Contacts of the helix formed by residues 50 - 68 (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 ASN 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ARG* 3.2 16.5 + - + +
48A LYS* 3.3 8.7 + - + -
49A GLY* 1.3 72.7 - - - +
51A ILE* 1.3 56.6 + - - +
52A GLN* 3.4 10.9 - - - +
53A LEU* 2.8 50.8 - - + +
54A THR* 2.7 30.7 + - - +
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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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49A GLY* 2.9 19.8 + - - +
50A ASN* 1.3 71.5 - - - +
52A GLN* 1.3 64.4 + - - +
54A THR* 3.3 8.0 + - + +
55A ASN* 2.8 45.9 + - - +
290A ASP* 3.6 20.9 - - + +
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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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50A ASN* 3.4 9.1 - - - +
51A ILE* 1.3 79.4 - - - +
53A LEU* 1.3 68.8 + - + +
55A ASN* 3.9 8.4 - - - +
56A SER* 3.1 26.4 + - - -
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ARG* 3.2 35.3 + - + +
50A ASN* 2.8 35.1 - - - +
52A GLN* 1.3 90.2 - - + +
54A THR* 1.3 58.5 + - - +
56A SER* 3.6 9.0 - - - -
57A ALA* 2.8 28.8 + - - +
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Residues in contact with THR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 4.3 5.7 - - - +
45A ARG* 3.3 13.5 - - + -
46A MET* 3.3 50.7 - - + +
49A GLY 5.2 0.2 - - - -
50A ASN 2.7 30.0 + - - +
51A ILE* 3.6 8.8 + - + +
53A LEU* 1.3 73.1 - - - +
55A ASN* 1.3 73.3 + - - +
57A ALA* 3.7 4.2 - - - +
58A ILE* 3.1 32.1 + - - +
287A PHE 5.4 1.0 + - - -
290A ASP* 5.4 0.3 + - - -
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Residues in contact with ASN 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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51A ILE* 2.8 39.0 + - - +
52A GLN* 3.9 7.6 - - - +
54A THR* 1.3 85.5 + - - +
56A SER* 1.3 58.3 + - - +
58A ILE* 3.6 1.9 - - - +
59A SER* 2.8 31.9 + - - -
287A PHE 3.6 2.1 - - - +
288A ALA* 3.0 36.2 - - + +
290A ASP* 2.8 26.5 + - - +
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Residues in contact with SER 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLN* 3.1 17.5 + - - -
53A LEU* 3.6 14.2 - - - +
55A ASN* 1.3 78.5 - - - +
57A ALA* 1.3 59.0 + - - +
59A SER* 3.5 6.3 - - - -
60A ASP* 2.9 46.2 + - - +
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Residues in contact with ALA 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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38A ILE* 5.5 1.0 - - - +
41A LEU* 3.8 32.7 - - + +
42A ILE* 4.1 17.8 - - + +
45A ARG* 5.4 2.2 - - + +
53A LEU 2.8 18.4 + - - +
54A THR* 3.7 8.3 - - - +
56A SER* 1.3 72.4 - - - +
58A ILE* 1.3 65.7 + - - +
60A ASP* 3.2 9.6 + - - +
61A ALA* 3.0 21.8 + - - +
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Residues in contact with ILE 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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20A PHE* 5.0 3.6 - - + -
42A ILE* 3.8 29.8 - - + -
46A MET* 4.9 2.0 - - + -
54A THR* 3.1 21.7 + - - +
55A ASN 3.6 4.5 - - - +
57A ALA* 1.3 75.0 - - - +
59A SER* 1.3 65.7 + - - +
61A ALA* 2.8 21.1 + - + +
62A LEU* 2.9 19.8 + - + +
284A LEU* 3.5 36.8 - - + +
287A PHE* 3.9 15.0 - - + -
288A ALA* 3.4 35.9 - - + +
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Residues in contact with SER 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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55A ASN 2.8 19.1 + - - -
56A SER* 3.5 9.8 + - - -
58A ILE* 1.3 77.0 - - - +
60A ASP* 1.3 61.2 + - - +
62A LEU* 3.4 8.9 + - - +
63A LYS* 2.9 27.9 + - - +
288A ALA* 4.9 3.6 - - - +
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Residues in contact with ASP 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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56A SER* 2.9 35.6 + - - +
