Contacts of the helix formed by residues 42 - 60 (chain N) in PDB entry 3LUE
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 ALA 42 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43N TRP* 1.3 79.3 + - - +
44N GLU* 3.1 6.4 + - - +
45N LYS* 3.2 10.2 + - - +
46N GLN* 2.7 38.4 + - + +
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Residues in contact with TRP 43 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E ARG 6.0 1.8 - - - -
92E ASN 4.6 8.3 - - - -
93E GLU* 4.2 22.7 - - - +
42N ALA* 1.3 88.9 - - - +
44N GLU* 1.3 89.0 + - + +
46N GLN* 3.6 8.8 - - - +
47N GLN* 2.8 77.9 + - + +
135N LYS* 4.7 27.6 - - + -
138N LEU* 5.1 5.4 - - + -
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Residues in contact with GLU 44 (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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42N ALA 3.1 4.0 - - - +
43N TRP* 1.3 109.1 + - + +
45N LYS* 1.3 62.1 + - - +
47N GLN* 4.6 1.6 - - - -
48N ARG* 3.1 25.7 + - - +
134N LEU* 3.2 37.2 - - + +
135N LYS* 3.7 31.7 + - + +
138N LEU* 3.9 11.7 - - + +
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Residues in contact with LYS 45 (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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42N ALA* 3.2 6.8 + - - +
44N GLU* 1.3 78.0 - - - +
46N GLN* 1.3 78.3 + - - +
48N ARG* 3.5 10.8 + - - +
49N LYS* 3.2 21.9 + - + +
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Residues in contact with GLN 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42N ALA* 2.7 40.0 + - + +
43N TRP* 3.3 7.6 + - - +
45N LYS* 1.3 90.9 - - - +
47N GLN* 1.3 66.8 + - - +
49N LYS* 2.9 18.4 + - - +
50N THR* 2.9 28.9 + - - +
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Residues in contact with GLN 47 (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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92E ASN 4.3 1.8 + - - +
93E GLU 4.4 2.0 + - - -
95E ARG* 2.3 61.6 + - + +
43N TRP* 2.8 56.2 + - - +
44N GLU 4.0 3.6 - - - +
46N GLN* 1.3 73.6 - - - +
48N ARG* 1.3 57.1 + - - +
50N THR* 4.6 3.8 - - - +
51N PHE* 2.9 52.7 + - + -
138N LEU* 4.0 15.4 - - + +
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Residues in contact with ARG 48 (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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44N GLU 3.1 18.6 + - - +
45N LYS* 3.6 11.1 + - - +
46N GLN 3.1 0.8 - - - -
47N GLN* 1.3 77.0 - - - +
49N LYS* 1.3 57.7 + - - +
51N PHE* 4.2 0.3 - - - +
52N THR* 2.5 41.0 + - - +
67N GLU 4.6 2.3 + - - -
68N ASN* 3.0 29.6 - - - +
69N ILE* 3.7 17.3 - - + +
70N GLU* 2.5 43.7 + - - -
134N LEU* 4.2 16.2 - - - -
138N LEU* 3.9 15.7 - - + +
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Residues in contact with LYS 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45N LYS* 3.2 9.6 + - + +
46N GLN* 2.9 19.1 + - - +
48N ARG* 1.3 81.8 - - - +
50N THR* 1.3 73.8 + - - +
52N THR* 3.6 4.8 - - - -
53N ALA* 3.0 30.8 + - + +
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Residues in contact with THR 50 (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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46N GLN* 2.9 17.4 + - - +
47N GLN* 4.1 4.7 - - - -
49N LYS* 1.3 89.6 + - - +
51N PHE* 1.3 68.6 + - + +
53N ALA* 3.3 6.5 + - - +
54N TRP* 2.9 30.5 + - + +
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Residues in contact with PHE 51 (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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95E ARG* 0.9 148.7 - - - -
47N GLN* 2.9 40.2 + - + +
50N THR* 1.3 81.1 - - + +
52N THR* 1.3 58.0 + - - +
54N TRP* 3.2 6.5 + - - +
55N CYS* 2.8 33.6 + - - -
69N ILE* 4.0 16.8 - - + -
138N LEU* 3.3 29.2 - - + -
141N ILE* 4.0 13.5 - - + -
142N TRP* 3.7 2.9 - + + -
145N ILE* 3.7 15.3 - - + -
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Residues in contact with THR 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48N ARG* 2.5 29.5 + - - +
