Contacts of the helix formed by residues 39 - 53 (chain A) in PDB entry 1TBX
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 SER 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A TYR* 3.9 2.9 - - - -
38A MSE 1.3 82.6 - - - +
40A THR* 1.3 55.4 + - - +
41A ALA* 3.5 10.1 + - - +
42A THR* 2.8 37.8 + - - +
43A PHE* 2.7 30.0 + - - +
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Residues in contact with THR 40 (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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26A TYR* 4.6 10.8 - - + +
29A TYR* 3.7 30.1 - - + +
39A SER* 1.3 70.0 - - - +
41A ALA* 1.3 70.3 + - - +
43A PHE* 4.2 7.2 - - - +
44A TYR* 2.8 42.5 + - + +
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Residues in contact with ALA 41 (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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39A SER* 3.3 9.1 + - - +
40A THR* 1.3 85.0 + - - +
42A THR* 1.3 66.7 + - + +
44A TYR* 3.9 2.5 - - - +
45A ASP* 3.0 26.2 + - - +
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Residues in contact with THR 42 (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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9A PRO* 3.5 18.1 - - - +
38A MSE 3.4 24.4 - - + +
39A SER* 2.8 47.4 + - - +
41A ALA* 1.3 73.9 - - + +
43A PHE* 1.3 62.1 + - - +
45A ASP* 3.3 8.1 + - - +
46A ALA* 3.1 17.5 + - - +
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Residues in contact with PHE 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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13A VAL* 3.9 26.0 - - + +
25A THR* 3.6 42.6 - - + -
28A LEU* 3.9 26.5 - - + -
29A TYR* 3.5 44.6 - + + -
32A VAL* 4.5 4.7 - - + -
38A MSE 2.9 18.1 - - + +
39A SER 2.7 21.5 + - - +
40A THR* 3.8 2.9 - - - +
42A THR* 1.3 72.7 - - - +
44A TYR* 1.3 78.7 + + - +
46A ALA* 3.1 7.4 + - - +
47A LYS* 2.9 28.2 + - + -
67A LEU* 4.8 2.2 - - + -
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Residues in contact with TYR 44 (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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25A THR* 3.6 32.5 - - + +
26A TYR* 3.9 32.1 + + - +
29A TYR* 5.3 0.9 - - + -
40A THR* 2.8 40.9 + - - +
41A ALA* 4.2 2.5 - - - +
43A PHE* 1.3 84.1 - + - +
45A ASP* 1.3 66.6 + - - +
47A LYS* 3.1 31.0 + - + +
48A LYS* 2.8 25.5 + - - +
58A GLU* 5.4 0.2 - - - -
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Residues in contact with ASP 45 (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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41A ALA* 3.0 16.9 + - - +
42A THR* 3.4 13.4 - - - +
44A TYR* 1.3 76.8 - - - +
46A ALA* 1.3 57.5 + - - +
48A LYS* 3.3 11.1 + - - +
49A PHE* 3.0 28.1 + - - +
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Residues in contact with ALA 46 (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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9A PRO* 3.9 6.5 - - + -
10A GLU* 3.8 31.6 - - + +
13A VAL* 3.9 17.9 - - + -
38A MSE 4.1 0.2 - - + -
42A THR 3.1 7.9 + - - +
43A PHE 3.1 11.1 + - - +
45A ASP* 1.3 77.2 - - - +
47A LYS* 1.3 66.0 + - - +
49A PHE* 3.2 6.0 + - - +
50A LEU* 3.0 31.2 + - - +
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Residues in contact with LYS 47 (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 VAL* 5.2 4.4 - - + +
25A THR* 3.8 14.8 - - + -
43A PHE* 2.9 24.7 + - + +
44A TYR* 3.1 30.2 + - + +
46A ALA* 1.3 74.6 - - - +
48A LYS* 1.3 71.2 + - - +
50A LEU* 3.3 8.5 + - - +
51A ILE* 3.0 42.9 + - + +
56A VAL* 5.4 3.3 - - + +
58A GLU* 3.1 37.6 + - - +
67A LEU* 4.2 15.7 - - + -
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Residues in contact with LYS 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 TYR 2.8 13.1 + - - +
45A ASP* 3.3 16.4 - - - +
47A LYS* 1.3 85.7 - - - +
49A PHE* 1.3 56.2 + - - +
51A ILE* 3.3 6.7 + - - +
52A GLN* 2.9 66.4 + - - +
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Residues in contact with PHE 49 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLU* 3.9 24.2 - - + -
45A ASP 3.0 16.6 + - - +
46A ALA* 3.2 5.6 + - - +
48A LYS* 1.3 76.7 - - - +
50A LEU* 1.3 61.9 + - + +
52A GLN* 2.9 12.6 + - + +
53A GLU* 2.8 59.7 + - + +
55A PHE* 5.2 0.2 - + - -
5B PRO* 3.6 30.7 - - + -
6B PHE* 3.8 28.3 - + - -
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Residues in contact with LEU 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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10A GLU* 3.7 26.2 - - + +
13A VAL* 3.8 25.8 - - + -
14A LEU* 4.0 11.7 - - + +
46A ALA 3.0 17.6 + - - +
47A LYS* 4.0 4.5 - - - +
49A PHE* 1.3 80.1 - - + +
51A ILE* 1.3 60.2 + - - +
54A GLY 3.1 2.4 + - - -
55A PHE* 2.8 40.0 + - + -
56A VAL* 3.2 29.2 + - + -
6B PHE* 3.6 37.9 - - + -
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Residues in contact with ILE 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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47A LYS* 3.0 49.3 + - + +
48A LYS* 3.6 8.5 - - - +
50A LEU* 1.3 75.8 - - - +
52A GLN* 1.3 68.8 + - + +
54A GLY* 3.1 13.2 + - - -
56A VAL* 3.5 30.8 - - + +
57A LYS* 5.9 0.2 - - - -
58A GLU* 3.8 25.8 - - + +
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Residues in contact with GLN 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 LYS* 2.9 54.0 + - - +
49A PHE* 2.9 12.9 + - + +
51A ILE* 1.3 81.7 - - + +
53A GLU* 1.3 71.6 - - - +
54A GLY* 3.3 1.1 + - - -
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Residues in contact with GLU 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 PHE* 2.8 51.7 + - + +
52A GLN* 1.3 82.6 - - - +
54A GLY* 1.3 58.1 + - - +
55A PHE* 3.4 24.3 + - + -
72A LYS* 2.9 28.4 + - - -
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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