57A ALA* 3.6 8.1 - - - +
58A ILE 3.2 0.2 - - - -
59A SER* 1.3 76.4 + - - +
61A ALA* 1.3 53.5 + - - +
63A LYS* 2.8 11.3 + - - +
64A GLU* 2.8 34.4 + - - +
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Residues in contact with ALA 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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34A ILE* 4.8 10.5 - - + -
38A ILE* 4.0 28.9 - - + +
42A ILE* 4.8 0.9 - - + -
57A ALA 3.0 11.8 + - - +
58A ILE* 2.8 15.1 + - + +
60A ASP* 1.3 77.3 - - - +
62A LEU* 1.3 58.7 + - + +
64A GLU* 3.4 11.5 + - - +
65A ILE* 3.1 34.6 + - + +
284A LEU* 5.9 2.5 - - + -
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Residues in contact with LEU 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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33A ILE* 5.3 0.2 - - + -
58A ILE* 2.9 30.1 + - + +
59A SER* 3.8 9.9 - - - +
61A ALA* 1.3 75.2 - - + +
63A LYS* 1.3 66.1 + - - +
65A ILE* 3.7 14.8 - - + +
66A ASP* 3.0 33.0 + - - +
281A ARG* 4.3 31.9 - - + +
284A LEU* 3.7 29.4 - - + -
285A GLU* 4.0 26.9 - - + +
288A ALA* 5.6 1.8 - - + -
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Residues in contact with LYS 63 (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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59A SER* 2.9 15.3 + - - +
60A ASP* 2.8 18.3 + - - +
62A LEU* 1.3 78.6 - - - +
64A GLU* 1.3 59.5 + - - +
66A ASP* 3.9 3.3 - - - +
67A SER* 2.8 46.7 + - - +
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Residues in contact with GLU 64 (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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38A ILE* 3.7 25.3 - - - +
60A ASP 2.8 10.8 + - - +
61A ALA* 3.6 10.5 - - - +
63A LYS* 1.3 79.9 - - - +
65A ILE* 1.3 65.4 + - - +
67A SER* 3.2 7.6 + - - -
68A SER* 3.1 21.9 + - - -
254A TYR* 3.7 45.5 - - + +
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Residues in contact with ILE 65 (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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33A ILE* 3.6 43.7 - - + +
34A ILE* 5.4 3.1 - - + -
61A ALA* 3.1 17.6 + - + +
62A LEU* 3.7 21.8 - - + +
63A LYS 3.4 0.2 - - - -
64A GLU* 1.3 80.2 - - - +
66A ASP* 1.3 67.0 + - - +
68A SER* 3.2 9.2 - - - -
254A TYR* 3.7 21.6 - - + +
257A HIS* 3.6 40.2 - - + +
258A ASN* 3.0 18.5 - - - +
281A ARG* 5.0 3.8 - - - +
284A LEU* 4.9 3.1 - - + -
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Residues in contact with ASP 66 (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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62A LEU* 3.0 21.5 + - - +
63A LYS* 4.0 3.9 - - - +
65A ILE* 1.3 78.9 - - - +
67A SER* 1.3 59.0 + - - +
68A SER 2.9 10.5 + - - -
121A ASN* 3.3 11.4 + - - -
257A HIS* 4.6 2.8 - - - -
258A ASN* 2.9 23.2 + - - +
281A ARG* 2.6 34.5 + - - -
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Residues in contact with SER 67 (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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63A LYS* 2.8 47.1 + - - +
64A GLU* 3.2 10.6 + - - -
66A ASP* 1.3 71.8 - - - +
68A SER* 1.3 62.5 + - - +
69A VAL* 3.3 8.8 + - - +
121A ASN* 3.6 10.1 + - - +
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Residues in contact with SER 68 (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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64A GLU 3.1 10.3 + - - -
65A ILE 3.2 17.7 - - - -
66A ASP 2.9 2.6 + - - -
67A SER* 1.3 76.4 - - - +
69A VAL* 1.3 57.2 + - - +
70A LEU* 4.2 0.7 + - - +
121A ASN* 3.1 14.5 + - - +
254A TYR* 3.8 17.1 - - - -
255A LYS* 3.3 41.2 + - - +
258A ASN* 3.1 19.4 - - - +
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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