Contacts of the helix formed by residues 841 - 849 (chain D) in PDB entry 6M04
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 GLU 841 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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815D ALA* 4.7 7.0 - - + +
818D GLY* 3.7 23.6 - - - +
819D GLN* 5.9 4.0 - - - +
838D LEU* 3.4 39.7 + - + +
840D LEU* 1.3 89.5 + - - +
842D VAL* 1.3 60.8 + - + +
843D LYS 3.5 0.2 - - - -
844D GLU* 4.2 0.2 - - - +
845D ALA* 2.9 28.9 + - - +
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Residues in contact with VAL 842 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814D PRO 4.7 4.7 - - - +
817D LEU* 3.6 17.3 - - + +
818D GLY* 3.4 27.1 - - - +
834D LEU* 3.3 48.2 - - + +
835D PHE* 4.4 2.6 - - + -
837D THR 3.3 14.4 - - - +
838D LEU* 3.3 12.5 + - + +
841D GLU* 1.3 80.2 - - + +
843D LYS* 1.3 62.7 + - + +
845D ALA* 3.6 5.3 - - - +
846D LEU* 2.9 36.6 + - + +
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Residues in contact with LYS 843 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835D PHE* 3.3 52.2 + - + +
838D LEU 3.6 3.0 + - - +
839D PRO* 3.3 34.8 + - + +
841D GLU 3.5 0.6 - - - -
842D VAL* 1.3 76.8 - - + +
844D GLU* 1.3 60.9 + - - +
846D LEU 3.7 0.5 - - - -
847D ASN* 2.9 47.3 + - - +
778E ARG* 3.0 25.1 - - - +
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Residues in contact with GLU 844 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839D PRO 4.0 12.0 + - - +
840D LEU* 3.3 27.1 + - + +
841D GLU 3.8 1.2 + - - +
843D LYS* 1.3 76.7 - - - +
845D ALA* 1.3 58.2 + - - +
847D ASN* 4.5 5.5 + - - +
848D GLN* 2.9 63.3 + - - +
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Residues in contact with ALA 845 (chain D).
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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817D LEU 4.5 6.5 - - - +
818D GLY 3.8 16.8 - - - +
820D CYS 5.2 0.9 - - - -
821D ARG* 4.5 20.1 - - + +
841D GLU 2.9 21.2 + - - +
842D VAL* 3.6 9.0 - - - +
843D LYS 3.2 0.2 - - - -
844D GLU* 1.3 77.3 - - - +
846D LEU* 1.3 61.1 + - + +
847D ASN 3.1 0.2 - - - -
848D GLN* 3.8 2.4 - - - +
849D ASP* 3.0 38.0 + - - +
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Residues in contact with LEU 846 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817D LEU* 5.9 2.7 - - + +
820D CYS 5.4 3.4 - - - +
823D LEU* 5.3 2.9 - - + +
824D LYS 3.6 24.2 - - - +
825D LYS* 6.3 0.7 - - - +
830D VAL* 4.9 13.9 - - + -
834D LEU* 4.4 18.6 - - + -
835D PHE* 3.6 38.1 - - + -
842D VAL* 2.9 21.7 + - + +
843D LYS 3.7 0.9 - - - -
845D ALA* 1.3 75.0 - - + +
847D ASN* 1.3 57.1 + - - +
849D ASP* 3.9 19.7 - - + +
850D ILE* 3.5 19.2 - - - +
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Residues in contact with ASN 847 (chain D).
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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843D LYS* 2.9 33.2 + - - +
844D GLU* 4.2 5.4 + - - +
846D LEU* 1.3 78.0 - - - +
848D GLN* 1.3 60.7 + - + +
849D ASP 3.3 1.1 - - - -
850D ILE* 3.2 28.5 - - - +
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Residues in contact with GLN 848 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821D ARG* 4.3 27.4 + - - +
844D GLU* 2.9 47.3 + - - +
845D ALA* 4.1 2.5 - - - +
847D ASN* 1.3 74.2 - - + +
849D ASP* 1.3 65.4 + - - +
850D ILE* 3.2 2.6 - - - +
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Residues in contact with ASP 849 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820D CYS 4.1 0.3 - - - +
821D ARG* 2.9 51.6 + - - +
823D LEU 3.7 9.1 - - - +
824D LYS* 2.5 39.8 + - + +
845D ALA 3.0 24.8 + - - +
846D LEU* 3.9 18.9 - - + +
847D ASN 3.3 0.2 - - - -
848D GLN* 1.3 79.4 - - - +
850D ILE* 1.3 58.4 + - + +
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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
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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