Contacts of the helix formed by residues 845 - 855 (chain N) in PDB entry 4G7Z
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 ASN 845 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83L LYS 5.6 1.0 + - - -
84L GLU* 3.5 33.3 - - - +
175L ARG* 4.6 19.0 + - - +
843N PHE* 4.1 1.0 - - - +
844N ALA* 1.3 78.7 - - - +
846N PRO* 1.3 76.2 - - + +
847N ASP* 3.5 11.8 + - + +
848N GLU* 2.8 43.7 + - - +
849N ALA* 3.4 8.0 + - - +
866N VAL* 4.0 10.0 - - - +
867N ARG 3.7 3.4 - - - -
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Residues in contact with PRO 846 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845N ASN* 1.3 87.0 - - + +
847N ASP* 1.3 73.0 + - - +
849N ALA* 3.1 6.2 + - + +
850N LEU* 3.1 29.2 + - + +
866N VAL* 4.3 6.7 - - + -
867N ARG 4.2 9.4 - - - +
868N TYR* 4.6 23.1 - - + -
880N ILE* 3.7 28.9 - - + -
884N ARG* 5.7 7.4 - - + +
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Residues in contact with ASP 847 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175L ARG* 3.3 57.0 - - + +
176L ARG* 4.6 6.9 - - - +
200L TRP* 5.4 1.0 - - - +
845N ASN* 3.3 10.9 + - - +
846N PRO* 1.3 85.9 - - - +
848N GLU* 1.3 58.3 + - - +
850N LEU* 3.2 7.8 + - - +
851N LEU* 2.8 29.0 + - - +
884N ARG* 5.0 10.6 + - - +
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Residues in contact with GLU 848 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83L LYS* 3.1 28.2 + - - +
150L TYR* 3.0 34.1 + - + -
168L ASP* 4.3 0.2 - - - +
170L VAL* 3.9 15.6 - - + +
175L ARG* 6.0 1.1 - - - +
843N PHE* 3.6 12.4 - - + -
844N ALA* 2.6 41.7 + - - +
845N ASN* 2.8 23.0 + - - +
846N PRO 3.2 0.2 - - - -
847N ASP* 1.3 69.8 - - - +
849N ALA* 1.3 66.5 + - - +
851N LEU* 3.0 11.1 + - - +
852N ALA* 2.9 21.5 + - - +
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Residues in contact with ALA 849 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843N PHE* 3.7 34.7 - - + -
845N ASN 3.4 4.4 + - - +
846N PRO* 3.1 11.5 + - + +
848N GLU* 1.3 78.5 - - - +
850N LEU* 1.3 66.2 + - + +
852N ALA* 3.1 6.6 + - - +
853N VAL* 3.0 30.2 + - - +
858N VAL* 4.3 1.4 - - - +
866N VAL* 4.0 16.6 - - + -
877N PRO* 4.8 9.0 - - + -
880N ILE* 5.8 2.2 - - + -
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Residues in contact with LEU 850 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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846N PRO* 3.1 19.0 + - + +
847N ASP* 3.8 6.1 - - - +
849N ALA* 1.3 74.4 - - + +
851N LEU* 1.3 60.2 + - - +
853N VAL* 3.6 8.4 + - + +
854N ALA* 3.1 25.8 + - - +
860N LEU* 4.5 7.2 - - + -
877N PRO* 3.7 38.1 - - + +
880N ILE* 5.3 4.3 - - + -
881N LEU* 4.1 20.4 - - + +
884N ARG* 3.1 41.3 - - + +
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Residues in contact with LEU 851 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L LEU* 3.9 33.7 - - + +
149L GLY 4.8 6.3 - - - +
150L TYR* 4.1 25.1 - - + -
170L VAL* 4.5 16.2 - - + -
172L SER* 4.9 7.9 - - - +
174L VAL 4.7 12.3 - - - +
175L ARG* 5.7 4.3 - - - +
847N ASP 2.8 14.3 + - - +
848N GLU* 3.0 13.0 + - - +
850N LEU* 1.3 76.0 - - - +
852N ALA* 1.3 63.8 + - - +
854N ALA* 3.2 10.8 + - + +
855N HIS* 2.8 52.5 + - + -
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Residues in contact with ALA 852 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150L TYR* 4.1 12.3 - - + -
843N PHE* 3.5 32.5 - - + -
848N GLU 2.9 6.9 + - - +
849N ALA 3.1 10.1 + - - +
851N LEU* 1.3 74.5 - - - +
853N VAL* 1.3 66.4 + - - +
855N HIS 3.0 10.6 + - - -
857N ILE* 3.0 42.2 + - + +
858N VAL* 3.9 3.4 - - + -
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Residues in contact with VAL 853 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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849N ALA 3.0 17.1 + - - +
850N LEU* 3.7 11.0 - - + +
852N ALA* 1.3 74.2 - - - +
854N ALA* 1.3 61.7 + - - +
856N GLY* 3.1 11.6 + - - -
858N VAL* 3.3 31.2 - - + +
859N ASP* 4.2 6.1 - - - +
860N LEU* 3.9 26.5 - - + +
877N PRO* 3.6 29.2 - - + -
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Residues in contact with ALA 854 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L ARG* 5.1 8.5 - - - +
45L LEU* 4.6 17.3 - - + -
850N LEU 3.1 15.2 + - - +
851N LEU* 3.3 18.4 - - + +
852N ALA 3.1 0.4 - - - -
853N VAL* 1.3 78.3 - - - +
855N HIS* 1.3 63.9 + - + +
856N GLY 3.4 0.4 + - - -
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Residues in contact with HIS 855 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ARG* 3.6 40.7 + - - +
45L LEU* 3.2 28.5 + - + -
46L SER* 4.2 11.5 - - - -
149L GLY* 4.1 4.2 - - - -
150L TYR* 3.8 35.0 + - + +
851N LEU* 2.8 35.9 + - + +
852N ALA 3.0 3.0 + - - +
854N ALA* 1.3 81.1 - - + +
856N GLY* 1.3 62.0 + - - +
857N ILE* 3.2 25.8 - - + +
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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