49N LYS* 3.6 5.3 - - - -
51N PHE* 1.3 76.5 - - - +
53N ALA* 1.3 63.9 + - - +
55N CYS* 3.2 2.9 + - - +
56N ASN* 2.9 38.8 + - - +
66N ILE* 4.0 17.3 - - + +
67N GLU 4.0 20.7 + - - +
69N ILE* 3.6 24.9 + - + +
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Residues in contact with ALA 53 (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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49N LYS* 3.0 18.8 + - + +
50N THR* 3.6 6.1 - - - +
52N THR* 1.3 77.6 - - - +
54N TRP* 1.3 64.1 + - - +
56N ASN* 3.7 6.8 - - - +
57N SER* 3.0 23.9 + - - -
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Residues in contact with TRP 54 (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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50N THR* 2.9 17.8 + - + +
51N PHE* 3.5 9.2 - - - +
53N ALA* 1.3 76.9 - - - +
55N CYS* 1.3 85.3 + - - +
57N SER* 2.7 26.0 + - - -
58N HIS* 3.5 35.6 + + - -
82N LEU* 4.1 25.4 - - + -
86N ILE* 4.1 25.1 - - + -
141N ILE* 4.9 1.1 - - + -
144N ILE* 4.2 6.1 - - + -
145N ILE* 3.6 46.8 - - + +
148N PHE 5.8 0.4 - - - -
149N ALA* 4.2 24.8 - - + +
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Residues in contact with CYS 55 (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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51N PHE 2.8 27.3 + - - +
52N THR 3.6 4.0 - - - +
54N TRP* 1.3 82.8 - - - +
56N ASN* 1.3 59.0 + - - +
58N HIS* 3.1 5.9 + - - +
59N LEU* 2.9 34.4 + - + +
66N ILE* 4.1 15.3 - - + -
69N ILE* 4.7 2.0 - - - -
73N PHE* 3.9 13.9 - - + -
82N LEU* 3.7 26.5 - - + +
141N ILE* 3.8 31.2 - - - -
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Residues in contact with ASN 56 (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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52N THR* 2.9 25.7 + - - +
53N ALA* 3.7 7.2 - - - +
55N CYS* 1.3 73.5 - - - +
57N SER* 1.3 56.4 + - - +
58N HIS 3.0 5.6 - - - -
59N LEU* 4.2 3.9 - - - +
60N ARG* 3.0 18.6 + - - +
65N GLN* 2.7 49.6 + - - +
66N ILE* 2.7 54.0 - - - +
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Residues in contact with SER 57 (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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53N ALA 3.0 15.1 + - - -
54N TRP* 2.7 25.9 + - - -
56N ASN* 1.3 74.7 - - - +
58N HIS* 1.3 64.6 + - - +
60N ARG* 2.9 43.8 + - - +
61N LYS* 3.5 11.6 + - - -
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Residues in contact with HIS 58 (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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54N TRP* 3.5 57.2 + + - -
55N CYS 3.1 6.8 + - - +
56N ASN 3.0 0.4 - - - -
57N SER* 1.3 85.3 + - - +
59N LEU* 1.3 66.4 + - - +
60N ARG 3.1 2.0 - - - -
61N LYS* 3.0 47.4 + - - +
62N ALA 4.1 0.5 + - - -
82N LEU* 3.8 13.9 - - + -
85N VAL* 3.6 16.9 - - + +
86N ILE* 3.5 21.0 - - + +
149N ALA* 5.8 1.2 - - - +
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Residues in contact with LEU 59 (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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55N CYS* 2.9 23.9 + - + +
56N ASN* 4.2 11.0 - - - +
58N HIS* 1.3 76.6 - - - +
60N ARG* 1.3 53.6 + - - +
62N ALA* 2.7 29.3 + - - +
63N GLY 3.3 6.2 + - - -
64N THR* 3.3 35.2 + - + +
65N GLN* 4.2 1.8 - - - +
66N ILE* 3.8 29.6 - - + +
73N PHE* 4.4 13.2 - - + -
78N LYS* 3.6 13.0 - - + +
81N LEU* 4.3 8.5 - - + +
82N LEU* 3.6 35.7 - - + +
85N VAL* 5.0 2.0 - - + -
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Residues in contact with ARG 60 (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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56N ASN 3.0 18.3 + - - +
57N SER* 2.9 37.3 + - - +
59N LEU* 1.3 76.8 - - - +
61N LYS* 1.3 67.1 + - + +
63N GLY* 3.1 17.9 + - - +
64N THR 3.3 10.3 + - - +
65N GLN* 3.5 13.2 - - + +
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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