Contacts of the helix formed by residues 41 - 52 (chain B) in PDB entry 3BGD
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 HIS 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B GLN* 3.2 27.5 + - - +
40B GLY* 1.3 70.2 - - - -
42B GLN* 1.3 61.6 + - - +
43B LEU* 3.5 26.6 + - + -
44B LEU* 3.4 23.9 + - + +
45B LYS* 3.1 26.0 + - - +
70B GLU* 2.7 18.6 + - - +
73B TRP* 3.7 5.9 - - - -
145B TRP* 3.7 27.7 - + + -
147B ARG* 3.7 23.5 + - + -
178B ALA* 4.3 4.6 - - + +
232B GLU* 2.8 37.4 + - - -
234B LEU* 5.3 0.4 - - + -
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Residues in contact with GLN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B GLN* 5.8 0.4 - - - -
39B GLN* 3.3 37.5 + - - +
40B GLY 3.0 22.5 + - - +
41B HIS* 1.3 73.9 + - - +
43B LEU* 1.3 67.3 + - + +
45B LYS* 3.5 26.3 + - - +
46B LYS* 3.3 20.8 + - - +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B HIS* 3.5 18.3 + - + -
42B GLN* 1.3 76.2 - - + +
44B LEU* 1.3 64.7 + - - +
45B LYS 3.2 0.9 - - - -
46B LYS* 3.4 5.4 + - + +
47B HIS* 2.9 32.9 + - + +
213B GLU* 3.8 32.8 - - + +
215B VAL* 4.3 22.4 - - + -
232B GLU* 3.8 32.5 - - + +
234B LEU* 4.3 31.6 - - + +
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B HIS* 3.4 17.9 + - + +
43B LEU* 1.3 78.1 - - - +
45B LYS* 1.3 64.0 + - - +
47B HIS* 3.1 2.3 + - - -
48B LEU* 2.9 43.7 + - + +
51B PHE* 4.7 1.1 - - + -
70B GLU* 3.7 33.2 - - + -
73B TRP* 4.1 8.1 - - + -
74B PHE* 4.0 18.8 - - + -
145B TRP* 3.8 38.5 - - + +
176B LEU* 3.9 26.5 - - + -
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Residues in contact with LYS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLN* 3.6 33.3 + - - +
41B HIS 3.1 14.6 + - - +
42B GLN* 3.5 28.0 - - - +
43B LEU 3.2 0.2 - - - -
44B LEU* 1.3 78.8 - - - +
46B LYS* 1.3 61.0 + - - +
47B HIS 3.3 0.9 + - - -
48B LEU* 3.7 13.5 + - - +
49B ASP 5.1 0.9 + - - -
73B TRP* 3.5 35.4 - - + -
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Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLN 3.3 12.7 + - - +
43B LEU* 3.4 9.2 + - + +
44B LEU 3.2 0.4 - - - -
45B LYS* 1.3 78.6 - - - +
47B HIS* 1.3 71.9 + - + +
48B LEU 3.6 0.4 - - - -
49B ASP* 5.4 0.5 + - - +
50B THR* 5.0 3.8 + - - -
213B GLU* 2.5 41.0 + - - +
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Residues in contact with HIS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU 2.9 24.9 - - - +
44B LEU* 3.1 7.1 + - - +
46B LYS* 1.3 97.6 + - + +
48B LEU* 1.3 59.3 + - - +
49B ASP 3.5 1.8 - - - -
50B THR* 3.4 6.5 + - - -
51B PHE* 2.8 29.7 + - - +
176B LEU* 4.7 3.8 - - + -
212B LEU* 3.7 13.7 - - + +
213B GLU* 2.9 38.2 + - + +
234B LEU* 3.6 20.6 - - + +
302B PM6 2.8 47.5 + + - -
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 2.9 24.2 + - + +
45B LYS* 3.7 9.6 + - + +
46B LYS 3.6 1.6 - - - -
47B HIS* 1.3 75.1 - - - +
49B ASP* 1.3 71.1 + - - +
51B PHE* 3.3 5.1 + - + +
52B LEU* 2.9 39.3 + - + +
73B TRP* 4.1 28.0 - - + -
74B PHE* 3.5 39.0 - - + -
77B ARG* 3.9 35.7 - - - +
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LYS 5.1 1.0 + - - -
46B LYS 5.4 0.8 + - - +
47B HIS 3.5 0.4 - - - -
48B LEU* 1.3 80.5 - - - +
50B THR* 1.3 58.6 + - - +
52B LEU* 3.5 3.9 + - - +
53B LYS* 2.9 28.2 + - - +
77B ARG* 5.1 8.7 + - - -
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Residues in contact with THR 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LYS 5.0 3.1 + - - -
47B HIS* 3.4 10.7 + - - -
48B LEU 3.2 0.4 - - - -
49B ASP* 1.3 75.6 - - - +
51B PHE* 1.3 64.7 + - - +
52B LEU 3.1 1.3 - - - -
53B LYS* 3.1 32.0 + - + +
174B GLN* 4.5 1.6 - - - +
302B PM6 3.3 51.9 + - + +
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Residues in contact with PHE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 4.7 0.7 - - + -
47B HIS 2.8 21.5 + - - +
48B LEU* 3.5 11.0 - - + +
50B THR* 1.3 73.2 - - - +
52B LEU* 1.3 58.7 + - + +
53B LYS 3.8 0.2 + - - -
60B VAL* 5.1 0.4 - - + -
74B PHE* 3.7 38.8 - + - -
143B ARG* 2.7 57.6 + - + -
144B ILE 3.7 23.6 - - - -
145B TRP* 4.8 3.6 - - + -
174B GLN* 3.6 42.0 - - + +
176B LEU* 3.5 38.1 - - + -
236B LEU* 4.6 0.2 - - + -
302B PM6 3.7 10.7 - - - -
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 2.9 38.3 + - + +
49B ASP* 3.5 3.6 - - - +
51B PHE* 1.3 81.2 - - + +
53B LYS* 1.3 67.6 + - - +
54B GLY 3.1 2.9 + - - -
55B GLN* 3.2 20.9 + - - +
58B LEU* 3.6 26.2 - - + -
74B PHE* 3.9 26.0 - - + -
77B ARG* 4.3 14.4 - - - -
79B HIS* 3.6 36.3 - - + +
143B ARG* 4.7 7.4 - - + +
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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