Contacts of the helix formed by residues 48 - 62 (chain A) in PDB entry 1Z6T
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 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A GLU 3.2 0.8 + - - -
47A PRO* 1.3 90.3 - - + +
49A GLN* 1.3 59.7 + - - +
50A GLN* 3.8 4.9 + - - +
51A GLN* 3.2 39.4 + - - +
52A ARG* 2.9 36.0 + - - +
409A GLU* 3.7 14.6 - - - +
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Residues in contact with GLN 49 (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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17A GLU 5.6 0.2 - - - +
18A LYS 4.1 13.3 + - - -
19A ASP* 3.8 20.8 + - - +
20A ILE 3.8 13.2 + - - +
21A LYS* 3.6 37.7 - - + +
22A THR* 5.1 1.2 + - - +
48A THR* 1.3 74.3 - - - +
50A GLN* 1.3 61.0 + - + +
52A ARG* 3.6 9.7 + - - +
53A ALA* 3.1 24.6 + - - +
408A THR* 4.6 10.2 - - - +
409A GLU* 3.2 25.3 + - + +
412A GLU* 5.0 0.5 - - - +
431A LYS* 5.8 0.8 - - - +
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Residues in contact with GLN 50 (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* 3.4 24.6 - - + +
18A LYS* 3.5 38.7 + - - +
48A THR* 3.3 5.8 + - - +
49A GLN* 1.3 81.0 - - + +
51A GLN* 1.3 62.6 + - + +
53A ALA* 3.4 2.1 + - - +
54A ALA* 2.8 27.4 + - - +
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Residues in contact with GLN 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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46A GLU* 3.5 24.8 - - + +
47A PRO* 3.4 24.1 - - - +
48A THR* 3.2 30.5 + - - +
50A GLN* 1.3 76.6 - - + +
52A ARG* 1.3 60.6 + - - +
54A ALA* 3.7 7.6 - - + +
55A MET* 3.0 30.1 + - - +
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Residues in contact with ARG 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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22A THR* 3.5 24.3 + - - +
23A SER* 5.9 4.0 - - - -
26A MET* 6.2 0.2 - - - -
43A VAL* 3.1 37.4 - - + +
44A ARG* 3.5 29.9 + - - +
46A GLU* 3.3 20.4 + - - +
47A PRO 5.4 2.2 + - - -
48A THR 2.9 23.7 + - - +
49A GLN* 3.6 8.7 - - - +
51A GLN* 1.3 76.9 - - - +
53A ALA* 1.3 56.0 + - - +
55A MET* 3.4 0.3 + - - +
56A LEU* 3.0 25.8 + - - +
409A GLU* 4.2 22.6 + - - +
413A ASP* 2.9 41.0 + - - -
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Residues in contact with ALA 53 (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* 3.7 25.4 - - - +
20A ILE* 3.7 28.2 - - + +
22A THR* 3.7 10.7 - - + +
49A GLN 3.1 15.1 + - - +
50A GLN 3.5 8.1 - - - +
51A GLN 3.3 0.2 - - - -
52A ARG* 1.3 76.0 - - - +
54A ALA* 1.3 55.6 + - - +
56A LEU* 3.5 1.8 + - - +
57A ILE* 3.1 35.0 + - - +
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Residues in contact with ALA 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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13A ARG* 4.1 1.0 + - - -
17A GLU* 3.7 27.5 - - - +
50A GLN 2.8 17.0 + - - +
51A GLN* 3.7 10.1 - - + +
53A ALA* 1.3 72.4 - - - +
55A MET* 1.3 66.7 + - - +
57A ILE* 3.5 1.8 + - - +
58A LYS* 3.0 42.5 + - - +
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Residues in contact with MET 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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42A LYS* 3.8 40.6 - - + +
43A VAL* 3.7 26.9 - - + +
46A GLU* 3.9 27.4 - - + +
51A GLN 3.0 16.8 + - - +
52A ARG 3.6 4.7 - - - +
54A ALA* 1.3 76.5 - - - +
56A LEU* 1.3 62.7 + - - +
