Contacts of the helix formed by residues 60 - 75 (chain A) in PDB entry 1ZTD
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 ALA 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A ILE* 3.5 21.0 - - + +
56A VAL 5.5 1.1 - - - +
57A ASP* 2.9 17.4 + - - +
59A HIS* 1.3 79.4 - - - +
61A LYS* 1.3 64.2 + - - +
62A GLY 3.2 3.1 - - - +
63A ASP* 3.2 19.6 + - + +
64A TYR* 3.0 17.8 + - - +
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Residues in contact with LYS 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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41A ALA* 3.7 33.4 - - + +
44A LEU* 3.7 16.8 - - + +
45A GLU* 3.6 19.7 + - - +
50A SER* 4.1 24.5 + - - -
53A LEU* 3.9 15.7 - - + -
57A ASP 3.7 0.9 + - - -
58A LYS* 3.6 36.7 - - - +
59A HIS 3.6 2.4 + - - -
60A ALA* 1.3 77.1 - - - +
62A GLY* 1.3 61.7 + - - +
64A TYR* 3.3 5.7 + - - +
65A ALA* 3.1 20.1 + - - +
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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
----------------------------------------------------------
37A ASN* 3.7 23.8 + - - +
40A LEU* 3.7 25.1 - - - +
41A ALA* 4.3 4.2 - - - +
60A ALA 3.2 1.2 - - - -
61A LYS* 1.3 76.3 - - - +
63A ASP* 1.3 64.3 + - - +
65A ALA* 3.2 4.2 + - - +
66A GLU* 3.0 30.3 + - - +
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Residues in contact with ASP 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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3A ILE* 4.1 17.0 - - + -
5A LYS* 5.5 5.0 + - - +
8A ALA* 3.7 13.5 - - + +
37A ASN* 4.0 11.8 - - - +
60A ALA* 3.2 25.3 + - + +
62A GLY* 1.3 74.7 - - - +
64A TYR* 1.3 62.8 + - - +
66A GLU* 3.3 17.7 + - - +
67A ALA* 3.0 24.8 + - - +
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Residues in contact with TYR 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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2A GLU* 4.7 25.9 + - + -
3A ILE* 3.8 27.7 - - + +
44A LEU* 3.9 27.4 - - + -
49A LEU* 5.2 8.0 + - + +
52A ASN* 5.4 6.1 + - - +
53A LEU* 3.3 33.1 - - + +
57A ASP* 4.9 3.8 - - + -
60A ALA 3.0 13.8 + - - +
61A LYS* 3.5 11.0 - - - +
63A ASP* 1.3 78.7 - - - +
65A ALA* 1.3 64.9 + - - +
67A ALA* 3.3 3.7 + - - +
68A LEU* 3.0 39.3 + - + +
121A TYR* 5.8 0.3 + - - -
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.2 24.9 - - + +
44A LEU* 4.3 6.7 - - + -
61A LYS 3.1 12.3 + - - +
62A GLY 3.2 7.8 + - - +
64A TYR* 1.3 80.0 - - - +
66A GLU* 1.3 63.0 + - - +
68A LEU* 3.3 8.5 + - - +
69A ILE* 3.1 30.0 + - - +
113A LEU* 4.2 26.4 - - + +
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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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7A LEU 4.2 0.4 - - - -
8A ALA* 3.3 22.5 - - - +
11A GLY* 3.3 16.5 - - - +
12A ASP* 3.3 41.6 - - - +
15A ILE* 4.8 4.0 - - + +
37A ASN* 6.0 0.7 - - - -
40A LEU* 3.5 25.2 - - + +
62A GLY 3.0 15.7 + - - +
63A ASP* 3.6 23.2 - - - +
64A TYR 3.3 0.2 - - - -
65A ALA* 1.3 77.0 - - - +
67A ALA* 1.3 56.6 + - - +
69A ILE* 3.3 6.7 + - - +
70A ALA* 2.9 23.7 + - - +
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Residues in contact with ALA 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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2A GLU 5.9 0.7 - - - +
3A ILE* 4.5 9.0 - - + -
4A ASP 4.3 8.5 - - - +
7A LEU* 3.8 35.7 - - + +
8A ALA* 3.9 6.4 - - + +
63A ASP 3.0 16.1 + - - +
64A TYR* 3.7 4.7 - - - +
66A GLU* 1.3 73.5 - - - +
68A LEU* 1.3 65.2 + - - +
70A ALA* 3.7 1.0 - - - +
71A LYS* 2.9 28.1 + - - +
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Residues in contact with LEU 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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44A LEU* 5.0 3.4 - - + -
