Contacts of the helix formed by residues 799 - 813 (chain A) in PDB entry 4U6R
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 799 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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796A HIS* 3.5 27.7 + - + +
798A GLU* 1.3 77.8 - - - +
800A HIS* 1.3 66.5 + - - +
801A GLU* 3.3 16.2 - - - +
802A ASP* 3.0 28.8 + - - +
803A VAL* 2.9 24.8 + - - +
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Residues in contact with HIS 800 (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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799A LYS* 1.3 71.7 - - - +
801A GLU* 1.3 81.5 + - + +
803A VAL* 3.3 1.9 + - - +
804A ILE* 3.0 45.3 + - + +
835A LEU* 5.9 3.6 - - + -
838A GLN* 2.9 31.6 + - - -
934A THR* 3.5 49.6 + - + +
935A SER* 4.9 2.4 - - - +
937A PHE 5.2 0.2 + - - -
938A PRO* 3.6 25.1 + - - +
941A LEU* 3.6 33.3 + - + +
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Residues in contact with GLU 801 (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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799A LYS* 4.0 18.1 - - - +
800A HIS* 1.3 101.6 + - + +
802A ASP* 1.3 62.2 + - - +
804A ILE* 4.0 4.9 - - - +
805A ALA* 3.1 27.0 + - - +
831A PHE* 5.3 2.1 - - - -
931A CYS* 6.1 1.0 - - - -
934A THR* 5.4 0.9 + - - -
935A SER* 6.1 0.5 - - - -
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Residues in contact with ASP 802 (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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794A CYS 3.8 5.2 - - - +
795A LEU* 3.7 27.7 - - - +
796A HIS* 2.9 47.8 + - - +
799A LYS* 3.0 22.6 + - + +
801A GLU* 1.3 82.4 - - - +
803A VAL* 1.3 59.1 + - - +
805A ALA* 3.6 1.6 - - - +
806A ARG* 2.8 30.2 + - - +
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Residues in contact with VAL 803 (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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796A HIS 3.9 1.8 - - - +
797A PRO* 3.4 33.4 - - + +
798A GLU* 4.5 0.9 - - - -
799A LYS 2.9 22.9 + - - +
800A HIS 3.7 4.7 - - - +
802A ASP* 1.3 73.8 - - - +
804A ILE* 1.3 65.1 + - - +
806A ARG* 3.4 9.8 + - - +
807A GLU* 3.0 24.1 + - + +
938A PRO 3.8 15.7 - - - +
939A HIS* 3.8 28.5 - - + +
942A ALA* 4.0 17.0 - - + -
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Residues in contact with ILE 804 (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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800A HIS* 3.0 37.6 + - + +
801A GLU* 4.0 5.8 - - - +
803A VAL* 1.3 76.2 - - + +
805A ALA* 1.3 63.6 + - - +
807A GLU* 3.4 3.2 + - - +
808A LEU* 3.3 16.8 + - - +
829A HIS* 3.4 13.9 - - + -
830A PRO* 3.7 14.1 - - + +
831A PHE* 3.3 37.5 - - + +
938A PRO 5.7 0.4 - - - +
941A LEU* 3.8 18.4 - - + -
942A ALA* 3.6 37.2 - - + +
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Residues in contact with ALA 805 (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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768A ILE* 3.9 19.7 - - + -
795A LEU* 4.2 7.2 - - + -
801A GLU 3.1 19.7 + - - +
802A ASP 3.6 5.2 - - - +
804A ILE* 1.3 77.6 - - - +
806A ARG* 1.3 56.5 + - - +
808A LEU* 3.4 3.5 + - - +
809A ILE* 2.9 35.9 + - + +
831A PHE* 3.9 30.0 - - + -
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Residues in contact with ARG 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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792A LEU* 3.2 26.4 + - + +
793A ASP 5.2 0.2 + - - -
795A LEU* 2.9 43.4 + - + +
796A HIS 5.3 1.2 + - - -
797A PRO* 5.2 12.1 - - - +
802A ASP 2.8 18.1 + - - +
803A VAL* 3.7 10.7 - - - +
805A ALA* 1.3 73.8 - - - +
807A GLU* 1.3 66.6 + - - +
809A ILE* 4.5 2.2 - - - +
