Contacts of the helix formed by residues 44 - 57 (chain N) in PDB entry 5NO6
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 SER 44 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40N GLU* 5.0 5.8 - - - +
41N GLY 3.9 10.5 + - - +
42N VAL 2.9 13.0 + - - -
43N TRP* 1.3 77.7 - - - +
45N PRO* 1.3 65.7 - - - +
46N ASP* 3.1 27.5 + - - -
47N ILE* 2.8 19.5 + - - +
48N GLU 2.8 21.0 + - - -
91N LYS* 5.6 3.3 - - - -
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Residues in contact with PRO 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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40N GLU* 3.1 34.1 - - + +
43N TRP 3.5 1.3 - - - +
44N SER* 1.3 88.2 - - - +
46N ASP* 1.3 62.1 + - - +
48N GLU* 3.4 10.5 - - + +
49N GLN* 3.0 31.8 + - - +
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Residues in contact with ASP 46 (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 SER* 3.1 22.8 + - - -
45N PRO* 1.3 82.5 - - - +
47N ILE* 1.3 68.6 + - - +
49N GLN* 3.2 25.8 + - - +
50N SER* 3.6 8.7 + - - -
89N THR* 4.2 9.4 - - + +
91N LYS* 5.8 3.5 - - - +
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Residues in contact with ILE 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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42N VAL 3.9 15.5 - - - +
43N TRP* 3.9 26.7 - - + -
44N SER* 2.8 34.0 + - - +
46N ASP* 1.3 77.0 - - - +
48N GLU* 1.3 68.1 + - - +
50N SER* 2.8 14.6 + - - -
51N PHE* 2.9 10.2 + - - +
85N ILE* 3.9 25.4 - - + -
89N THR* 4.2 15.7 - - + -
91N LYS* 4.5 28.0 - - + -
93N ARG* 4.5 17.5 - - + +
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Residues in contact with GLU 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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43N TRP* 4.0 13.4 + - - +
44N SER 2.8 12.2 + - - +
45N PRO* 3.4 15.5 - - + +
47N ILE* 1.3 75.0 - - - +
49N GLN* 1.3 56.9 + - - +
51N PHE* 2.8 13.9 + - - +
52N GLN* 2.8 51.1 + - + +
101N HIS* 2.4 42.3 + - - -
105N LEU* 4.4 6.1 - - - +
108N ARG* 5.8 2.1 + - - -
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Residues in contact with GLN 49 (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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45N PRO 3.0 16.3 + - - +
46N ASP* 3.2 25.2 - - - +
48N GLU* 1.3 74.4 - - - +
50N SER* 1.3 57.7 + - - +
52N GLN* 3.0 13.0 + - + +
53N GLU* 2.8 47.0 + - - +
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Residues in contact with SER 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 ASP 3.6 2.8 + - - -
47N ILE* 2.8 13.7 + - - -
49N GLN* 1.3 78.0 + - - +
51N PHE* 1.3 55.6 + - - +
53N GLU* 3.4 10.9 + - - -
54N ALA* 2.8 31.0 + - - +
84N TYR* 3.6 7.5 - - - -
85N ILE* 4.5 14.4 - - - -
88N ARG* 3.2 30.8 - - - +
89N THR* 3.6 21.9 - - - +
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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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43N TRP* 4.0 18.6 - + + -
47N ILE 2.9 9.3 + - - +
48N GLU* 2.8 13.4 + - - +
50N SER* 1.3 77.3 - - - +
52N GLN* 1.3 69.8 + - - -
54N ALA* 3.3 5.6 + - - +
55N LEU* 2.8 62.1 + - + +
81N ILE* 3.8 20.0 - - + -
85N ILE* 4.6 4.4 - - + +
98N VAL* 4.2 14.6 - - + -
101N HIS* 3.6 28.9 - + - -
102N ILE* 3.6 31.2 - - + -
105N LEU* 3.8 21.8 - - + -
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Residues in contact with GLN 52 (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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48N GLU* 2.8 47.4 + - + +
49N GLN* 3.0 11.0 + - - +
51N PHE* 1.3 81.3 - - - +
53N GLU* 1.3 65.5 + - - +
55N LEU* 3.9 18.1 - - - +
56N ALA* 3.6 18.5 + - - +
105N LEU* 4.8 6.9 - - - +
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Residues in contact with GLU 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 GLN* 2.8 33.6 + - + +
50N SER* 3.7 8.3 + - - +
52N GLN* 1.3 72.3 - - - +
54N ALA* 1.3 67.4 + - - +
56N ALA* 2.8 7.3 + - - +
57N ILE* 2.8 31.7 + - + +
84N TYR* 2.7 40.0 + - + +
88N ARG* 3.5 25.8 + - - +
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Residues in contact with ALA 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 SER 2.8 21.5 + - - +
51N PHE* 3.5 5.4 - - - +
53N GLU* 1.3 71.0 - - - +
55N LEU* 1.3 53.8 + - - +
57N ILE* 3.3 12.1 - - - +
58N TYR* 2.8 41.6 + - + +
81N ILE* 3.8 37.5 - - + +
84N TYR* 3.7 16.5 - - + -
85N ILE* 5.5 0.4 - - + -
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Residues in contact with LEU 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 58.9 + - + +
52N GLN* 3.9 18.6 - - - +
53N GLU 2.9 0.6 + - - -
54N ALA* 1.3 70.9 - - - +
56N ALA* 1.3 56.5 + - - +
58N TYR 3.0 1.2 + - - -
59N PRO* 2.8 42.0 - - - +
77N ARG* 3.4 32.1 - - - +
81N ILE* 3.7 13.9 - - + -
102N ILE* 5.0 5.2 - - + -
105N LEU* 6.1 0.2 - - + -
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Residues in contact with ALA 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 GLN 3.6 15.6 + - - +
53N GLU* 2.8 9.5 + - - +
55N LEU* 1.3 77.9 - - - +
57N ILE* 1.3 63.0 + - + +
58N TYR 3.8 0.2 + - - -
59N PRO 3.9 15.7 - - - -
60N PRO* 3.9 13.3 - - - +
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Residues in contact with ILE 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 GLU* 2.8 35.2 + - + +
54N ALA* 3.3 18.8 - - - +
56N ALA* 1.3 74.7 - - + +
58N TYR* 1.3 75.0 + - + +
84N TYR* 4.1 27.4 - - + +
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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