58A LYS* 3.2 29.4 - - + +
59A MET* 3.0 28.9 + - - +
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Residues in contact with LEU 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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20A ILE* 4.7 3.4 - - + -
22A THR* 3.8 22.7 - - + -
25A ILE* 4.1 20.0 - - + -
26A MET* 4.0 26.9 - - + -
29A MET* 5.0 2.2 - - - -
35A LEU* 3.9 28.3 - - + -
43A VAL* 3.9 11.6 - - + +
52A ARG 3.0 17.9 + - - +
53A ALA 3.8 3.8 - - - +
55A MET* 1.3 76.1 - - - +
57A ILE* 1.3 58.7 + - + +
59A MET* 2.9 9.4 + - + +
60A ILE* 2.9 42.8 + - + +
71A PHE* 4.3 11.2 - - + -
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Residues in contact with ILE 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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9A LEU* 4.4 14.4 - - + -
13A ARG* 3.5 32.8 - - + +
16A LEU* 3.4 36.3 - - + -
17A GLU* 3.9 18.2 - - + +
20A ILE* 4.7 7.0 - - + -
53A ALA 3.1 19.0 + - - +
54A ALA 4.0 3.1 - - - +
56A LEU* 1.3 79.4 - - + +
58A LYS* 1.3 55.9 + - - +
60A ILE* 3.4 7.6 + - - +
61A LEU* 2.9 36.5 + - + +
71A PHE* 4.4 19.7 - - + -
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Residues in contact with LYS 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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13A ARG* 2.8 29.1 - - - +
17A GLU* 5.6 0.7 - - - -
54A ALA* 3.0 35.0 + - - +
55A MET* 3.2 28.2 - - + +
57A ILE* 1.3 76.2 - - - +
59A MET* 1.3 63.0 + - + +
61A LEU* 3.5 14.4 + - - +
62A LYS* 3.7 18.7 + - - +
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Residues in contact with MET 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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35A LEU* 4.8 4.9 - - + -
39A GLU* 3.4 67.1 - - + +
42A LYS* 3.8 30.3 - - + +
43A VAL* 3.8 17.7 - - - -
55A MET* 3.0 18.3 + - - +
56A LEU* 2.9 12.3 + - + +
58A LYS* 1.3 72.4 - - + +
60A ILE* 1.3 66.2 + - - +
62A LYS* 3.0 19.4 + - - +
63A LYS* 3.4 18.8 - - - +
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Residues in contact with ILE 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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1A MET* 3.5 10.8 - - + +
9A LEU* 4.0 17.3 - - + -
29A MET* 3.7 22.7 - - + -
35A LEU* 5.4 1.8 - - + -
56A LEU* 2.9 34.1 + - + +
57A ILE* 3.8 6.3 - - - +
59A MET* 1.3 76.4 - - + +
61A LEU* 1.3 62.3 + - - +
63A LYS* 3.2 25.6 + - + +
67A SER* 4.7 3.6 - - - -
68A TYR* 4.6 19.1 - - - +
71A PHE* 3.5 47.8 - - + -
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Residues in contact with LEU 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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1A MET* 4.5 10.2 + - - +
6A ARG* 4.4 22.5 + - + -
9A LEU* 3.3 36.3 - - + -
10A LEU* 3.5 36.3 - - + -
13A ARG* 3.5 36.8 - - + +
57A ILE* 2.9 20.6 + - + +
58A LYS* 3.7 7.6 - - - +
59A MET 3.2 0.6 - - - -
60A ILE* 1.3 76.6 - - - +
62A LYS* 1.3 59.0 + - + +
63A LYS 3.2 6.7 + - - +
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Residues in contact with LYS 62 (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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58A LYS* 3.7 14.8 + - - +
59A MET* 3.0 10.7 + - - +
61A LEU* 1.3 77.7 - - + +
63A LYS* 1.3 64.8 + - - +
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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