810A GLU* 2.9 46.4 + - - +
1002A SO4 2.9 44.0 + - - -
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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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803A VAL* 3.0 18.0 + - + +
804A ILE* 3.7 7.0 - - - +
805A ALA 3.3 0.2 - - - -
806A ARG* 1.3 76.2 - - - +
808A LEU* 1.3 62.2 + - - +
810A GLU* 3.9 12.1 - - - +
811A LYS* 2.9 51.1 + - - +
829A HIS* 2.7 34.9 + - + +
942A ALA* 4.5 16.4 - - + -
945A TYR* 4.8 6.1 - - - -
946A ARG* 3.1 41.8 + - + +
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Residues in contact with LEU 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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764A PHE* 3.7 28.5 - - + -
804A ILE 3.3 4.3 + - - +
805A ALA 3.7 6.5 - - - +
806A ARG 3.2 0.4 - - - -
807A GLU* 1.3 79.0 + - - +
809A ILE* 1.3 66.4 + - + +
811A LYS* 3.1 7.8 + - + +
812A MET* 3.0 43.6 + - + +
821A PRO* 4.7 6.7 - - + -
826A VAL* 4.2 19.1 - - + -
829A HIS* 3.5 40.4 - - + +
831A PHE* 3.7 29.6 - - + -
832A PHE* 4.7 0.2 - - + -
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Residues in contact with ILE 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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761A GLY 3.8 16.2 - - - +
764A PHE* 4.0 25.4 - - + -
765A TYR* 3.9 24.7 - - + +
768A ILE* 3.6 30.3 - - + -
792A LEU* 4.2 26.9 - - + -
795A LEU* 4.7 2.2 - - + -
805A ALA* 2.9 23.2 + - + +
806A ARG 4.2 1.8 - - - +
808A LEU* 1.3 79.7 - - + +
810A GLU* 1.3 64.3 + - - +
812A MET* 3.2 8.1 + - - +
813A ILE* 3.0 29.5 + - + +
831A PHE* 5.4 2.0 - - + -
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Residues in contact with GLU 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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792A LEU* 4.3 10.9 - - + +
806A ARG* 2.9 43.7 + - - +
807A GLU* 3.9 13.9 - - - +
809A ILE* 1.3 77.1 - - - +
811A LYS* 1.3 64.6 + - + +
813A ILE* 3.8 12.2 + - + +
814A ALA* 3.3 23.2 + - - +
946A ARG* 4.6 11.4 + - - -
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Residues in contact with LYS 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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807A GLU* 2.9 38.8 + - - +
808A LEU* 3.1 9.9 + - + +
810A GLU* 1.3 82.6 - - + +
812A MET* 1.3 63.7 + - - +
813A ILE 3.2 1.8 - - - -
814A ALA* 3.2 16.3 + - + +
819A LYS* 4.3 11.9 - - + +
820A ARG* 3.3 18.5 - - - +
821A PRO* 3.9 16.4 - - + -
829A HIS* 6.5 0.2 - - + -
946A ARG* 4.1 21.2 - - - +
949A GLU* 5.8 2.0 + - - -
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Residues in contact with MET 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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673A THR* 5.6 0.9 - - + +
757A ILE* 3.4 25.6 - - + +
758A PHE* 3.2 21.7 + - - -
760A ALA* 3.9 8.5 - - + -
761A GLY* 3.6 31.2 - - - +
764A PHE* 3.7 35.9 - - + -
808A LEU* 3.0 43.5 + - + +
809A ILE* 3.6 9.2 - - - +
811A LYS* 1.3 75.5 - - - +
813A ILE* 1.3 58.1 + - - +
814A ALA 3.4 0.2 - - - -
820A ARG* 3.3 11.6 - - - -
821A PRO* 4.0 7.4 - - + -
826A VAL* 4.1 13.7 - - + -
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Residues in contact with ILE 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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758A PHE* 3.6 29.8 - - + +
761A GLY* 3.6 34.1 - - - +
762A CYS* 3.7 12.1 - - - +
774A PRO* 3.9 27.8 - - + -
775A PHE* 4.2 10.8 - - + -
790A CYS* 4.2 19.5 - - - -
792A LEU* 4.4 4.7 - - + -
809A ILE* 3.0 25.2 + - + +
810A GLU* 3.9 11.0 - - - +
812A MET* 1.3 74.4 - - - +
814A ALA* 1.3 67.6 + - - +
815A MET* 3.5 5.7 + - - +
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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