Contacts of the helix formed by residues 53 - 72 (chain A) in PDB entry 1LTQ
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 THR 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A TYR* 1.3 77.4 + - - +
54A LYS* 1.3 67.5 + - + +
55A LYS* 3.0 20.5 + - + +
56A LYS* 3.3 35.8 + - + +
57A GLU* 3.2 27.4 + - - +
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Residues in contact with LYS 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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52A TYR 4.0 2.0 + - - -
53A THR* 1.3 75.1 - - + +
55A LYS* 1.3 59.3 + - - +
57A GLU* 4.0 9.3 - - - +
58A GLY* 3.3 15.9 + - - -
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Residues in contact with LYS 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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53A THR* 3.0 13.2 - - + +
54A LYS* 1.3 78.2 - - - +
56A LYS* 1.3 68.5 + - + +
57A GLU 3.2 0.2 - - - -
58A GLY* 2.9 12.3 + - - -
59A ILE* 3.0 18.8 + - + +
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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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38A ARG* 6.2 4.3 - - + -
41A ILE* 4.5 11.1 - - + +
42A MSE 3.3 46.3 - - + +
45A GLU* 4.9 5.8 - - - +
52A TYR 4.6 9.0 - - - +
53A THR* 3.3 38.0 + - + +
55A LYS* 1.3 77.0 - - + +
57A GLU* 1.3 64.1 + - - +
59A ILE* 2.8 26.0 + - - +
60A VAL* 2.9 19.2 + - + +
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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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34A ARG* 3.0 18.2 + - - +
38A ARG* 2.5 49.0 + - - -
52A TYR* 5.5 5.1 - - - -
53A THR 3.2 22.0 + - - +
54A LYS* 4.0 8.5 - - - +
56A LYS* 1.3 80.6 - - - +
58A GLY* 1.3 57.0 + - - +
60A VAL* 4.5 2.5 - - - -
61A THR* 2.9 33.7 + - - +
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Residues in contact with GLY 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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54A LYS 3.3 10.3 + - - -
55A LYS* 2.9 9.8 + - - -
57A GLU* 1.3 79.2 - - - +
59A ILE* 1.3 63.8 + - - +
61A THR* 3.5 7.1 + - - +
62A GLY* 3.1 18.4 + - - -
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Residues in contact with ILE 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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41A ILE* 4.5 17.3 - - + -
55A LYS* 3.0 17.8 + - + +
56A LYS* 2.8 12.1 + - - +
58A GLY* 1.3 77.1 - - - +
60A VAL* 1.3 60.3 - - - +
62A GLY* 3.1 3.9 + - - -
63A MSE 2.8 46.4 + - + +
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Residues in contact with VAL 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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34A ARG* 3.3 55.6 - - + +
37A TYR* 3.9 7.2 - - + -
38A ARG* 4.1 34.1 - - + +
41A ILE* 4.2 12.6 - - + -
56A LYS* 2.9 19.1 + - + +
57A GLU* 3.9 5.6 - - - +
59A ILE* 1.3 75.3 - - - +
61A THR* 1.3 63.3 + - - +
63A MSE 3.3 11.0 + - - +
64A GLN* 3.0 22.3 + - - +
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Residues in contact with THR 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 ARG* 3.3 9.1 + - - +
57A GLU 2.9 22.2 + - - -
58A GLY* 3.6 7.8 - - - +
59A ILE 3.1 0.2 - - - -
60A VAL* 1.3 74.0 - - - +
62A GLY* 1.3 67.8 + - - +
64A GLN* 3.1 9.3 + - - +
65A PHE* 3.1 36.7 - - + -
92A ARG* 2.5 40.2 + - - +
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Residues in contact with GLY 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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58A GLY 3.1 9.2 + - - -
59A ILE 3.1 6.5 + - - -
61A THR* 1.3 81.3 - - - +
63A MSE 1.3 62.5 + - - +
65A PHE* 3.3 3.3 + - - -
66A ASP* 2.9 38.0 + - - +
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Residues in contact with MSE 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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37A TYR* 3.4 53.8 - - + -
40A SER* 5.5 4.7 - - - +
41A ILE* 3.8 28.0 - - + -
59A ILE* 2.8 28.7 + - + +
60A VAL* 3.4 10.8 - - - +
