Contacts of the helix formed by residues 5 - 25 (chain A) in PDB entry 1ZH5
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 GLY 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ASP* 1.3 67.5 + - - -
7A ASN* 3.4 2.7 - - - -
8A GLU* 3.1 26.4 + - - +
9A LYS* 3.0 31.8 + - - +
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Residues in contact with ASP 6 (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 GLY* 1.3 71.2 - - - -
7A ASN* 1.3 57.3 + - - +
9A LYS* 3.3 16.4 + - - +
10A MSE 2.8 34.2 + - - +
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Residues in contact with ASN 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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5A GLY* 3.4 1.0 - - - -
6A ASP* 1.3 75.6 - - - +
8A GLU* 1.3 57.7 + - - +
10A MSE 3.3 7.0 + - - +
11A ALA* 2.9 31.8 + - - +
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Residues in contact with GLU 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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5A GLY* 3.1 26.2 + - - +
7A ASN* 1.3 79.5 - - - +
9A LYS* 1.3 65.8 + - + +
11A ALA* 3.4 6.5 + - - +
12A ALA* 3.2 22.0 + - - +
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Residues in contact with LYS 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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5A GLY 3.0 22.3 + - - +
6A ASP* 3.8 20.0 - - - +
8A GLU* 1.3 79.2 - - + +
10A MSE 1.3 64.8 + - - +
12A ALA* 3.4 6.6 + - - +
13A LEU* 3.1 23.4 + - - +
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Residues in contact with MSE 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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6A ASP* 2.8 20.6 + - + +
7A ASN* 3.7 8.3 - - - +
9A LYS* 1.3 76.7 - - - +
11A ALA* 1.3 57.6 + - - +
13A LEU* 3.5 16.7 + - + +
14A GLU* 3.0 56.5 + - - +
67A VAL* 4.2 28.3 - - + -
70A GLU* 4.7 4.9 - - - +
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Residues in contact with ALA 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 ASN 2.9 18.1 + - - +
8A GLU* 3.8 6.7 - - - +
9A LYS 3.2 0.2 - - - -
10A MSE 1.3 75.2 - - - +
12A ALA* 1.3 63.8 + - - +
14A GLU* 3.5 8.5 + - - +
15A ALA* 3.1 23.0 + - - +
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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 GLU 3.2 14.2 + - - +
9A LYS* 3.8 9.2 - - - +
10A MSE 3.4 0.2 - - - -
11A ALA* 1.3 75.7 - - - +
13A LEU* 1.3 60.3 + - - +
15A ALA* 3.4 7.7 + - - +
16A LYS* 3.4 29.3 + - - +
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Residues in contact with LEU 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 LYS 3.1 17.1 + - - +
10A MSE 3.8 27.1 - - + +
11A ALA 3.3 0.2 - - - -
12A ALA* 1.3 76.0 - - - +
14A GLU* 1.3 63.6 + - - +
16A LYS* 3.1 11.9 + - + +
17A ILE* 3.0 36.9 + - + +
61A LEU* 3.7 48.9 - - + +
62A THR* 4.9 2.0 - - - -
67A VAL* 4.6 5.4 - - + -
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Residues in contact with GLU 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 MSE 3.0 43.2 + - - +
11A ALA* 3.9 7.7 - - - +
12A ALA 3.4 0.2 - - - -
13A LEU* 1.3 75.3 - - - +
15A ALA* 1.3 63.0 + - - +
17A ILE* 3.3 6.8 + - - +
18A CYS* 3.0 28.0 + - - -
67A VAL* 4.1 13.0 - - + +
70A GLU* 2.6 30.3 - - - +
71A ALA* 3.7 32.2 + - + +
74A LYS* 3.7 25.1 + - - +
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Residues in contact with ALA 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 ALA 3.1 13.8 + - - +
12A ALA* 3.7 10.8 - - - +
13A LEU 3.3 0.4 - - - -
14A GLU* 1.3 75.7 - - - +
16A LYS* 1.3 62.9 + - + +
18A CYS* 3.4 8.2 + - - +
19A HIS* 3.1 41.2 + - + +
501A SO4 4.6 0.2 - - - -
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Residues in contact with LYS 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* 3.4 15.1 + - - +
13A LEU* 3.1 13.8 + - + +
15A ALA* 1.3 74.6 - - + +
17A ILE* 1.3 61.8 + - - +
19A HIS* 3.5 2.6 + - - +
20A GLN* 3.0 29.8 + - - +
61A LEU* 3.9 27.6 - - + +
501A SO4 3.7 35.9 + - - +
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Residues in contact with ILE 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 LEU* 3.0 26.9 + - + +
14A GLU* 3.5 12.3 - - - +
