Contacts of the helix formed by residues 17 - 30 (chain D) in PDB entry 1WNT
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 17 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D GLY 3.6 3.3 - - - +
15D ALA 3.1 0.6 + - - -
16D GLY* 1.3 75.0 - - - +
18D GLY* 1.3 65.6 + - - +
20D GLY* 2.8 8.3 + - - -
21D ARG* 2.7 31.6 + - - +
43D ASP* 2.8 33.8 + - - +
185D SER* 4.4 18.5 + - - +
3245D NAP 2.8 45.3 + - - +
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Residues in contact with GLY 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LYS* 1.3 79.1 - - - +
19D ILE* 1.3 65.6 + - - -
21D ARG* 3.6 2.2 - - - +
22D GLY* 3.1 19.2 + - - -
184D THR* 3.8 17.9 - - - -
212D VAL* 4.3 8.7 - - - +
3245D NAP 3.6 14.2 + - - -
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Residues in contact with ILE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D GLY* 1.3 71.2 - - - -
20D GLY* 1.3 54.3 + - - +
23D THR* 2.3 49.3 + - - +
83D ASN* 3.1 24.2 - - - +
134D VAL* 4.8 2.9 - - + -
179D PRO* 5.2 0.9 - - + -
182D VAL* 4.0 26.2 - - + -
184D THR* 4.7 0.2 - - + -
212D VAL* 3.9 23.6 - - + +
215D VAL* 3.3 36.6 - - + -
216D VAL* 4.6 0.2 - - + -
219D ILE* 4.0 5.6 - - + -
3245D NAP 2.9 48.0 + - + +
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Residues in contact with GLY 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 3.8 5.8 - - - +
14D GLY 3.2 18.2 - - - -
15D ALA* 3.7 9.4 - - - -
17D LYS 2.8 9.4 + - - -
19D ILE* 1.3 76.7 - - - +
21D ARG* 1.3 63.4 + - - -
23D THR* 3.3 5.6 + - - -
24D VAL* 2.9 26.2 + - - +
83D ASN* 3.7 15.0 + - - -
3245D NAP 4.1 0.4 + - - -
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Residues in contact with ARG 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ALA 3.1 11.1 + - - +
16D GLY 3.3 18.5 + - - +
17D LYS* 2.7 27.1 + - - +
18D GLY 3.6 2.2 - - - +
20D GLY* 1.3 70.3 - - - +
22D GLY* 1.3 51.7 + - - +
24D VAL* 2.5 34.4 + - - +
25D GLN* 2.8 39.2 + - - +
43D ASP* 3.7 7.4 + - - +
46D SER* 3.0 25.1 + - - -
47D LEU* 3.0 39.1 - - + +
50D GLU* 3.3 24.9 + - - -
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Residues in contact with GLY 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D GLY 3.1 10.7 + - - -
19D ILE 4.2 0.4 - - - -
21D ARG* 1.3 76.1 - - - +
23D THR* 1.3 56.0 + - - +
25D GLN* 2.8 16.7 + - - +
26D ALA* 2.9 33.6 + - - +
212D VAL* 4.4 12.8 - - - -
216D VAL* 4.1 6.1 - - - -
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Residues in contact with THR 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 4.3 12.1 - - + -
19D ILE* 2.3 43.3 + - - +
20D GLY* 3.4 7.0 - - - -
22D GLY* 1.3 75.5 - - - +
24D VAL* 1.3 57.5 + - - +
26D ALA* 4.2 0.7 - - - +
27D LEU* 3.0 42.1 + - + +
81D VAL* 4.3 5.6 - - + -
83D ASN* 6.1 0.2 - - - -
216D VAL* 3.5 15.7 - - + +
219D ILE* 3.5 31.6 - - + +
220D LEU* 4.8 4.7 - - + +
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Residues in contact with VAL 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 4.1 13.2 - - + -
15D ALA* 3.4 25.4 - - + -
20D GLY 2.9 15.5 + - - +
21D ARG 2.5 18.5 + - - +
23D THR* 1.3 69.5 - - - +
25D GLN* 1.3 66.8 + - - +
27D LEU* 3.0 8.4 + - - +
28D HIS* 2.9 20.3 + - - +
34D VAL* 4.2 16.7 - - + +
36D ALA* 3.9 9.9 - - + -
47D LEU* 3.7 30.3 - - + -
51D CYS* 4.3 6.7 - - - -
54D ILE* 4.5 9.6 - - + -
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Residues in contact with GLN 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ARG* 2.8 33.9 + - - +
22D GLY* 2.8 40.7 + - - +
24D VAL* 1.3 74.0 - - - +
26D ALA* 1.3 55.3 + - - +
28D HIS* 2.6 32.2 + - - +
29D ALA* 3.1 7.4 + - - +
47D LEU* 4.4 4.0 - - + -
50D GLU* 4.3 12.2 + - + +
51D CYS* 4.1 23.6 - - - -
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Residues in contact with ALA 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D GLY 2.9 15.8 + - - +
23D THR 4.4 0.9 - - - +
25D GLN* 1.3 77.3 - - - +
27D LEU* 1.3 60.8 + - - +
29D ALA* 3.8 7.6 + - - +
30D THR* 3.4 19.9 + - - -
216D VAL* 3.7 24.5 - - + -
220D LEU* 4.1 16.4 - - + +
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Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LEU* 4.0 26.7 - - + -
10D VAL* 3.3 44.2 - - + -
12D VAL* 3.6 19.5 - - + -
23D THR* 3.0 26.3 + - + +
24D VAL* 3.0 7.1 + - - +
25D GLN 2.9 1.0 + - - -
26D ALA* 1.3 76.9 - - - +
28D HIS* 1.3 63.0 + - - +
30D THR* 3.4 10.1 - - + +
32D ALA* 3.2 27.7 + - + +
34D VAL* 4.1 11.9 - - + -
79D LEU* 5.2 0.4 - - + -
220D LEU* 4.1 13.7 - - + -
223D LEU* 4.6 9.4 - - + -
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Residues in contact with HIS 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D VAL 2.9 9.7 + - - +
25D GLN 2.6 20.2 + - - +
27D LEU* 1.3 68.6 - - - +
29D ALA* 1.3 55.9 + - - +
30D THR 3.0 1.3 - - - -
31D GLY* 2.5 30.8 + - - -
32D ALA 3.8 12.5 + - - +
34D VAL* 4.6 2.7 - - + -
50D GLU 4.5 1.9 + - - -
51D CYS* 3.3 45.1 - - + +
52D PRO* 3.0 32.1 + - + -
53D GLY 4.9 1.5 - - - -
54D ILE* 3.5 14.6 - - + -
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Residues in contact with ALA 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D GLN 3.1 6.2 + - - +
26D ALA* 4.1 10.3 - - - +
28D HIS* 1.3 81.3 + - - +
30D THR* 1.3 61.4 + - - +
31D GLY* 3.1 1.7 + - - -
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Residues in contact with THR 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 5.2 5.2 - - - +
4D PHE 5.7 0.2 + - - -
5D LEU* 3.3 44.3 + - + +
6D ALA* 3.1 25.5 - - - +
26D ALA 3.4 12.8 + - - -
27D LEU* 3.4 16.4 - - - +
28D HIS 3.0 1.2 + - - -
29D ALA* 1.3 77.2 - - - +
31D GLY* 1.3 58.1 + - - +
32D ALA* 3.5 4.7 - - + +
220D LEU* 4.8 5.0 - - - +
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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