Contacts of the helix formed by residues 46 - 59 (chain N) in PDB entry 4B2Q
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 THR 46 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43N ILE* 3.3 32.0 - - + +
44N LYS 2.9 0.6 - - - -
45N ASP* 1.3 81.2 + - - +
47N VAL* 1.3 61.4 + - + +
49N PRO* 3.2 16.7 - - - +
50N MET* 3.0 25.7 - - + +
37O VAL* 6.1 2.5 - - + -
44O LYS* 3.2 40.6 + - + +
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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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33N LEU* 3.6 15.3 - - + -
37N VAL* 5.8 1.1 - - + -
43N ILE* 3.5 31.0 - - + +
44N LYS* 3.4 2.0 + - - +
46N THR* 1.3 76.4 - - + +
48N PHE* 1.3 61.8 + - - +
49N PRO 3.4 0.4 - - - -
50N MET* 3.1 7.8 - - + +
51N ALA* 2.9 27.2 + - - +
34O ILE* 3.5 38.1 - - + -
37O VAL* 3.5 29.2 - - + -
38O SER* 4.1 11.4 - - - +
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Residues in contact with PHE 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M MET* 4.6 30.1 - - + -
53M LEU* 4.8 16.4 - - + -
30N PHE* 6.3 1.8 - + - -
33N LEU* 4.1 21.6 - - + +
44N LYS* 3.1 33.9 + - + +
45N ASP* 4.8 2.7 - - - +
47N VAL* 1.3 78.5 - - - +
49N PRO* 1.3 66.9 - - + +
51N ALA* 3.3 7.3 + - - +
52N ILE* 3.3 44.5 + - + +
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Residues in contact with PRO 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 ASP* 3.7 19.3 - - - +
46N THR* 3.2 22.7 - - - +
48N PHE* 1.3 99.2 - - + +
50N MET* 1.3 65.3 + - + +
52N ILE* 3.3 20.0 + - + +
53N LEU* 3.4 17.0 + - + +
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Residues in contact with MET 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 THR* 3.0 33.9 - - + +
47N VAL* 3.1 28.0 - - + +
49N PRO* 1.3 78.2 - - + +
51N ALA* 1.3 64.7 + - - +
53N LEU* 3.0 20.6 + - + +
30O PHE* 2.9 32.4 - - + -
33O LEU* 4.1 28.9 - - + +
34O ILE* 4.9 5.6 - - + -
37O VAL* 4.6 19.5 - - + -
44O LYS* 4.7 7.2 - - + -
48O PHE* 4.4 29.6 - - + -
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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
----------------------------------------------------------
29N VAL* 4.2 8.9 - - - +
30N PHE* 6.1 2.7 - - + -
33N LEU* 3.8 25.8 - - + -
47N VAL 2.9 19.7 + - - +
48N PHE 3.4 7.2 - - - +
49N PRO 3.2 0.2 - - - -
50N MET* 1.3 79.3 - - - +
52N ILE* 1.3 61.4 + - + +
54N GLY* 3.2 10.6 + - - -
55N PHE* 3.3 10.2 + - - +
30O PHE* 4.3 6.7 - - - -
34O ILE* 4.4 17.3 - - + -
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Residues in contact with ILE 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48N PHE* 3.3 40.4 - - + +
49N PRO* 3.6 11.2 - - + +
50N MET 3.2 0.4 - - - -
51N ALA* 1.3 74.9 - - + +
53N LEU* 1.3 67.6 + - + +
55N PHE* 3.0 32.0 + - + +
56N ALA* 3.5 6.6 + - - +
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Residues in contact with LEU 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 PRO* 3.4 11.9 + - + +
50N MET* 3.0 24.3 + - + +
52N ILE* 1.3 79.3 - - + +
54N GLY* 1.3 60.9 - - - +
55N PHE 3.3 0.3 + - - -
56N ALA* 3.5 7.4 + - - +
57N LEU* 3.1 25.2 + - + +
30O PHE* 4.1 9.4 - - + -
48O PHE* 4.7 16.2 - - + -
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Residues in contact with GLY 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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29N VAL* 4.3 12.0 - - - +
50N MET 3.1 10.1 + - - -
51N ALA 3.2 5.6 + - - -
52N ILE 3.2 0.4 - - - -
53N LEU* 1.3 74.3 - - - +
55N PHE* 1.3 63.2 + - - +
57N LEU* 3.4 4.2 + - - +
58N SER* 3.1 24.3 + - - -
26O ILE* 5.6 1.0 - - - +
30O PHE* 3.3 34.9 - - - +
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Residues in contact with PHE 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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57M LEU* 3.2 49.4 - - + -
26N ILE* 3.5 30.5 - - + -
29N VAL* 5.4 2.0 - - - -
30N PHE* 6.4 0.7 - - + -
51N ALA 3.3 7.8 + - - +
52N ILE* 3.0 26.8 + - + +
54N GLY* 1.3 77.7 - - - +
56N ALA* 1.3 56.0 + - + +
58N SER* 3.1 4.8 + - - -
59N GLU* 2.7 69.5 + - + +
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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 ILE 3.5 6.4 + - - +
53N LEU* 3.5 8.7 + - - +
55N PHE* 1.3 83.0 - - + +
57N LEU* 1.3 64.0 + - + +
59N GLU* 3.8 8.9 - - - +
60N ALA* 3.5 17.3 + - - +
63N LEU* 5.9 0.7 - - - +
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Residues in contact with LEU 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 LEU* 3.1 14.6 - - + +
54N GLY 3.6 5.6 - - - +
55N PHE 3.1 0.4 - - - -
56N ALA* 1.3 82.3 - - + +
58N SER* 1.3 59.5 + - - +
60N ALA* 3.5 18.2 - - - +
61N THR* 4.8 1.6 + - - +
22O ALA 5.0 0.7 - - - +
26O ILE* 4.2 20.1 - - + +
30O PHE* 3.6 36.6 - - + -
55O PHE* 3.3 53.5 - - + -
59O GLU* 4.8 0.7 - - - +
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Residues in contact with SER 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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21N GLY 3.7 3.3 + - - -
22N ALA* 3.9 7.3 - - - +
25N GLY 3.7 1.1 - - - -
26N ILE* 3.3 35.3 + - - +
29N VAL* 4.8 7.0 - - - -
54N GLY 3.1 15.7 + - - -
55N PHE 3.9 0.2 - - - -
57N LEU* 1.3 72.5 - - - +
59N GLU* 1.3 57.2 + - - +
60N ALA 3.1 5.2 - - - -
61N THR* 3.1 24.7 + - - +
22O ALA 5.1 5.2 - - - -
23O GLY 3.3 23.1 + - - -
26O ILE* 5.5 3.1 - - - -
27O ALA* 5.2 2.5 - - - -
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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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57M LEU 4.8 2.9 - - - +
60M ALA* 5.1 7.7 - - - +
64M PHE* 4.9 9.7 - - - -
22N ALA* 5.0 2.5 - - - +
26N ILE* 3.3 23.6 - - + +
55N PHE* 2.7 39.2 + - + +
56N ALA* 3.9 11.9 - - - +
57N LEU 3.3 0.4 - - - -
58N SER* 1.3 75.9 - - - +
60N ALA* 1.3 65.0 + - - +
61N THR 3.4 0.2 - - - -
62N GLY* 3.0 20.8 + - - +
63N LEU* 3.1 41.4 + - + +
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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