Contacts of the helix formed by residues 805 - 818 (chain A) in PDB entry 4FYT
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 GLY 805 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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801A ILE* 5.1 2.0 - - - +
804A GLY* 1.3 76.2 - - - -
806A GLU* 1.3 66.5 + - - -
807A GLU 3.2 4.1 + - - -
808A GLU* 2.8 12.8 + - - +
809A TRP* 3.1 21.9 + - - +
837A GLU* 3.7 15.0 - - - -
840A ILE* 4.9 1.1 - - - -
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Residues in contact with GLU 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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805A GLY* 1.3 72.1 - - - -
807A GLU* 1.3 56.6 + - - +
809A TRP* 3.3 6.0 + - - +
810A ASP* 2.9 54.3 + - - +
837A GLU* 4.0 5.6 + - - +
839A TRP* 3.5 39.2 - - + -
840A ILE* 4.4 5.8 - - + -
843A ARG* 4.7 4.6 + - - +
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Residues in contact with GLU 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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780A MET* 3.7 20.8 - - + +
805A GLY 3.2 1.0 - - - -
806A GLU* 1.3 78.7 - - - +
808A GLU* 1.3 72.3 + - - +
810A ASP* 3.6 5.4 + - - +
811A PHE* 3.1 24.1 + - - +
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Residues in contact with GLU 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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776A PHE* 3.9 33.1 - - + -
780A MET* 4.1 12.9 - - - +
800A ALA* 4.2 17.7 - - + +
801A ILE* 4.6 8.3 - - - -
804A GLY* 4.0 6.5 - - - -
805A GLY* 2.8 35.4 + - - +
807A GLU* 1.3 83.5 + - - +
809A TRP* 1.3 64.9 + - - +
811A PHE* 3.4 2.4 + - - +
812A ALA* 3.0 24.6 + - - +
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Residues in contact with TRP 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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801A ILE* 3.9 21.7 - - + +
805A GLY 3.1 13.9 + - - +
806A GLU* 3.7 10.8 - - - +
808A GLU* 1.3 76.3 - - - +
810A ASP* 1.3 61.9 + - - +
812A ALA* 3.2 2.1 + - - -
813A TRP* 2.8 54.7 + + + -
832A LEU* 2.8 46.7 + - + +
835A SER* 4.0 4.0 - - - -
840A ILE* 3.4 30.6 - - + +
843A ARG* 3.5 26.9 - - - +
844A TYR* 3.6 42.4 - + + -
847A TYR* 4.0 18.6 - + - -
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Residues in contact with ASP 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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806A GLU* 2.9 35.7 + - - +
807A GLU* 4.0 5.6 - - - +
809A TRP* 1.3 80.2 - - - +
811A PHE* 1.3 63.6 + - - +
813A TRP* 3.4 5.5 + - - +
814A GLU* 3.0 30.7 + - + +
843A ARG* 3.3 28.9 + - - -
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Residues in contact with PHE 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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776A PHE* 3.9 11.9 - + - -
779A TRP* 3.6 45.1 - + - -
780A MET* 3.5 53.6 - - + -
783A PRO* 4.1 15.5 - - + -
807A GLU 3.1 18.9 + - - +
808A GLU 3.6 3.8 - - - +
810A ASP* 1.3 75.5 - - - +
812A ALA* 1.3 58.8 + - - +
814A GLU* 3.3 6.8 + - + +
815A GLN* 3.0 56.2 + - + +
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Residues in contact with ALA 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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776A PHE* 4.3 8.7 - - + -
801A ILE* 3.7 16.2 - - + -
808A GLU 3.0 16.5 + - - +
809A TRP 3.7 3.6 - - - +
811A PHE* 1.3 80.9 - - - +
813A TRP* 1.3 57.4 + - - +
815A GLN* 3.3 4.2 + - - +
816A PHE* 2.8 28.2 + - - +
828A LEU* 3.9 25.4 - - + +
832A LEU* 3.7 17.0 - - + -
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Residues in contact with TRP 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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809A TRP* 2.8 44.1 + + + +
810A ASP* 3.7 7.0 - - - +
812A ALA* 1.3 75.2 - - - +
814A GLU* 1.3 76.1 + - - +
816A PHE* 3.2 30.0 + + - +
817A ARG* 2.9 63.0 + - + +
832A LEU* 3.7 20.7 - - + +
844A TYR* 3.9 18.6 - + - -
847A TYR* 3.5 41.3 + + + -
853A LEU* 4.1 22.4 - - + -
854A ILE* 4.4 3.4 - - + -
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Residues in contact with GLU 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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810A ASP* 3.0 20.7 + - + +
811A PHE* 3.3 5.8 + - + +
813A TRP* 1.3 94.6 + - - +
815A GLN* 1.3 65.6 + - + +
817A ARG* 3.2 19.4 + - - +
818A ASN* 3.0 27.5 + - - +
1011A NAG 6.5 0.4 - - + -
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Residues in contact with GLN 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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779A TRP* 3.6 24.6 + - + -
783A PRO* 4.1 16.1 + - - +
811A PHE* 3.0 53.5 + - + +
812A ALA 3.5 8.1 - - - +
814A GLU* 1.3 77.3 - - - +
816A PHE* 1.3 61.2 + - - +
818A ASN* 3.4 8.2 + - - +
819A ALA* 3.1 24.4 + - - +
828A LEU* 3.8 18.1 - - + +
1011A NAG 4.4 13.1 + - - -
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Residues in contact with PHE 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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812A ALA 2.8 13.9 + - - +
813A TRP* 3.2 37.9 + + - +
815A GLN* 1.3 75.5 - - - +
817A ARG* 1.3 68.6 + - - +
819A ALA* 3.1 19.1 + - - +
825A ALA* 3.3 43.0 - - + +
828A LEU* 3.6 15.1 - - + +
829A ARG* 3.8 33.4 - - + -
832A LEU* 4.4 5.6 - - + -
853A LEU 3.5 26.0 - - - -
854A ILE* 4.1 9.0 - - + -
855A ARG 5.7 0.9 - - - -
858A ASP* 5.9 1.3 - - - -
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Residues in contact with ARG 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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813A TRP* 2.9 60.9 + - + +
814A GLU* 3.2 20.9 + - - +
816A PHE* 1.3 82.5 - - + +
818A ASN* 1.3 60.2 + - - +
819A ALA 3.7 1.0 + - - +
852A ASP 4.6 8.5 + - - -
853A LEU* 3.6 33.8 - - - +
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Residues in contact with ASN 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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814A GLU 3.0 17.6 + - - +
815A GLN* 3.6 8.9 + - - +
817A ARG* 1.3 75.2 - - - +
819A ALA* 1.3 65.5 + - - +
820A THR* 3.5 10.0 + - - +
1011A NAG 1.4 68.0 + - - +
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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