Contacts of the helix formed by residues 45 - 57 (chain N) in PDB entry 3Q2K
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 45 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43N ASP* 2.9 15.8 + - - +
44N THR* 1.3 78.5 - - - +
46N PRO* 1.3 59.7 - - - +
47N GLU* 2.8 18.0 + - - +
48N ALA* 2.8 26.0 + - + -
49N LEU* 2.8 35.0 + - - +
500N NAI 3.5 13.7 + - - +
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Residues in contact with PRO 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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43N ASP 5.4 0.2 - - - +
44N THR 3.7 7.8 - - - +
45N ASN* 1.3 87.4 - - - +
47N GLU* 1.3 68.9 + - + +
49N LEU* 3.8 9.3 - - + +
50N GLN* 2.8 35.0 + - - +
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Residues in contact with GLU 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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45N ASN* 2.8 18.6 + - - +
46N PRO* 1.3 77.3 - - + +
48N ALA* 1.3 55.4 + - - +
50N GLN* 3.3 12.1 - - - +
51N ALA* 2.9 29.2 + - - +
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Residues in contact with ALA 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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18N CYS* 3.7 24.2 - - - +
19N GLY* 5.5 0.2 - - - -
43N ASP* 4.0 11.7 - - - +
45N ASN* 2.8 21.4 + - - +
47N GLU* 1.3 73.3 - - - +
49N LEU* 1.3 64.7 + - - +
51N ALA* 3.3 7.0 + - - +
52N ALA* 2.9 26.7 + - - +
500N NAI 4.1 7.0 - - - +
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Residues in contact with LEU 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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18N CYS* 4.7 2.5 - - - -
41N ILE* 3.9 22.2 - - + +
42N CYS* 4.2 1.3 - - - +
43N ASP* 3.9 25.5 - - + +
45N ASN 2.8 17.7 + - - +
46N PRO* 3.8 8.1 - - + +
48N ALA* 1.3 78.9 - - - +
50N GLN* 1.3 64.8 + - - +
52N ALA* 3.3 2.5 + - - +
53N GLU* 3.2 17.2 + - - +
60N PRO* 3.8 27.4 - - + -
61N PHE 3.1 34.3 - - - +
62N SER* 4.3 7.2 - - - -
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Residues in contact with GLN 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 PRO* 2.8 33.0 + - - +
47N GLU* 3.3 10.9 - - - +
49N LEU* 1.3 72.5 - - - +
51N ALA* 1.3 56.9 + - - +
53N GLU* 2.7 47.3 + - - +
54N ALA* 3.2 11.3 + - - +
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Residues in contact with ALA 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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47N GLU 2.9 18.9 + - - +
48N ALA* 3.7 8.3 - - - +
50N GLN* 1.3 73.7 - - - +
52N ALA* 1.3 61.5 + - - +
53N GLU 3.4 0.3 + - - -
54N ALA* 3.5 9.4 + - - +
55N ALA* 3.5 18.4 + - - +
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Residues in contact with ALA 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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15N LEU* 6.1 0.4 - - + -
18N CYS* 3.8 28.9 - - + -
26N ILE* 5.1 11.7 - - + -
41N ILE* 3.7 8.0 - - + +
48N ALA 2.9 17.2 + - - +
49N LEU 3.7 4.7 - - - +
50N GLN 3.0 0.2 + - - -
51N ALA* 1.3 76.3 - - - +
53N GLU* 1.3 61.4 + - - +
55N ALA* 3.5 8.1 - - - +
56N THR* 2.9 28.0 + - + +
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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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41N ILE* 3.9 8.5 - - + -
49N LEU 3.2 8.5 + - - +
50N GLN* 2.7 38.1 + - - +
52N ALA* 1.3 68.8 - - - +
54N ALA* 1.3 62.7 + - - +
55N ALA 2.7 10.7 + - - -
56N THR* 4.0 2.0 - - - -
57N GLY* 2.7 30.7 + - - +
58N ALA 4.4 4.5 - - - +
60N PRO* 3.8 29.8 - - + +
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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 GLN 3.2 6.7 + - - +
51N ALA* 3.8 10.3 - - - +
52N ALA 3.4 0.2 - - - -
53N GLU* 1.3 87.1 - - + +
55N ALA* 1.3 57.3 + - - +
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Residues in contact with ALA 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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26N ILE* 5.3 9.1 - - + +
51N ALA 3.5 11.7 - - - +
52N ALA* 3.5 13.7 - - - +
53N GLU 2.7 2.6 - - - -
54N ALA* 1.3 83.4 - - - +
56N THR* 1.3 66.0 + - + +
57N GLY 3.8 0.2 - - - -
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Residues in contact with THR 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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26N ILE* 3.9 29.4 - - + -
38N LEU* 3.8 32.5 - - + +
41N ILE* 3.8 7.2 - - + +
52N ALA* 2.9 18.2 + - + +
55N ALA* 1.3 79.7 - - + +
57N GLY* 1.3 74.5 + - - +
58N ALA* 3.0 18.2 + - - +
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Residues in contact with GLY 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* 2.7 25.2 + - - -
56N THR* 1.3 74.5 + - - +
58N ALA* 1.3 64.8 + - - +
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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