Contacts of the helix formed by residues 42 - 57 (chain A) in PDB entry 1TAU
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 GLN 42 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR 3.4 10.0 - - - +
27A PHE* 3.5 22.7 + - - +
29A ALA 3.0 27.6 - - - +
30A LEU* 3.5 19.5 - - + +
31A LYS* 2.7 30.7 + - - +
33A LEU* 3.4 31.1 + - + -
34A THR* 5.2 0.6 - - - +
40A PRO* 4.1 8.3 - - - +
41A VAL* 1.3 78.3 - - - +
43A ALA* 1.3 59.0 + - - +
46A GLY* 2.8 28.1 + - - -
95A GLN* 2.7 32.8 + - - +
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Residues in contact with ALA 43 (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 ALA 4.0 4.0 - - - +
26A THR* 2.7 30.9 + - - +
27A PHE* 3.6 24.7 - - + +
42A GLN* 1.3 73.3 - - - +
44A VAL* 1.3 58.5 + - - +
47A PHE* 2.8 24.3 + - - +
92A PHE* 5.6 1.8 - - + -
95A GLN* 2.8 35.2 + - + +
99A ILE* 4.1 6.1 - - + -
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 3.3 14.6 + - + -
43A ALA* 1.3 76.4 - - - +
45A TYR* 1.3 69.2 + - - +
47A PHE* 3.7 1.6 - - - +
48A ALA* 3.0 20.9 + - + +
95A GLN* 3.2 24.2 + - + +
98A LEU* 3.4 42.2 - - + -
99A ILE* 3.7 11.3 - - + +
102A LEU* 4.9 7.2 - - + +
272A PHE* 4.3 9.6 - - + -
273A LEU* 6.4 0.2 - - + -
276A LEU* 3.6 24.7 - - + -
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Residues in contact with TYR 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.5 20.4 - - + -
33A LEU* 4.0 14.6 - - + -
41A VAL* 2.8 22.2 + - - +
42A GLN 3.8 2.9 - - - +
44A VAL* 1.3 71.7 - - - +
46A GLY* 1.3 69.4 + - - +
48A ALA* 2.8 20.0 + - + +
49A LYS* 3.0 50.9 + - + +
278A PHE* 3.1 47.3 - + + -
281A LEU* 3.6 21.3 - - + +
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Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A THR* 3.3 19.1 - - - +
29A ALA* 5.9 0.9 - - - -
30A LEU* 4.3 7.2 - - - -
42A GLN 2.8 21.0 + - - -
45A TYR* 1.3 83.0 - - - +
47A PHE* 1.3 61.1 + - - +
49A LYS* 3.5 8.5 + - - +
50A SER* 3.3 23.9 + - - -
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Residues in contact with PHE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 4.1 9.4 - - + -
19A GLY* 3.4 27.1 - - - -
22A LEU* 3.8 24.6 - - + +
23A ALA* 3.8 9.4 - - - -
26A THR* 3.3 8.3 - - - +
43A ALA 2.8 13.3 + - - +
44A VAL 3.7 0.7 - - - +
45A TYR 2.9 1.0 + - - -
46A GLY* 1.3 73.1 - - - +
48A ALA* 1.3 62.0 + - - +
50A SER* 3.2 5.8 + - - -
51A LEU* 3.1 44.4 + - + +
64A VAL* 3.7 24.0 - - + -
99A ILE* 3.3 48.7 - - + -
102A LEU* 4.2 9.9 - - + -
103A VAL* 4.0 8.1 - - + -
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Residues in contact with ALA 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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44A VAL* 3.0 13.0 + - + +
45A TYR* 2.8 16.0 + - + +
47A PHE* 1.3 72.3 - - - +
49A LYS* 1.3 56.6 + - - +
51A LEU* 3.0 7.0 + - - +
52A LEU* 2.8 35.4 + - - +
102A LEU* 3.9 25.1 - - + +
273A LEU* 5.8 3.1 - - + -
281A LEU* 5.8 4.7 - - + -
285A PHE* 4.2 19.1 - - + -
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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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30A LEU* 5.7 7.9 - - - +
45A TYR* 3.0 46.1 + - + +
46A GLY* 3.7 12.1 - - - +
48A ALA* 1.3 77.7 - - - +
50A SER* 1.3 71.2 + - - +
52A LEU* 3.5 10.6 + - - +
53A LYS* 3.4 17.7 + - - +
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Residues in contact with SER 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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22A LEU* 4.1 14.6 - - - +
26A THR* 5.3 1.6 - - - +
