Contacts of the helix formed by residues 815 - 827 (chain A) in PDB entry 3H0G
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 THR 815 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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808A ASN* 4.1 16.4 - - - +
813A GLY 5.0 0.4 - - - +
814A LEU* 1.3 78.1 - - - +
816A PRO* 1.3 64.5 - - - -
817A GLN* 4.2 5.9 + - - +
818A GLU* 2.4 65.6 + - - +
819A PHE* 2.6 16.1 + - - -
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Residues in contact with PRO 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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814A LEU 4.2 2.4 - - - +
815A THR* 1.3 80.9 - - - +
817A GLN* 1.3 56.3 + - - +
818A GLU 2.3 18.2 + - - -
819A PHE* 2.6 25.1 + - + +
820A PHE* 3.7 7.4 + - - +
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Residues in contact with GLN 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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790A LEU* 5.3 5.4 - - + -
792A HIS* 2.7 50.5 + - + +
793A PHE* 2.6 43.8 - - + -
801A GLU 4.4 3.1 - - - +
802A SER 4.6 1.2 - - - +
815A THR* 3.3 6.0 + - - +
816A PRO* 1.3 77.3 - - - +
818A GLU* 1.3 59.2 + - + +
820A PHE* 5.2 0.9 - - - -
821A PHE* 2.8 32.3 - - - -
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Residues in contact with GLU 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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802A SER 6.0 1.3 - - - +
805A PHE 4.0 10.1 - - - +
806A ILE* 3.1 55.4 - - + +
807A GLU* 3.9 8.1 + - - +
808A ASN* 4.8 2.2 + - - +
813A GLY 4.8 0.3 - - - +
814A LEU* 4.1 2.1 - - - -
815A THR* 2.4 50.5 + - - +
816A PRO 2.3 12.9 + - - -
817A GLN* 1.3 74.3 - - + +
819A PHE* 1.3 61.5 + - - +
820A PHE 3.2 2.5 - - - -
821A PHE* 3.0 21.4 + - + +
822A HIS* 3.2 10.7 + - - +
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Residues in contact with PHE 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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814A LEU* 4.0 22.0 - - + +
815A THR 2.6 14.8 + - - +
816A PRO* 2.6 17.5 + - + +
818A GLU* 1.3 71.1 - - - +
820A PHE* 1.3 62.3 + + + +
822A HIS* 3.5 10.5 - + - +
823A ALA* 3.2 32.0 + - + +
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Residues in contact with PHE 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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790A LEU* 4.9 26.0 - - + -
816A PRO 3.7 7.1 + - - +
817A GLN 5.7 0.2 - - - -
819A PHE* 1.3 83.2 - + + +
821A PHE* 1.3 76.4 + + + +
822A HIS 2.9 1.3 - - - -
823A ALA* 2.8 19.8 + - + +
824A MET* 3.0 40.8 + - + +
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Residues in contact with PHE 821 (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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774A GLN* 4.6 3.9 - - + +
781A ILE* 2.8 40.5 - - + +
789A THR* 3.0 25.6 - - + -
790A LEU* 3.5 28.5 - - + -
793A PHE* 4.3 4.0 - + - -
802A SER 3.2 17.3 - - - -
804A GLY* 3.2 30.7 - - - -
805A PHE 5.1 1.8 - - - +
806A ILE* 6.2 1.1 - - + -
817A GLN 2.8 31.2 - - - -
818A GLU* 3.0 9.7 + - - +
820A PHE* 1.3 81.6 - + + +
822A HIS* 1.3 61.9 + - - +
824A MET* 3.3 11.9 - - - +
825A ALA* 3.3 21.0 + - - +
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Residues in contact with HIS 822 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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771A VAL* 5.2 2.1 - - + +
774A GLN* 4.0 29.6 + - + +
806A ILE* 4.3 8.1 - - + -
810A TYR* 3.8 31.7 + + - -
814A LEU* 4.0 26.5 - - + -
818A GLU 3.2 3.9 + - - +
819A PHE* 3.5 16.2 - + - +
820A PHE 2.8 3.4 + - - -
821A PHE* 1.3 75.4 - - - +
823A ALA* 1.3 62.2 + - - +
825A ALA* 3.2 2.6 + - - +
826A GLY* 2.9 28.8 + - - -
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Residues in contact with ALA 823 (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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819A PHE* 3.2 23.5 + - + +
820A PHE* 2.8 18.3 + - + +
822A HIS* 1.3 79.4 - - + +
824A MET* 1.3 55.4 + - - +
826A GLY* 3.4 2.7 + - - +
827A ARG* 3.1 30.2 + - - +
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Residues in contact with MET 824 (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 VAL* 5.2 11.4 - - + +
781A ILE* 3.5 32.8 - - + -
782A PRO* 4.9 7.2 - - + -
820A PHE* 3.0 40.6 + - + +
821A PHE* 3.3 17.5 - - - +
823A ALA* 1.3 75.6 - - + +
825A ALA* 1.3 63.6 + - - +
826A GLY 3.2 0.9 - - - -
827A ARG* 3.8 13.6 + - - +
828A GLU* 4.2 8.1 + - - +
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Residues in contact with ALA 825 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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774A GLN* 3.6 33.2 - - + +
775A ILE* 3.4 34.4 - - + +
776A VAL* 5.4 0.4 - - - -
821A PHE 3.3 10.5 + - - +
822A HIS* 3.2 5.0 + - - +
824A MET* 1.3 77.3 - - + +
826A GLY* 1.3 65.5 + - - +
827A ARG 3.2 0.4 - - - -
828A GLU* 3.2 19.3 + - - +
829A GLY 3.9 3.1 + - - -
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Residues in contact with GLY 826 (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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822A HIS* 2.9 19.9 + - - -
823A ALA* 3.4 4.7 + - - -
824A MET 3.2 0.2 - - - -
825A ALA* 1.3 75.3 - - - +
827A ARG* 1.3 56.4 + - - +
828A GLU 3.0 10.2 + - - -
829A GLY* 3.6 3.6 + - - -
830A LEU* 3.1 20.8 + - - +
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Residues in contact with ARG 827 (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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823A ALA* 3.1 18.6 + - - +
824A MET* 3.8 10.2 - - - +
825A ALA 3.2 1.2 - - - -
826A GLY* 1.3 74.9 - - - +
828A GLU* 1.3 58.1 + - - +
830A LEU* 3.5 26.7 - - + +
831A ILE* 3.6 28.6 - - + +
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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