Contacts of the helix formed by residues 35 - 49 (chain A) in PDB entry 1TQ6
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 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ILE* 1.3 79.2 - - - +
36A GLN* 1.3 60.5 + - - +
37A GLU* 3.5 18.8 + - - +
38A ILE* 3.1 34.9 + - - +
39A LEU* 2.9 28.7 + - - +
253A ILE* 3.9 29.9 - - - +
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Residues in contact with GLN 36 (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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21A THR* 6.0 1.4 - - - +
32A LYS* 4.9 12.1 - - - -
34A ILE 4.0 0.2 + - - -
35A SER* 1.3 70.8 - - - +
37A GLU* 1.3 65.2 + - + +
39A LEU* 3.0 26.4 + - - +
40A ASN* 2.8 65.8 + - - +
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Residues in contact with GLU 37 (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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35A SER* 3.5 15.5 - - - +
36A GLN* 1.3 91.4 + - + +
38A ILE* 1.3 64.1 + - + +
40A ASN* 3.1 14.9 + - - +
41A LEU* 3.1 19.8 + - - +
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Residues in contact with ILE 38 (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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34A ILE* 3.5 30.3 - - + -
35A SER* 3.1 20.0 + - - +
37A GLU* 1.3 79.3 - - + +
39A LEU* 1.3 61.7 + - - +
41A LEU* 3.2 15.1 + - + +
42A ILE* 3.2 25.1 + - + +
57A ALA 5.5 0.7 - - - +
61A ALA* 4.0 22.0 - - + -
64A GLU* 3.7 23.6 - - - +
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Residues in contact with LEU 39 (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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20A PHE* 3.6 31.9 - - + -
21A THR* 3.8 20.3 - - + +
24A PHE* 3.7 44.4 - - + -
32A LYS* 6.1 1.8 - - - -
34A ILE* 4.0 18.2 - - + +
35A SER 2.9 18.8 + - - +
36A GLN* 3.0 28.7 + - - +
38A ILE* 1.3 77.1 - - - +
40A ASN* 1.3 62.3 + - - +
42A ILE* 3.5 3.5 + - + +
43A GLU* 3.2 21.3 + - - +
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Residues in contact with ASN 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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21A THR* 5.8 0.9 - - - +
36A GLN* 2.8 44.0 + - - +
37A GLU* 3.1 11.7 + - - +
39A LEU* 1.3 74.8 - - - +
41A LEU* 1.3 65.5 + - - +
43A GLU* 3.0 11.5 + - - +
44A LEU* 2.8 40.6 + - + +
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Residues in contact with LEU 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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37A GLU 3.1 11.6 + - - +
38A ILE* 3.3 17.7 - - + +
40A ASN* 1.3 78.4 - - - +
42A ILE* 1.3 63.6 + - + +
44A LEU* 3.2 4.8 + - + +
45A ARG* 2.8 56.0 + - - +
57A ALA* 3.8 28.7 - - + +
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Residues in contact with ILE 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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20A PHE* 3.6 28.7 - - + -
34A ILE* 3.6 30.7 - - + -
38A ILE* 3.2 15.4 + - + +
39A LEU* 3.7 7.4 - - - +
41A LEU* 1.3 78.0 - - + +
43A GLU* 1.3 57.1 + - - +
45A ARG* 3.4 4.4 + - - +
46A MET* 3.0 40.8 + - + +
54A THR* 4.3 4.7 - - - +
57A ALA* 4.1 22.9 - - + -
58A ILE* 3.8 36.1 - - + +
61A ALA* 4.8 2.0 - - + -
284A LEU* 4.5 3.8 - - + -
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Residues in contact with GLU 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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17A PRO* 3.6 34.7 - - + +
18A SER* 4.0 3.8 + - - -
20A PHE* 5.1 2.0 - - + -
21A THR* 3.6 34.5 + - + +
39A LEU 3.2 10.2 + - - +
40A ASN* 3.0 15.4 + - - +
42A ILE* 1.3 77.3 - - - +
44A LEU* 1.3 58.9 + - + +
46A MET* 3.5 5.8 - - - +
47A ARG* 2.6 51.6 + - - +
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Residues in contact with LEU 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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40A ASN* 2.8 41.8 + - + +
41A LEU* 3.6 10.1 - - + +
43A GLU* 1.3 74.3 - - + +
45A ARG* 1.3 77.5 + - - +
47A ARG* 3.3 30.0 + - - +
48A LYS* 3.1 32.2 + - + +
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Residues in contact with ARG 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 LEU* 2.8 39.9 + - + +
42A ILE* 3.6 7.6 - - - +
44A LEU* 1.3 89.4 - - - +
46A MET* 1.3 62.9 + - - +
48A LYS* 3.2 12.6 + - - +
49A GLY 3.1 16.6 + - - -
50A ASN* 3.2 17.0 + - + +
53A LEU* 3.2 57.0 + - + +
54A THR* 3.3 15.5 - - + +
57A ALA* 5.4 2.1 - - + +
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Residues in contact with MET 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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16A LEU* 4.4 14.4 - - + -
17A PRO* 3.9 27.7 - - + +
20A PHE* 3.8 37.2 - - + -
42A ILE* 3.0 38.5 + - + +
43A GLU* 3.5 6.1 - - - +
45A ARG* 1.3 75.4 - - - +
47A ARG* 1.3 65.3 + - - +
49A GLY* 2.9 14.5 + - - +
54A THR* 3.3 22.1 - - + +
58A ILE* 4.9 1.8 - - + -
287A PHE* 3.9 25.4 - - + -
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Residues in contact with ARG 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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17A PRO* 4.0 19.6 - - + +
43A GLU* 2.6 35.1 + - - +
44A LEU* 3.3 29.5 - - - +
46A MET* 1.3 73.8 - - - +
48A LYS* 1.3 83.0 + - + +
49A GLY* 3.2 1.2 + - - -
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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 LEU* 3.1 18.9 + - + +
45A ARG* 3.6 14.8 - - - +
47A ARG* 1.3 97.6 - - + +
49A GLY* 1.3 60.8 + - - +
50A ASN* 3.3 9.1 + - + +
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Residues in contact with GLY 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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45A ARG 3.1 0.4 + - - -
46A MET* 2.9 18.5 + - - -
47A ARG 3.1 0.8 - - - -
48A LYS* 1.3 79.5 - - - +
50A ASN* 1.3 60.3 + - - +
51A ILE* 2.9 21.0 + - - +
54A THR* 5.2 0.4 - - - -
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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