16A LYS* 1.3 73.8 - - - +
18A CYS* 1.3 65.7 + - - +
20A GLN* 3.3 2.6 + - - +
21A ILE* 3.1 43.3 + - + +
58A LEU* 4.2 8.7 - - + -
61A LEU* 4.0 24.9 - - + -
62A THR* 3.5 27.1 - - + -
67A VAL* 3.7 24.7 - - + +
68A ILE* 4.5 9.4 - - + -
71A ALA* 4.0 13.7 - - + -
72A LEU* 5.6 0.9 - - + -
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Residues in contact with CYS 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 GLU 3.0 15.1 + - - -
15A ALA* 3.6 10.8 - - - +
16A LYS 3.4 0.2 - - - -
17A ILE* 1.3 75.1 - - - +
19A HIS* 1.3 60.7 + - + +
21A ILE* 3.4 1.0 + - - +
22A GLU* 2.9 47.9 + - - +
71A ALA* 3.1 37.7 - - - -
72A LEU* 4.0 14.1 - - - +
75A SER* 3.8 21.1 - - - +
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Residues in contact with HIS 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 ALA* 3.1 25.1 + - + +
16A LYS 3.8 2.5 - - - +
17A ILE 3.4 0.2 - - - -
18A CYS* 1.3 81.0 - - + +
20A GLN* 1.3 57.1 + - - +
22A GLU* 3.5 15.6 + - - +
23A TYR* 3.0 28.9 + - - +
501A SO4 2.8 39.3 + - - +
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Residues in contact with GLN 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 LYS 3.0 17.4 + - - +
17A ILE* 3.8 4.3 - - - +
19A HIS* 1.3 75.8 - - - +
21A ILE* 1.3 64.8 + - + +
23A TYR* 3.2 5.7 + - - +
24A TYR* 3.1 62.5 + - + +
57A ARG* 3.0 43.7 + - + +
58A LEU* 4.2 10.5 - - + +
61A LEU* 4.4 10.9 - - + +
128A LYS* 4.8 4.2 + - - -
8D U 3.1 22.3 + - - +
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Residues in contact with ILE 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 ILE* 3.1 27.4 + - + +
18A CYS 4.1 2.2 - - - +
20A GLN* 1.3 76.0 - - + +
22A GLU* 1.3 61.3 + - - +
24A TYR* 3.1 11.1 + - + +
25A PHE* 3.1 43.0 + - + -
49A LEU* 5.8 0.4 - - + -
52A MSE 5.1 2.9 - - + -
58A LEU* 4.2 28.0 - - + -
68A ILE* 3.8 28.5 - - + -
72A LEU* 4.2 14.6 - - + -
80A MSE 4.0 13.9 - - + -
89A ILE* 4.0 20.2 - - + -
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Residues in contact with GLU 22 (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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18A CYS* 2.9 31.6 + - - +
19A HIS* 3.9 17.2 + - - +
21A ILE* 1.3 74.9 - - - +
23A TYR* 1.3 62.3 + - - +
25A PHE 3.7 1.4 + - - -
26A GLY* 3.2 21.3 + - - -
72A LEU* 4.6 4.8 - - + +
75A SER* 2.7 31.9 + - - -
77A ALA* 3.7 20.0 - - + +
79A LEU* 3.9 31.5 + - + +
80A MSE 4.2 15.9 + - + +
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Residues in contact with TYR 23 (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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19A HIS 3.0 15.0 + - - +
20A GLN* 3.6 13.9 - - - +
21A ILE 3.2 0.2 - - - -
22A GLU* 1.3 74.8 - - - +
24A TYR* 1.3 68.6 + - - +
26A GLY* 3.1 13.6 + - - -
28A PHE* 3.8 9.8 + - + -
29A ASN* 3.5 28.1 - - + +
32A ARG* 3.1 20.0 + - - -
138A LEU 3.8 17.9 - - - -
139A ASN* 2.7 29.1 + - - -
8D U 3.4 70.7 - + - +
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Residues in contact with TYR 24 (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 GLN* 3.1 43.2 + - + -
21A ILE* 3.1 10.5 + - - +
23A TYR* 1.3 77.5 - + - +
25A PHE* 1.3 61.1 + - + +
26A GLY 3.2 2.0 + - - -
29A ASN* 3.0 26.4 - - - +
30A LEU* 3.7 6.9 + - - -
36A LEU* 3.4 22.6 - - + +
52A MSE 3.8 14.6 - - + -
55A PHE* 3.6 40.9 - + + +
57A ARG* 3.5 4.3 + - - +
58A LEU* 3.3 29.8 + - + -
8D U 3.5 23.3 - - - -
9D U 2.7 30.4 + - - -
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Residues in contact with PHE 25 (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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21A ILE* 3.1 23.9 + - + +
22A GLU 3.8 2.9 - - - +
24A TYR* 1.3 78.1 - - + +
26A GLY* 1.3 52.0 + - - +
30A LEU* 3.7 12.0 - - + +
36A LEU* 4.1 9.6 - - + -
40A ILE* 3.7 31.0 - - + -
45A GLY 4.9 0.2 - - - -
47A VAL* 4.0 17.3 - - + -
52A MSE 3.9 38.8 - - + -
79A LEU* 4.6 3.0 - - + +
80A MSE 3.3 44.9 - - + -
89A ILE* 4.1 7.6 - - + -
90A ARG* 4.7 3.1 - - - -
91A ARG* 2.8 53.9 + - + -
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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
------------------------------------------------------------
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