Contacts of the helix formed by residues 47 - 62 (chain A) in PDB entry 3DEW
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 GLY 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ILE 3.2 1.2 + - - -
43A SER 4.3 9.2 + - - -
44A TYR 5.0 1.0 - - - -
45A HIS 3.6 2.8 + - - -
46A PHE* 1.3 74.9 - - - +
48A GLY* 1.3 60.8 + - - +
50A GLU* 4.0 4.9 + - - +
51A GLY* 2.9 28.6 + - - -
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Residues in contact with GLY 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 4.4 4.3 - - - -
42A ILE* 2.9 29.7 + - - -
43A SER* 3.9 12.3 - - - +
47A GLY* 1.3 72.5 - - - +
49A LYS* 1.3 64.7 + - - -
50A GLU* 3.1 7.4 - - - -
52A LEU* 3.0 25.5 + - - +
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Residues in contact with LYS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 3.6 18.6 - - + -
23A PHE* 2.8 53.8 + - + -
24A TYR* 4.7 4.4 + - - +
26A VAL* 2.7 30.4 + - + +
27A SER* 4.7 0.9 - - - +
28A ILE* 4.2 24.3 - - + +
31A LEU* 4.2 20.0 - - + -
42A ILE* 4.3 0.2 - - - +
48A GLY* 1.3 70.7 - - - +
50A GLU* 1.3 69.6 + - - +
52A LEU* 3.4 0.7 + - - +
53A TYR* 2.9 28.4 + - - +
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Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 4.3 25.5 - - + -
47A GLY 4.2 2.7 - - - +
48A GLY* 4.0 5.4 - - - -
49A LYS* 1.3 97.1 + - - +
51A GLY* 1.3 57.2 - - - +
53A TYR* 3.2 4.2 + - - +
54A ALA* 2.9 30.6 + - - +
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Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE 4.0 5.2 - - - -
47A GLY* 2.9 28.5 + - - -
50A GLU* 1.3 76.2 - - - +
52A LEU* 1.3 61.2 + - - +
54A ALA* 3.3 8.1 + - - +
55A ALA* 3.0 24.5 + - - +
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.0 33.9 - - + +
11A MSE 5.2 11.2 - - + +
14A ALA* 4.3 17.7 - - + -
18A PHE* 4.1 4.5 - - + -
31A LEU* 3.9 23.6 - - + -
42A ILE* 3.9 16.4 - - + -
46A PHE* 3.7 27.7 + - + +
48A GLY 3.0 20.9 + - - +
49A LYS 3.8 2.9 - - - +
51A GLY* 1.3 76.9 - - - +
53A TYR* 1.3 58.2 + - - +
55A ALA* 3.3 6.9 + - + +
56A VAL* 3.0 32.2 + - - +
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Residues in contact with TYR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 3.6 46.8 - + + -
22A GLY* 5.7 0.2 - - - -
23A PHE* 3.5 36.3 + + + +
49A LYS 2.9 19.1 + - - +
50A GLU 3.5 4.3 - - - +
52A LEU* 1.3 76.2 - - - +
54A ALA* 1.3 57.7 + - - +
56A VAL* 3.2 3.9 + - + +
57A LEU* 2.9 47.5 + - + +
101A PHE* 4.2 16.9 - + - -
104A SER* 5.6 2.9 + - - -
105A GLU* 2.5 40.0 + - - +
110A THR* 3.5 16.9 - - + +
112A CYS* 4.0 11.9 - - + -
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLU 2.9 16.9 + - - +
51A GLY* 3.3 8.5 + - - +
53A TYR* 1.3 76.2 - - - +
55A ALA* 1.3 56.8 + - - +
57A LEU* 3.4 1.4 + - - -
58A GLN* 2.9 31.1 + - - +
112A CYS* 4.1 11.4 - - - -
