Contacts of the helix formed by residues 814 - 819 (chain F) 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 PRO 814 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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789F SER* 3.9 22.2 - - - +
790F LEU 4.0 7.6 - - - +
812F ARG* 3.8 4.0 - - + -
813F LEU* 1.3 94.2 - - - +
815F ALA* 1.3 61.9 + - - +
816F GLN* 3.2 20.2 - - + +
817F LEU* 3.1 41.8 + - + +
818F GLY 3.3 6.2 + - - -
838F LEU* 4.1 3.9 - - - +
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Residues in contact with ALA 815 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814F PRO* 1.3 73.6 - - - +
816F GLN* 1.3 65.9 + - - +
817F LEU 3.3 0.2 - - - -
818F GLY* 3.0 18.1 + - - +
819F GLN* 3.3 16.1 + - - +
838F LEU* 4.9 5.4 - - - -
841F GLU* 5.4 10.3 - - + +
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Residues in contact with GLN 816 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790F LEU 4.4 4.0 - - - +
791F PRO 3.8 4.0 - - - +
792F GLU* 3.3 46.3 + - - +
794F VAL* 3.6 26.2 - - + +
795F GLY* 4.0 6.8 + - - +
814F PRO* 3.5 21.1 - - + +
815F ALA* 1.3 79.8 + - - +
817F LEU* 1.3 63.9 + - - +
818F GLY 3.2 0.2 - - - -
819F GLN* 3.3 24.5 + - - +
820F CYS* 3.9 2.3 - - - -
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Residues in contact with LEU 817 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790F LEU* 3.8 20.2 - - + -
794F VAL* 3.7 25.1 - - + -
803F LEU* 4.7 8.1 - - + -
813F LEU* 4.0 30.1 - - + -
814F PRO* 3.1 35.0 + - + +
816F GLN* 1.3 75.7 - - - +
818F GLY* 1.3 64.2 + - - +
819F GLN 3.2 0.4 - - - -
820F CYS* 3.3 37.4 - - - +
829F VAL* 4.6 16.2 - - + -
834F LEU* 5.1 2.6 - - + +
838F LEU* 4.8 1.3 - - + -
842F VAL* 3.6 10.5 - - - +
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Residues in contact with GLY 818 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814F PRO 3.3 6.1 + - - -
815F ALA 3.0 12.3 + - - -
817F LEU* 1.3 77.9 - - - +
819F GLN* 1.3 59.9 + - - +
820F CYS 3.2 5.0 + - - -
821F ARG* 4.5 3.5 + - - +
838F LEU* 3.8 13.6 - - - +
841F GLU* 3.9 23.7 - - - +
842F VAL* 3.7 20.5 - - - +
845F ALA* 5.1 2.6 - - - +
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Residues in contact with GLN 819 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794F VAL 4.5 0.3 - - - +
795F GLY* 4.1 20.0 - - - +
798F SER* 5.8 4.0 - - - -
815F ALA 3.3 11.2 + - - +
816F GLN* 3.3 17.3 + - - +
817F LEU 3.2 1.0 - - - -
818F GLY* 1.3 78.1 + - - +
820F CYS* 1.3 59.0 + - - +
821F ARG* 3.5 19.2 + - - +
822F MET 5.4 0.2 + - - -
841F GLU* 4.9 11.3 - - - +
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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
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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