Contacts of the helix formed by residues 43 - 66 (chain N) in PDB entry 2ZQK
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 LYS 43 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A SER* 3.1 32.2 + - - +
160A VAL* 4.4 8.3 - - + +
174A GLY* 4.6 21.2 - - - -
24N ASP* 3.1 30.2 + - - +
25N ASN* 2.7 22.6 + - - +
26N GLN 4.2 8.1 - - - -
27N LYS* 3.9 19.8 - - + +
42N LEU* 1.3 73.8 - - - +
44N ASP* 1.3 65.3 + - - +
45N ASP* 3.4 4.9 - - - +
46N VAL* 3.0 13.7 + - + +
47N VAL 3.0 18.2 + - - -
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Residues in contact with ASP 44 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A GLN 5.3 0.4 - - - -
157A ARG 3.2 16.4 - - - +
158A SER 2.8 21.8 + - - +
159A GLY* 2.9 10.4 - - - -
27N LYS* 2.8 25.1 + - - -
42N LEU 3.4 1.0 + - - +
43N LYS* 1.3 70.1 - - - +
45N ASP* 1.3 62.2 + - - +
47N VAL* 3.3 9.5 + - - +
48N ALA* 3.0 22.0 + - - +
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Residues in contact with ASP 45 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A SER* 4.5 2.3 - - - +
157A ARG* 3.4 17.3 + - + +
158A SER* 3.0 38.8 + - - -
43N LYS* 3.8 5.0 - - - +
44N ASP* 1.3 72.9 - - - +
46N VAL* 1.3 63.5 + - - +
48N ALA* 3.3 7.4 + - - +
49N ASN* 2.9 31.0 + - - +
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Residues in contact with VAL 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19N ALA* 4.1 19.3 - - + -
25N ASN* 4.0 41.3 - - + +
42N LEU* 4.6 6.1 - - + -
43N LYS* 3.0 26.1 + - + +
45N ASP* 1.3 80.7 + - - +
47N VAL* 1.3 60.4 + - - +
49N ASN* 3.5 8.4 + - - +
50N ILE* 2.8 37.4 + - + +
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Residues in contact with VAL 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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41N VAL* 5.8 0.9 - - + -
42N LEU* 3.2 32.3 - - + +
43N LYS 3.0 15.8 + - - +
44N ASP* 3.7 8.3 - - - +
46N VAL* 1.3 75.8 - - - +
48N ALA* 1.3 64.7 + - - +
50N ILE* 3.3 10.8 + - + +
51N GLU* 3.2 27.1 + - + +
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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
----------------------------------------------------------
44N ASP 3.0 13.2 + - - +
45N ASP* 3.4 11.2 - - - +
47N VAL* 1.3 71.6 - - - +
49N ASN* 1.3 58.4 + - - +
50N ILE 2.9 3.6 - - - -
51N GLU* 2.8 27.1 + - - +
52N GLU* 3.0 12.9 + - - +
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Residues in contact with ASN 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45N ASP 2.9 14.2 + - - +
46N VAL* 3.9 10.1 + - - +
48N ALA* 1.3 77.7 - - - +
50N ILE* 1.3 67.0 + - - +
52N GLU* 4.0 21.7 - - - +
53N GLN* 3.1 41.1 + - - +
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Residues in contact with ILE 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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12N ARG* 3.9 17.5 - - + +
15N LEU* 3.4 46.4 - - + +
16N THR* 3.6 24.2 - - - +
19N ALA* 4.5 2.2 - - + -
42N LEU* 5.4 2.2 - - + -
46N VAL* 2.8 35.6 + - + +
47N VAL* 3.3 11.7 - - + +
48N ALA 2.9 1.0 - - - -
49N ASN* 1.3 85.2 - - - +
51N GLU* 1.3 57.2 + - + +
53N GLN* 3.2 7.1 + - - +
54N ALA* 2.8 31.5 + - - +
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Residues in contact with GLU 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N ARG* 2.6 50.0 + - - +
47N VAL* 3.2 19.2 + - + +
48N ALA* 2.8 10.3 + - - +
50N ILE* 1.3 77.7 - - + +
52N GLU* 1.3 66.9 + - - +
54N ALA* 2.9 14.8 + - - -
55N LYS* 2.9 40.0 + - - +
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Residues in contact with GLU 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48N ALA 3.0 10.9 + - - +
49N ASN* 4.0 21.9 - - - +
51N GLU* 1.3 77.9 - - - +
53N GLN* 1.3 61.6 + - + +
55N LYS* 3.3 16.1 - - - +
56N ALA* 3.0 33.2 + - + +
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Residues in contact with GLN 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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11N THR* 3.9 3.5 - - - +
15N LEU* 3.5 29.0 - - + +
49N ASN* 3.1 38.0 + - - +
50N ILE* 3.2 5.7 + - - +
51N GLU 3.1 0.6 - - - -
52N GLU* 1.3 83.3 - - + +
54N ALA* 1.3 65.5 + - - +
56N ALA* 3.7 5.7 + - - +
57N ALA* 3.1 23.2 + - - +
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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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8N GLU* 3.1 36.9 - - + +