116A ILE* 3.9 5.6 - - + +
205A BME 3.9 23.3 - - + -
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A MSE 3.7 32.4 - - + +
51A GLY 3.0 17.4 + - - +
52A LEU* 3.6 8.3 - - + +
54A ALA* 1.3 74.8 - - - +
56A VAL* 1.3 63.1 + - - +
58A GLN* 3.4 7.2 + - - +
59A GLU* 3.1 22.3 + - - +
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A MSE 4.2 13.0 - - - +
14A ALA* 3.7 24.2 - - + -
15A THR* 3.6 27.6 - - + +
18A PHE* 4.4 4.3 - - + -
52A LEU 3.0 21.5 + - - +
53A TYR* 3.2 6.7 + - + +
55A ALA* 1.3 77.2 - - - +
57A LEU* 1.3 60.0 + - + +
59A GLU* 3.2 9.0 + - - +
60A GLN* 2.9 34.3 + - + +
101A PHE* 3.6 37.0 - - + -
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A TYR* 2.9 26.5 + - + +
54A ALA 4.0 3.1 - - - +
56A VAL* 1.3 77.5 - - - +
58A GLN* 1.3 63.0 + - - +
60A GLN* 3.1 5.0 + - + +
61A PHE* 2.9 55.1 + - + +
101A PHE* 3.9 29.8 - - + -
105A GLU* 3.5 19.3 - - + +
112A CYS* 3.2 33.9 - - + +
116A ILE* 4.2 9.4 - - + -
117A VAL* 4.0 14.1 - - + -
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Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA 2.9 19.0 + - - +
55A ALA* 3.7 7.6 - - - +
56A VAL 3.2 0.2 - - - -
57A LEU* 1.3 74.1 - - - +
59A GLU* 1.3 57.9 + - - +
61A PHE* 3.4 3.5 + - - +
62A ALA* 2.9 42.8 + - + +
116A ILE* 3.8 29.7 - - + +
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A MSE 4.6 17.4 - - - +
15A THR* 4.6 11.4 + - - -
55A ALA 3.1 12.5 + - - +
56A VAL* 3.6 9.6 - - - +
58A GLN* 1.3 74.3 - - - +
60A GLN* 1.3 71.9 + - - +
61A PHE 3.4 0.3 + - - -
62A ALA* 3.6 17.0 + - + +
63A CYS 5.2 0.2 + - - -
95A ASN* 5.6 0.2 + - - -
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A THR* 3.8 26.3 + - - +
56A VAL* 2.9 23.1 + - - +
57A LEU* 3.1 9.2 + - - +
59A GLU* 1.3 86.9 + - - +
61A PHE* 1.3 71.6 + - + +
62A ALA 3.8 0.2 + - - -
63A CYS* 5.1 2.9 + - - +
64A PHE* 4.9 1.7 - - - -
95A ASN* 2.5 41.1 + - - +
97A GLN* 3.9 1.4 - - - +
98A LEU* 3.4 30.1 + - + +
101A PHE* 3.6 35.3 - - + -
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Residues in contact with PHE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 2.9 39.6 + - + +
58A GLN* 3.6 5.0 + - - +
60A GLN* 1.3 80.0 - - + +
62A ALA* 1.3 66.1 + - - +
63A CYS 3.3 2.7 - - - -
64A PHE* 3.0 46.4 + + - +
65A GLY 4.2 0.7 + - - -
98A LEU* 4.1 10.5 - - + -
101A PHE* 4.7 1.6 - - + -
102A TYR* 3.7 43.3 - + - -
116A ILE* 3.9 16.6 - - + -
117A VAL* 3.7 40.8 - - + -
120A ALA* 3.9 18.4 - - + +
121A ILE* 4.8 0.9 - - + -
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLN* 2.9 27.1 + - + +
59A GLU* 3.6 13.7 + - + +
60A GLN 3.5 2.0 - - - -
61A PHE* 1.3 76.5 - - - +
63A CYS* 1.3 58.3 + - - +
65A GLY* 3.0 22.0 + - - -
66A GLN* 3.6 13.9 - - - +
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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