46A GLY 3.3 12.2 + - - -
47A PHE* 3.2 12.6 + - - -
49A LYS* 1.3 82.9 - - - +
51A LEU* 1.3 66.3 + - - +
53A LYS* 3.5 9.1 + - - +
54A ALA 3.3 17.0 + - - -
139A LEU* 3.9 15.3 - - - +
158A PRO* 4.5 25.8 - - - -
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Residues in contact with LEU 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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17A VAL* 4.0 32.1 - - + -
22A LEU* 6.2 0.2 - - - -
47A PHE* 3.1 35.7 + - + +
48A ALA 3.0 10.7 + - - +
50A SER* 1.3 75.3 + - - +
52A LEU* 1.3 66.2 + - + +
54A ALA* 3.3 3.8 + - - +
55A LEU* 3.0 46.2 + - + +
62A VAL* 5.0 0.2 - - + -
64A VAL* 4.6 1.6 - - + -
102A LEU* 4.5 8.5 - - + -
103A VAL* 4.3 5.6 - - + -
106A LEU* 4.2 12.8 - - + -
108A LEU* 3.6 30.1 - - + -
139A LEU* 4.3 5.6 - - + -
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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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48A ALA 2.8 15.1 + - - +
49A LYS* 3.7 11.7 - - - +
51A LEU* 1.3 75.7 - - + +
53A LYS* 1.3 53.6 + - - +
55A LEU* 2.8 10.4 + - + +
56A LYS* 2.6 43.9 + - + +
106A LEU* 4.5 7.4 - - + -
281A LEU* 5.0 6.1 - - + -
284A GLU* 4.0 26.9 - - + +
285A PHE* 3.1 52.5 - - + -
288A LEU* 4.5 18.3 - - + +
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Residues in contact with LYS 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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49A LYS 3.4 9.4 + - - +
50A SER* 3.5 13.0 - - - +
51A LEU 3.4 0.2 - - - -
52A LEU* 1.3 74.2 - - - +
54A ALA* 1.3 63.5 + - - +
56A LYS* 3.0 40.2 + - + +
57A GLU* 2.8 44.2 + - - +
158A PRO 4.7 15.3 - - - +
159A GLU 5.3 4.9 - - - -
160A GLY* 5.5 5.8 - - - -
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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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15A LEU* 3.7 16.2 - - + +
50A SER 3.3 2.2 + - - +
51A LEU 3.3 5.3 + - - +
52A LEU 3.2 0.8 - - - -
53A LYS* 1.3 79.5 - - - +
55A LEU* 1.3 53.7 + - - +
57A GLU* 3.3 3.7 + - - -
58A ASP* 2.7 27.0 + - - -
137A ARG* 3.1 13.5 + - - -
139A LEU* 3.5 37.5 - - + -
156A LEU* 4.0 17.7 - - + -
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Residues in contact with LEU 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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15A LEU* 3.4 26.7 - - + -
51A LEU* 3.0 32.7 + - + +
52A LEU* 2.8 14.9 + - + +
54A ALA* 1.3 68.4 - - - +
56A LYS* 1.3 64.6 + - - +
58A ASP* 3.1 24.6 + - - +
62A VAL* 4.1 9.9 - - + -
106A LEU* 4.5 7.6 - - + -
108A LEU* 3.9 28.7 - - + -
261A ARG* 4.0 17.3 + - - +
288A LEU* 3.9 38.7 - - + +
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Residues in contact with LYS 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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52A LEU* 2.6 21.9 + - + +
53A LYS* 3.0 44.7 + - - +
55A LEU* 1.3 72.7 - - - +
57A GLU* 1.3 71.6 + - - +
58A ASP* 3.8 7.3 - - - +
284A GLU* 4.8 14.8 - - - +
287A LEU* 4.6 18.4 - - + +
288A LEU* 5.3 3.1 - - + +
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Residues in contact with GLU 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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13A ARG* 5.1 1.9 + - - -
53A LYS* 2.8 55.3 + - - +
54A ALA* 3.3 9.0 + - - +
56A LYS* 1.3 87.6 - - - +
58A ASP* 1.3 77.8 + - - +
137A ARG* 3.3 26.8 + - - +
156A LEU* 5.0 5.1 - - + +
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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