Contacts of the helix formed by residues 6 - 21 (chain A) in PDB entry 1Z0X
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 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LYS 4.6 0.9 + - - -
5A LEU* 1.3 78.6 - - - +
7A LYS* 1.3 66.7 + - - +
8A ASP* 3.7 11.7 + - - +
9A THR* 2.9 29.5 + - - -
10A ILE* 2.9 16.9 + - - +
46A TYR* 3.5 13.9 - - - -
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Residues in contact with LYS 7 (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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6A SER* 1.3 72.5 - - - +
8A ASP* 1.3 64.7 + - - +
10A ILE* 3.2 9.1 + - - +
11A ILE* 2.8 38.4 + - + +
46A TYR* 3.7 35.3 + - + +
47A PHE* 4.0 23.6 - - + -
56A SER* 5.3 4.9 - - - +
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Residues in contact with ASP 8 (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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6A SER* 3.2 9.8 + - - +
7A LYS* 1.3 81.3 + - - +
9A THR* 1.3 57.1 + - - +
11A ILE* 3.6 7.8 + - - +
12A ALA* 3.0 29.1 + - - +
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Residues in contact with THR 9 (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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4A LYS* 2.7 34.2 + - + +
5A LEU* 4.1 10.1 - - + -
6A SER* 2.9 17.1 + - - -
8A ASP* 1.3 77.6 - - - +
10A ILE* 1.3 67.1 + - - +
12A ALA* 3.4 5.8 + - - +
13A ALA* 3.0 22.3 + - - +
36A LEU* 3.7 27.4 - - + +
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Residues in contact with ILE 10 (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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5A LEU* 3.9 21.8 - - + -
6A SER 2.9 20.4 + - - +
7A LYS* 3.6 4.7 - - - +
9A THR* 1.3 75.3 - - - +
11A ILE* 1.3 63.7 + - - +
13A ALA* 3.1 5.2 + - - +
14A ALA* 3.0 21.7 + - - +
32A VAL* 3.6 21.7 - - + +
36A LEU* 3.9 11.7 - - + -
43A ILE* 3.5 34.5 - - + -
46A TYR* 4.5 11.9 - - + -
47A PHE* 3.7 27.8 - - + -
53A LEU* 4.3 7.9 - - + -
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Residues in contact with ILE 11 (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 LYS* 2.8 30.3 + - + +
8A ASP* 3.7 7.2 - - - +
10A ILE* 1.3 76.2 - - - +
12A ALA* 1.3 64.1 + - - +
14A ALA* 3.2 6.8 + - - +
15A PHE* 3.1 44.0 + - + -
47A PHE* 3.5 14.6 - - + -
53A LEU* 3.3 30.5 - - + -
56A SER* 3.8 19.1 - - - +
57A MSE 4.1 8.3 - - + -
60A ALA* 4.1 17.7 - - + -
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Residues in contact with ALA 12 (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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8A ASP 3.0 18.8 + - - +
9A THR* 3.7 6.7 - - - +
10A ILE 3.2 0.2 - - - -
11A ILE* 1.3 74.7 - - - +
13A ALA* 1.3 59.0 + - - +
15A PHE* 3.0 10.0 + - - +
16A SER* 2.8 34.7 + - - +
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Residues in contact with ALA 13 (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 THR 3.0 7.7 + - - +
10A ILE 3.1 8.7 + - - +
12A ALA* 1.3 75.3 - - - +
14A ALA* 1.3 57.2 + - - +
16A SER* 3.6 5.1 - - - -
17A LEU* 2.9 31.2 + - - +
32A VAL* 4.4 2.9 - - + -
35A GLN* 3.6 23.1 - - + +
36A LEU* 3.4 40.6 - - + -
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Residues in contact with ALA 14 (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 ILE 3.0 10.6 + - - +
11A ILE* 3.3 11.4 - - - +
12A ALA 3.1 0.2 - - - -
13A ALA* 1.3 76.9 - - - +
15A PHE* 1.3 57.2 + - - +
17A LEU* 3.1 9.7 + - - +
18A LEU* 2.9 30.0 + - - +
27A LEU* 4.1 11.1 - - + +
32A VAL* 4.2 17.0 - - + +
53A LEU* 4.4 4.7 - - + -
57A MSE 3.4 28.9 - - + -
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Residues in contact with PHE 15 (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 ILE* 3.1 39.2 + - + -
12A ALA* 3.0 9.9 + - - +
14A ALA* 1.3 76.9 - - - +
16A SER* 1.3 59.6 + - - +
18A LEU* 3.1 6.4 + - + +
19A GLU* 2.8 33.3 + - + +
57A MSE 3.8 26.2 - - + -
60A ALA* 4.4 6.3 - - + -
61A ILE* 3.7 27.6 - - + -
92A PHE* 3.8 23.3 - + + -
93A PRO* 3.7 31.6 - - + +
98A ILE* 3.7 20.4 - - + -
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Residues in contact with SER 16 (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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12A ALA* 2.8 21.5 + - - +
13A ALA* 3.6 8.1 - - - -
15A PHE* 1.3 76.4 - - - +
17A LEU* 1.3 65.0 + - - +
19A GLU* 3.1 24.2 + - - +
20A LYS* 3.4 18.5 + - - +
35A GLN* 4.5 13.5 - - - -
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Residues in contact with LEU 17 (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 ALA 2.9 12.0 + - - +
14A ALA 3.1 11.9 - - - +
16A SER* 1.3 78.7 - - - +
18A LEU* 1.3 58.0 + - - -
20A LYS* 3.7 8.8 + - + +
21A SER* 3.4 18.4 + - - +
27A LEU* 3.5 28.0 - - + -
31A LYS* 3.7 42.8 - - + +
32A VAL* 3.8 8.7 - - + +
35A GLN* 3.1 28.4 + - + +
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Residues in contact with LEU 18 (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 ALA 2.9 12.6 + - - +
15A PHE* 3.1 10.3 + - + +
17A LEU* 1.3 76.6 - - - +
19A GLU* 1.3 62.3 + - - +
21A SER 3.8 5.6 - - - +
22A PRO* 2.6 33.1 - - - +
23A THR 4.1 6.5 - - - +
24A LEU* 3.8 33.7 - - + +
27A LEU* 4.5 19.7 - - + +
57A MSE 4.0 26.5 - - + -
93A PRO* 4.0 28.0 - - + +
94A CYS* 4.0 15.0 - - + -
98A ILE* 4.4 6.1 - - + -
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Residues in contact with GLU 19 (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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15A PHE* 2.8 15.0 + - + +
16A SER* 3.1 12.7 + - - +
18A LEU* 1.3 77.3 - - - +
20A LYS* 1.3 64.3 + - + +
22A PRO* 3.5 9.1 - - - +
91A GLN 5.7 0.3 - - - +
93A PRO* 3.4 28.7 - - + +
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Residues in contact with LYS 20 (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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16A SER* 3.4 16.1 + - - +
17A LEU* 4.0 8.7 - - + +
18A LEU 3.2 0.4 - - - -
19A GLU* 1.3 82.0 - - + +
21A SER* 1.3 66.9 + - - +
22A PRO* 3.7 3.8 - - - +
35A GLN* 4.4 23.0 + - - +
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Residues in contact with SER 21 (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 LEU 3.4 8.2 + - - +
18A LEU* 2.9 14.3 + - - +
20A LYS* 1.3 84.0 + - - +
22A PRO* 1.3 53.3 - - - +
23A THR* 2.6 26.5 + - - +
26A GLN* 4.0 17.5 - - - +
153A GLN* 5.7 1.6 - - - -
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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