA 3.7 7.6 - - - +
815A ALA* 1.3 73.6 - - - +
817A TYR* 1.3 59.1 + - - +
820A GLY* 2.7 32.9 + - - -
821A HIS 3.4 13.5 - - - +
823A VAL* 3.7 4.0 - - + +
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Residues in contact with TYR 817 (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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639A ASP 4.5 0.2 - - - -
641A PRO* 3.4 40.0 - - + +
753A PRO* 5.0 2.2 - - - -
758A GLY* 6.4 1.8 - - - -
760A MET* 3.9 10.7 - - + +
780A LEU* 3.6 22.7 - - + -
813A ALA 2.9 14.1 + - - +
814A LEU* 3.4 13.2 - - + +
816A ALA* 1.3 79.9 - - - +
818A LYS* 1.3 87.6 + - + +
820A GLY* 3.9 4.9 + - - -
95B LYS* 5.6 11.0 + - + -
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Residues in contact with LYS 818 (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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633A CYS* 5.6 2.9 - - - -
635A LEU* 3.9 23.3 - - + -
639A ASP* 3.3 46.7 + - + +
814A LEU* 2.9 16.6 + - + +
815A ALA 3.9 3.1 - - - +
817A TYR* 1.3 102.5 - - + +
819A THR* 1.3 63.5 + - + +
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Residues in contact with THR 819 (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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603A LEU* 3.8 27.0 - - + +
632A VAL* 4.3 14.6 - - + -
633A CYS* 4.5 12.6 - - - -
671A VAL* 4.3 9.0 - - + -
815A ALA* 2.9 21.1 + - - +
818A LYS* 1.3 79.1 - - + +
820A GLY* 1.3 56.9 + - - +
821A HIS* 3.0 45.5 + - - +
823A VAL* 4.0 1.0 - - - +
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Residues in contact with GLY 820 (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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601A ASN* 4.8 3.3 + - - -
753A PRO* 3.6 18.3 - - - +
816A ALA 2.7 19.9 + - - -
817A TYR 3.9 4.4 + - - -
818A LYS 3.5 1.8 - - - -
819A THR* 1.3 74.1 - - - +
821A HIS* 1.3 62.1 + - - +
822A PRO* 4.5 2.1 - - - +
95B LYS* 5.5 8.3 - - - -
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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