Contacts of the helix formed by residues 59 - 69 (chain A) in PDB entry 1TN9
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 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A SER* 3.4 2.9 - - - -
43A LYS* 3.1 28.6 - - - +
44A LEU 3.2 5.7 + - - -
45A VAL* 2.9 38.6 - - - -
46A ALA* 3.1 7.8 + - - +
58A ILE* 1.3 81.5 - - - +
60A LEU* 1.3 64.2 + - - +
61A ARG* 3.1 13.9 + - - +
62A GLU* 2.7 24.1 + - - +
63A LYS 3.1 5.0 + - - -
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Residues in contact with LEU 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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17A GLU* 4.7 8.5 - - + +
25A TYR* 3.9 15.9 - - + +
26A LEU* 3.6 17.7 - - - +
27A TYR* 3.4 38.8 - - + +
39A VAL* 3.6 27.4 - - + +
41A SER* 2.7 23.6 + - - +
43A LYS 3.1 6.9 + - - +
44A LEU* 4.8 4.7 - - + +
59A SER* 1.3 71.6 - - - +
61A ARG* 1.3 54.5 + - - +
63A LYS* 2.9 4.9 + - + -
64A ILE* 2.7 67.9 + - + +
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Residues in contact with ARG 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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14A LYS* 3.5 24.7 - - - +
17A GLU* 3.5 30.6 + - - +
44A LEU* 2.8 38.4 + - + +
45A VAL* 4.3 12.3 - - + +
59A SER* 3.0 5.5 + - - +
60A LEU* 1.3 78.8 - - - +
62A GLU* 1.3 58.8 + - + +
64A ILE* 4.0 11.5 - - - +
65A ALA* 3.0 26.9 + - - +
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Residues in contact with GLU 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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46A ALA* 4.2 20.6 - - + +
58A ILE* 3.5 27.8 - - + +
59A SER* 2.7 24.9 + - - +
61A ARG* 1.3 73.1 - - + +
63A LYS* 1.3 66.7 + - - +
65A ALA* 3.3 10.6 + - - +
66A GLU* 3.3 26.9 + - - +
69A LYS* 6.0 0.3 + - - -
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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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39A VAL* 3.6 31.2 - - + +
40A TYR* 3.0 26.3 + - - +
57A ALA* 4.1 19.6 - - - +
58A ILE* 3.3 39.5 - - + +
59A SER 3.1 6.4 + - - +
60A LEU* 2.9 6.9 + - - +
62A GLU* 1.3 76.8 - - - +
64A ILE* 1.3 64.6 + - - +
66A GLU* 2.8 22.8 + - - +
67A LEU* 3.3 11.2 + - + +
119C T 5.9 0.2 + - - -
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Residues in contact with ILE 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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17A GLU* 3.3 28.5 - - - +
27A TYR* 3.5 41.1 - - + +
60A LEU* 2.7 41.3 + - + +
61A ARG* 4.0 10.5 - - + +
63A LYS* 1.3 73.3 - - - +
65A ALA* 1.3 65.3 + - - +
67A LEU* 2.7 23.9 + - + +
68A GLN* 2.9 27.2 + - + +
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Residues in contact with ALA 65 (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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61A ARG 3.0 22.0 + - - +
62A GLU* 3.4 15.3 - - - +
63A LYS 3.2 0.2 - - - -
64A ILE* 1.3 77.6 - - - +
66A GLU* 1.3 58.3 + - - +
68A GLN* 3.4 21.5 - - - +
69A LYS* 2.9 53.2 + - + +
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Residues in contact with GLU 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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58A ILE* 5.1 6.7 - - + -
62A GLU* 3.3 20.3 + - - +
63A LYS* 2.8 12.3 + - - +
65A ALA* 1.3 81.0 - - - +
67A LEU* 1.3 68.3 + - + +
68A GLN 3.5 0.2 + - - -
69A LYS* 4.6 11.9 + - - +
70A ASP 3.5 9.0 + - - +
71A ILE* 3.3 57.8 + - + +
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Residues in contact with LEU 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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27A TYR* 4.2 10.8 - - + -
29A TYR* 3.8 40.2 - - + +
37A GLN* 5.1 3.1 - - - +
39A VAL* 4.5 11.9 - - + -
63A LYS* 3.4 15.0 - - + +
64A ILE* 2.7 24.4 + - + +
66A GLU* 1.3 80.6 - - + +
68A GLN* 1.3 61.1 + - - +
69A LYS 4.5 2.1 - - - +
70A ASP* 5.6 0.3 - - - -
71A ILE* 4.8 16.2 - - + +
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Residues in contact with GLN 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 ILE* 2.9 20.9 + - + +
65A ALA* 3.4 30.3 - - - +
67A LEU* 1.3 77.7 - - - +
69A LYS* 1.3 84.3 + - + +
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Residues in contact with LYS 69 (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 GLU* 6.0 0.2 + - - -
65A ALA* 2.9 38.8 + - + +
66A GLU* 3.9 11.8 + - - +
67A LEU 3.5 2.3 - - - +
68A GLN* 1.3 100.5 - - + +
70A ASP* 1.3 84.6 + - + +
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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