Contacts of the helix formed by residues 15 - 29 (chain A) in PDB entry 1EZW
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 LYS 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ASP* 1.3 90.1 + - - +
16A PRO* 1.3 74.9 - - + +
17A THR* 4.1 14.6 - - - +
18A LYS* 2.8 21.9 + - + +
19A ILE* 3.0 10.2 + - - +
43A TYR* 4.7 2.7 - - - +
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Residues in contact with PRO 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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14A ASP 3.6 5.8 - - - +
15A LYS* 1.3 82.9 - - + +
17A THR* 1.3 57.4 + - + +
19A ILE* 3.3 9.1 + - + +
20A ALA* 2.9 28.9 + - - +
43A TYR* 3.8 44.9 - - + +
47A GLY 6.1 0.7 - - - -
48A VAL* 4.4 16.6 - - + +
51A LEU* 3.6 18.5 - - + +
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Residues in contact with THR 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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15A LYS* 4.1 12.0 - - - +
16A PRO* 1.3 75.1 - - + +
18A LYS* 1.3 61.3 + - - +
20A ALA* 3.9 3.5 - - - +
21A HIS* 3.0 27.5 + - - +
51A LEU* 4.1 20.6 - - + -
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Residues in contact with LYS 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 ASP* 3.6 27.1 + - + +
15A LYS* 2.8 21.5 + - + +
17A THR* 1.3 78.2 + - - +
19A ILE* 1.3 61.3 + - + +
21A HIS* 3.2 16.5 + - + +
22A LEU* 2.8 53.6 + - + +
333A GLU* 5.9 0.9 - - - -
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Residues in contact with ILE 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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10A LEU* 4.0 22.6 - - + +
11A LEU 3.6 22.7 - - - +
12A PRO* 4.2 11.0 - - + -
14A ASP* 3.9 26.7 - - + +
15A LYS 3.0 16.4 + - - +
16A PRO* 3.6 7.9 - - + +
18A LYS* 1.3 79.7 - - + +
20A ALA* 1.3 60.5 + - - +
22A LEU* 3.2 7.3 + - + +
23A ILE* 3.0 26.1 + - + +
36A ILE* 3.6 21.5 - - + -
48A VAL* 3.6 25.6 - - + -
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Residues in contact with ALA 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 PRO 2.9 18.2 + - - +
17A THR* 3.9 4.7 - - - +
19A ILE* 1.3 77.2 - - - +
21A HIS* 1.3 61.1 + - - +
23A ILE* 3.2 4.5 + - - +
24A LYS* 3.0 21.1 + - - +
48A VAL* 5.2 1.5 - - - +
51A LEU* 4.0 18.2 - - + +
52A ALA* 4.0 32.8 - - - +
55A ILE* 4.3 15.5 - - + +
56A THR* 4.7 1.9 - - - +
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Residues in contact with HIS 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 THR 3.0 20.0 + - - +
18A LYS* 3.2 19.7 + - + +
20A ALA* 1.3 74.4 - - - +
22A LEU* 1.3 69.6 + - + +
24A LYS* 3.1 12.1 + - + +
25A VAL* 2.9 44.9 + - + +
55A ILE* 5.0 4.5 - - - +
333A GLU* 2.7 35.0 + - - -
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Residues in contact with LEU 22 (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 ILE* 5.2 0.4 - - - -
10A LEU* 3.9 22.9 - - + -
14A ASP* 5.9 0.2 - - - +
18A LYS* 2.8 43.5 + - + +
19A ILE* 3.8 8.5 - - + +
21A HIS* 1.3 81.6 - - + +
23A ILE* 1.3 58.5 + - - +
25A VAL* 3.2 5.2 + - + +
26A ALA* 2.8 29.3 + - - +
332A LYS* 4.0 29.4 - - + -
333A GLU* 3.8 38.6 - - + +
336A ILE* 3.9 14.8 - - + +
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Residues in contact with ILE 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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8A ILE* 4.9 2.7 - - + -
10A LEU* 3.8 13.0 - - + -
19A ILE* 3.0 27.6 + - + +
20A ALA* 3.6 8.1 - - - +
22A LEU* 1.3 78.0 - - - +
24A LYS* 1.3 56.6 + - - +
26A ALA* 3.2 7.1 + - - +
27A GLU* 2.9 27.2 + - - +
34A ALA* 3.7 34.3 - - + -
36A ILE* 4.2 18.2 - - + -
48A VAL* 5.5 0.2 - - + -
52A ALA* 3.8 22.0 - - + -
56A THR* 3.9 9.2 - - + -
59A ILE* 3.8 18.2 - - + -
61A LEU* 4.0 7.0 - - + -
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Residues in contact with LYS 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 ALA 3.0 12.2 + - - +
21A HIS* 3.1 12.8 + - - +
23A ILE* 1.3 77.4 - - - +
25A VAL* 1.3 57.9 + - + +
27A GLU* 3.2 18.8 + - - +
28A ASP* 2.7 67.4 + - - +
55A ILE* 3.4 35.2 - - + +
56A THR* 3.8 9.4 - - + +
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Residues in contact with VAL 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 HIS* 2.9 47.7 + - + +
22A LEU* 3.2 8.7 + - - +
24A LYS* 1.3 75.1 - - + +
26A ALA* 1.3 65.3 + - - +
28A ASP* 3.2 9.4 + - + +
29A ASN* 2.8 43.6 + - - +
333A GLU* 4.3 18.6 - - + +
336A ILE* 3.8 16.8 - - + -
337A GLU* 3.9 19.1 - - + +
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Residues in contact with ALA 26 (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 ILE* 3.9 24.9 - - + -
22A LEU 2.8 13.9 + - - +
23A ILE 3.5 7.6 - - - +
24A LYS 3.2 0.2 - - - -
25A VAL* 1.3 75.7 - - - +
27A GLU* 1.3 62.9 + - - +
29A ASN 3.0 7.4 + - - -
30A GLY 3.2 0.3 + - - -
31A PHE* 3.0 48.0 + - + -
59A ILE* 4.3 2.0 - - + -
336A ILE* 3.5 17.8 - - + +
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Residues in contact with GLU 27 (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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23A ILE 2.9 17.1 + - - +
24A LYS* 3.5 21.3 - - - +
26A ALA* 1.3 72.3 - - - +
28A ASP* 1.3 66.8 + - - +
29A ASN 3.1 1.0 + - - -
30A GLY* 3.1 12.5 + - - -
31A PHE 4.0 12.7 + - - +
56A THR* 3.3 13.8 - - - -
57A SER* 3.1 22.8 + - - -
58A LYS* 2.8 47.6 + - + +
59A ILE* 2.8 25.5 + - + +
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Residues in contact with ASP 28 (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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24A LYS* 2.7 55.3 + - - +
25A VAL* 3.2 12.4 + - - +
27A GLU* 1.3 81.6 - - - +
29A ASN* 1.3 64.8 + - - +
30A GLY 3.4 1.1 + - - -
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Residues in contact with ASN 29 (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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25A VAL* 2.8 39.7 + - - +
26A ALA 3.0 6.1 + - - +
28A ASP* 1.3 84.7 - - - +
30A GLY* 1.3 57.8 + - - +
31A PHE* 3.5 2.7 - - + -
336A ILE* 4.1 10.8 - - + +
337A GLU* 3.5 38.7 + - - +
340A GLY* 3.3 33.0 - - - +
341A GLN* 4.4 7.8 + - - +
344A ILE* 3.5 8.8 - - - +
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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