49A LEU* 4.1 26.7 - - + -
64A TYR* 3.0 34.5 + - + +
65A ALA 3.4 7.4 - - - +
67A ALA* 1.3 76.4 - - - +
69A ILE* 1.3 62.9 + - - +
71A LYS* 3.3 8.4 + - + +
72A ALA* 3.1 22.9 + - - +
113A LEU* 4.4 24.7 - - + +
116A ILE* 3.8 11.3 - - + +
117A SER* 4.5 8.7 - - - -
120A LEU* 3.5 25.3 - - + +
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Residues in contact with ILE 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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11A GLY* 5.1 1.8 - - - +
14A LEU* 3.8 24.5 - - + -
15A ILE* 3.8 39.9 - - + -
18A LEU* 4.9 5.2 - - + -
40A LEU* 4.8 8.1 - - + -
65A ALA 3.1 17.6 + - - +
66A GLU* 3.6 9.0 - - - +
68A LEU* 1.3 75.7 - - - +
70A ALA* 1.3 63.5 + - - +
72A ALA* 3.4 2.3 + - - +
73A TRP* 3.1 22.7 + - + +
78A ILE* 5.3 1.6 - - + +
109A LEU* 5.7 1.3 - - + -
112A LEU* 4.8 4.7 - - + -
113A LEU* 3.8 25.1 - - + -
116A ILE* 3.8 22.8 - - + +
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Residues in contact with ALA 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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7A LEU* 3.1 34.5 - - + +
10A PHE* 3.7 17.0 - - + -
11A GLY* 3.7 12.1 - - - +
14A LEU* 4.6 1.1 - - - -
66A GLU 2.9 12.4 + - - +
67A ALA 3.7 3.6 - - - +
68A LEU 3.3 0.2 - - - -
69A ILE* 1.3 75.8 - - - +
71A LYS* 1.3 58.8 + - - +
73A TRP* 3.3 4.4 + - - +
74A LEU* 2.8 39.5 + - + +
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Residues in contact with LYS 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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2A GLU 5.9 0.8 + - - -
7A LEU* 3.8 25.9 - - + +
67A ALA 2.9 18.1 + - - +
68A LEU* 3.6 8.4 - - + +
69A ILE 3.3 0.2 - - - -
70A ALA* 1.3 76.7 - - - +
72A ALA* 1.3 60.8 + - - +
74A LEU* 4.0 7.9 - - - +
75A MET* 3.1 30.4 + - + +
120A LEU* 4.0 24.5 - - + -
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Residues in contact with ALA 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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68A LEU 3.1 4.6 + - - +
69A ILE 3.8 3.6 - - - +
71A LYS* 1.3 79.5 - - - +
73A TRP* 1.3 60.5 + - - +
75A MET 3.5 0.5 + - - -
76A GLY 3.3 3.1 + - - -
77A LEU* 2.8 38.3 + - + +
78A ILE* 4.2 15.3 - - + -
116A ILE* 3.4 35.2 - - + +
120A LEU* 4.1 17.4 - - + +
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Residues in contact with TRP 73 (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 PHE* 3.6 31.4 - + - -
14A LEU* 3.5 26.5 - - + -
18A LEU* 5.7 2.2 - - + -
69A ILE* 3.1 16.7 + - + +
70A ALA 3.7 1.8 - - - +
72A ALA* 1.3 75.3 - - - +
74A LEU* 1.3 74.0 + - + +
76A GLY* 3.0 14.2 + - - -
78A ILE* 3.5 28.1 - - + +
79A SER* 3.9 2.7 - - - -
80A GLU* 3.3 46.0 - - + -
17B PHE* 3.9 24.9 - + - -
21B LEU* 4.6 6.1 - - + +
80B GLU* 4.5 10.8 - - - -
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Residues in contact with LEU 74 (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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7A LEU* 5.1 4.0 - - + -
10A PHE* 3.9 35.2 - - + -
70A ALA* 2.8 32.6 + - + +
71A LYS* 4.0 6.1 - - - +
73A TRP* 1.3 78.0 - - + +
75A MET* 1.3 65.8 + - - +
76A GLY 3.5 0.5 + - - -
21B LEU* 5.8 1.6 - - + -
24B THR* 5.4 8.3 - - + -
30B PRO* 3.9 29.6 - - + -
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Residues in contact with MET 75 (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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71A LYS* 3.1 21.5 + - + +
72A ALA 3.9 4.0 - - - +
73A TRP 3.2 0.2 - - - -
74A LEU* 1.3 81.4 - - - +
76A GLY* 1.3 60.9 + - - +
77A LEU* 4.2 22.7 - - + +
120A LEU* 5.4 2.7 - - + -
123A SER* 6.2 2.5 - - - -
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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