Contacts of the helix formed by residues 15 - 25 (chain D) in PDB entry 3ZWG
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 15 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D GLY 3.3 6.0 + - - -
14D LEU* 1.3 75.9 - - - +
16D PHE* 1.3 67.9 + - - -
17D ASP* 3.1 3.8 + - - -
18D VAL* 3.4 11.8 + - - +
19D LEU* 3.4 16.7 + - - +
173D GLU* 4.2 14.8 - - - -
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Residues in contact with PHE 16 (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 GLY* 1.3 74.3 - - - -
17D ASP* 1.3 85.8 + - + +
18D VAL 3.3 0.2 - - - -
19D LEU* 3.7 6.1 - - - +
20D LYS* 2.7 40.2 + - + +
171D ILE* 4.7 5.3 - - + +
173D GLU* 4.1 3.8 + - - -
2E ALA* 5.3 1.6 - - + -
4E VAL* 3.0 36.1 - - + -
5E ALA* 4.2 5.2 - - + -
6E GLY* 3.1 49.8 - - - +
7E ALA* 3.7 8.1 - - + -
58E ASP 6.0 0.2 - - - +
59E ILE* 4.8 10.8 - - + -
60E VAL* 3.9 34.5 - - + +
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Residues in contact with ASP 17 (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 GLY* 3.1 1.0 - - - -
16D PHE* 1.3 109.4 - - + +
18D VAL* 1.3 66.7 + - + +
20D LYS* 3.5 8.0 + - - +
21D THR* 3.1 36.4 + - - +
2E ALA* 4.4 9.9 - - + +
4E VAL* 3.9 16.9 - - - +
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Residues in contact with VAL 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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3D ASP* 3.7 18.6 - - + +
9D ILE* 4.7 6.1 - - + -
13D GLY 3.3 26.7 - - - +
14D LEU* 5.1 1.6 - - + -
15D GLY* 3.4 10.0 + - - +
16D PHE 3.3 0.4 - - - -
17D ASP* 1.3 77.5 - - + +
19D LEU* 1.3 59.5 + - + +
21D THR* 3.2 7.7 + - - -
22D VAL* 3.1 25.8 + - - +
72D LEU* 3.5 37.7 - - + -
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Residues in contact with LEU 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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14D LEU* 3.9 14.8 - - + -
15D GLY 3.4 14.6 + - - +
16D PHE* 3.4 6.9 + - - +
17D ASP 3.2 0.2 - - - -
18D VAL* 1.3 78.8 - - - +
20D LYS* 1.3 65.3 + - - +
22D VAL* 3.2 8.0 + - + +
23D LEU* 3.0 23.7 + - - +
34D ALA* 3.6 13.5 - - + +
35D VAL 3.8 10.1 - - - +
36D GLY* 3.7 26.5 - - - +
72D LEU* 4.7 9.4 - - + -
171D ILE* 3.7 32.5 - - + -
172D LEU 3.9 6.3 - - - +
173D GLU* 3.7 28.0 - - + +
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Residues in contact with LYS 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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16D PHE* 2.7 30.4 + - + +
17D ASP* 3.7 13.9 - - - +
19D LEU* 1.3 72.3 - - - +
21D THR* 1.3 64.7 + - + +
23D LEU* 3.2 11.8 + - + +
24D GLU* 3.2 47.6 + - + +
171D ILE* 4.1 18.3 - - + +
5E ALA* 6.2 0.6 - - - +
58E ASP* 5.5 12.0 - - + +
59E ILE* 5.0 13.7 - - - +
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Residues in contact with THR 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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3D ASP* 4.3 12.3 + - - +
17D ASP* 3.1 23.7 + - - +
18D VAL* 3.2 10.6 + - - -
19D LEU 3.2 0.4 - - - -
20D LYS* 1.3 75.5 - - + +
22D VAL* 1.3 70.3 + - - +
23D LEU 3.0 1.6 - - - -
24D GLU* 3.1 12.9 + - - +
25D ALA* 3.0 25.6 + - - +
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Residues in contact with VAL 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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3D ASP 3.9 16.4 - - - +
4D VAL* 4.3 15.0 - - - +
5D ALA* 4.3 7.0 - - + +
18D VAL 3.1 21.7 + - - +
19D LEU* 3.4 13.2 - - + +
21D THR* 1.3 81.8 + - - +
23D LEU* 1.3 61.7 + - - +
25D ALA* 3.7 14.6 + - - +
26D LEU* 4.0 10.9 + - - +
34D ALA* 3.5 19.1 - - + -
35D VAL 5.7 0.2 - - - +
72D LEU* 4.4 15.0 - - + -
73D TYR 3.9 15.3 - - - +
74D ASN* 4.1 17.3 + - + +
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Residues in contact with LEU 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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19D LEU 3.0 11.6 + - - +
20D LYS* 3.3 16.4 - - + +
21D THR 3.0 0.2 - - - -
22D VAL* 1.3 76.7 - - - +
24D GLU* 1.3 64.1 + - + +
25D ALA 3.3 0.4 - - - -
26D LEU* 3.4 15.0 - - + +
32D LYS* 2.8 53.2 + - + +
33D ILE 3.8 5.4 - - - +
34D ALA* 3.6 28.7 - - + +
169D HIS* 3.9 31.0 - - + +
170D ALA 3.7 9.2 - - - +
171D ILE* 4.1 14.8 - - + -
58E ASP* 5.1 4.3 - - - +
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Residues in contact with GLU 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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20D LYS* 3.2 44.0 + - + +
21D THR* 3.1 13.8 + - - +
23D LEU* 1.3 76.0 - - + +
25D ALA* 1.3 63.6 + - - +
26D LEU 3.0 6.3 + - - -
27D GLY* 3.1 14.9 + - - +
32D LYS* 3.9 7.2 - - - +
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Residues in contact with ALA 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 THR 3.0 16.0 + - - +
22D VAL* 3.8 10.1 - - - +
23D LEU 3.3 0.4 - - - -
24D GLU* 1.3 76.4 - - - +
26D LEU* 1.3 56.5 + - - +
27D GLY* 3.0 5.3 + - - -
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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