62A GLY* 1.3 76.6 - - - +
64A GLN* 1.3 55.5 + - - +
66A ASP* 4.0 3.7 - - - +
67A THR* 2.5 40.8 + - - +
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Residues in contact with GLN 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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32A ILE* 3.5 35.2 + - + +
34A ARG* 2.8 45.9 + - + +
37A TYR* 3.8 10.7 - - + -
60A VAL 3.0 16.4 + - - +
61A THR 3.1 8.0 + - - +
63A MSE 1.3 77.1 - - - +
65A PHE* 1.3 58.4 + - + +
67A THR* 3.5 2.1 + - - -
68A ALA* 3.0 27.4 + - - +
83A ILE* 3.8 9.3 - - - +
85A ASP* 2.7 26.2 + - - +
92A ARG* 4.0 7.4 + - - -
96A TRP* 3.9 19.6 + - + -
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Residues in contact with PHE 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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61A THR* 3.1 48.3 + - + +
62A GLY* 4.2 3.8 - - - +
64A GLN* 1.3 73.9 - - + +
66A ASP* 1.3 71.4 + - - +
68A ALA* 3.0 7.2 + - - +
69A LYS* 2.9 28.7 + - + +
92A ARG* 3.7 27.6 - - - -
95A ALA* 4.1 15.7 - - + -
96A TRP* 4.2 26.2 - + - -
99A PHE* 3.5 45.7 - + + -
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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 GLY* 2.9 25.5 + - - +
63A MSE 4.0 3.4 - - - +
65A PHE* 1.3 77.6 - - - +
67A THR* 1.3 61.4 + - - +
69A LYS* 3.6 14.6 + - - +
70A SER* 3.1 28.8 + - - -
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Residues in contact with THR 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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31A ASN 5.8 0.4 - - - +
32A ILE* 4.0 5.6 - - + -
37A TYR* 3.7 24.8 + - - +
63A MSE 2.5 26.9 + - - +
64A GLN 3.8 3.6 - - - -
66A ASP* 1.3 74.1 - - - +
68A ALA* 1.3 64.4 + - - +
70A SER* 4.1 4.8 - - - -
71A ILE* 2.9 52.1 + - + +
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Residues in contact with ALA 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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32A ILE* 4.8 4.5 - - + +
64A GLN 3.0 16.6 + - - +
65A PHE 3.0 6.1 + - - +
67A THR* 1.3 75.4 - - - +
69A LYS* 1.3 56.3 + - - +
71A ILE* 3.4 1.0 + - - -
72A LEU* 2.8 47.6 + - + +
81A VAL* 4.7 16.4 - - + -
96A TRP* 4.0 24.2 - - + -
99A PHE* 4.0 10.5 - - + -
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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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65A PHE* 2.9 20.1 + - + +
66A ASP* 3.7 15.7 - - - +
68A ALA* 1.3 76.4 - - - +
70A SER* 1.3 65.3 + - - +
72A LEU* 3.6 1.7 + - - +
73A TYR* 3.3 31.1 + - - +
99A PHE* 3.8 19.0 - - + -
103A TYR* 3.3 41.5 - - + +
105A TRP* 4.1 13.6 - - + -
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Residues in contact with SER 70 (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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66A ASP 3.1 16.2 + - - -
67A THR* 4.1 6.0 - - - -
69A LYS* 1.3 78.8 - - - +
71A ILE* 1.3 69.0 + - - +
73A TYR* 3.2 15.4 + - - +
74A GLY* 3.8 3.6 + - - -
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Residues in contact with ILE 71 (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 TYR* 3.5 45.8 - - + -
31A ASN 5.3 0.9 - - - +
32A ILE* 3.6 29.6 - - + -
67A THR* 2.9 37.3 + - + +
68A ALA 3.9 1.6 - - - +
70A SER* 1.3 76.6 - - - +
72A LEU* 1.3 54.6 + - - +
73A TYR 2.7 11.8 + - - -
74A GLY* 2.9 13.5 + - - -
78A VAL* 3.5 17.6 - - + +
81A VAL* 3.8 11.9 - - + -
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Residues in contact with LEU 72 (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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2A LYS* 3.7 39.3 - - + +
3A LYS 4.0 4.3 - - - +
4A ILE* 3.6 30.7 - - + -
68A ALA* 2.8 27.3 + - + +
69A LYS 3.8 0.7 - - - -
71A ILE* 1.3 70.5 - - - +
73A TYR* 1.3 60.1 + - - +
74A GLY 3.5 0.9 - - - -
78A VAL* 4.3 7.2 - - + -
80A GLY* 3.7 22.7 - - - -
81A VAL* 4.0 17.0 - - + -
105A TRP* 3.6 53.8 + - + -
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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