11N THR* 3.5 12.5 - - + +
12N ARG* 3.7 22.7 - - + +
50N ILE 2.8 16.6 + - - +
51N GLU* 2.9 10.6 + - - +
53N GLN* 1.3 72.1 - - - +
55N LYS* 1.3 57.8 + - - +
57N ALA* 2.9 19.8 + - - +
58N GLY 2.9 9.7 + - - -
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Residues in contact with LYS 55 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N GLU* 3.8 30.0 - - - +
12N ARG* 4.9 0.4 - - - +
51N GLU* 2.9 46.1 + - - +
52N GLU* 3.3 27.5 - - - +
54N ALA* 1.3 75.2 - - - +
56N ALA* 1.3 57.1 + - - +
58N GLY* 2.9 15.6 + - - -
59N GLU* 3.0 19.3 + - - +
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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 GLU* 3.0 24.1 + - + +
53N GLN* 3.9 7.0 - - - +
55N LYS* 1.3 76.4 - - - +
57N ALA* 1.3 58.0 + - - +
59N GLU* 4.2 6.8 - - - +
60N GLU* 3.4 21.7 + - - +
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Residues in contact with ALA 57 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7N THR* 3.7 4.5 - - + +
11N THR* 3.7 24.7 - - + +
53N GLN 3.1 13.4 + - - +
54N ALA 2.9 11.1 + - - +
56N ALA* 1.3 76.5 - - - +
58N GLY* 1.3 64.4 + - - +
60N GLU* 3.4 8.6 - - + +
61N ALA* 3.1 26.0 + - - +
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Residues in contact with GLY 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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6N ALA* 5.4 4.0 - - - -
7N THR* 3.8 15.9 - - - +
8N GLU* 4.0 12.8 - - - +
54N ALA 2.9 9.0 + - - -
55N LYS* 2.9 7.2 + - - -
57N ALA* 1.3 76.8 - - - +
59N GLU* 1.3 65.0 + - - +
61N ALA* 4.2 0.5 - - - +
62N LYS* 2.8 30.4 + - - +
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Residues in contact with GLU 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 LYS 3.0 16.5 + - - +
56N ALA* 4.4 5.2 - - - +
58N GLY* 1.3 73.9 - - - +
60N GLU* 1.3 68.2 + - - +
62N LYS* 3.3 30.6 + - - +
63N GLN* 2.9 35.3 + - + +
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Residues in contact with GLU 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 ALA 3.4 18.2 + - - +
57N ALA* 3.4 11.2 - - - +
59N GLU* 1.3 83.1 - - - +
61N ALA* 1.3 67.7 + - + +
63N GLN* 4.5 0.2 - - - +
64N GLN* 2.9 39.3 + - - +
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Residues in contact with ALA 61 (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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7N THR* 3.7 21.8 - - + +
57N ALA 3.1 12.7 + - - +
60N GLU* 1.3 81.2 - - + +
62N LYS* 1.3 63.4 + - - +
64N GLN* 3.3 17.5 + - - +
65N ALA* 2.9 26.5 + - - +
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Residues in contact with LYS 62 (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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6N ALA* 6.4 2.0 - - + -
7N THR* 5.1 0.8 - - - +
58N GLY 2.8 24.1 + - - +
59N GLU* 3.3 24.6 + - - +
61N ALA* 1.3 68.2 - - - +
63N GLN* 1.3 84.0 + - - +
64N GLN 2.7 14.6 + - - -
65N ALA* 2.9 16.4 + - - +
66N ILE* 3.2 24.8 + - + +
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Residues in contact with GLN 63 (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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59N GLU* 2.9 27.8 + - - +
60N GLU 4.5 0.4 - - - +
62N LYS* 1.3 94.3 + - - +
64N GLN* 1.3 55.6 + - - +
66N ILE* 2.9 33.1 - - + +
67N GLU* 3.9 7.8 - - - +
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Residues in contact with GLN 64 (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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60N GLU* 2.9 34.2 + - - +
61N ALA* 3.3 25.7 - - - +
62N LYS 2.7 4.9 + - - -
63N GLN* 1.3 72.3 - - - +
65N ALA* 1.3 60.9 + - - +
66N ILE 3.1 1.1 - - - -
67N GLU* 2.7 45.3 + - + +
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Residues in contact with ALA 65 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61N ALA 2.9 17.0 + - - +
62N LYS* 3.6 4.9 - - - +
64N GLN* 1.3 82.4 - - + +
66N ILE* 1.3 55.9 + - + +
67N GLU 2.6 21.1 + - - +
68N ASN 4.1 5.7 - - - +
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Residues in contact with ILE 66 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62N LYS* 3.5 23.1 - - + +
63N GLN* 2.9 39.7 - - + +
65N ALA* 1.3 74.2 - - + +
67N GLU* 1.3 63.3 + - - +
68N ASN* 2.6 20.7 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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