Contacts of the helix formed by residues 15 - 26 (chain D) in PDB entry 3GTU
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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10D TYR* 4.0 8.7 - - - -
13D ILE* 3.4 6.4 - - - +
14D ARG* 1.3 86.3 - - - +
16D LEU* 1.3 61.1 + - - -
18D HIS* 3.6 12.1 + - - +
19D ALA 5.1 0.2 + - - -
111D ARG* 5.9 0.4 + - - -
165D ASP* 4.1 12.0 - - - +
169D GLN* 5.2 5.4 - - - +
211D ILE 3.0 16.2 + - - -
212D ASN* 5.3 2.7 - - - -
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Residues in contact with LEU 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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10D TYR* 3.3 22.3 + - + +
15D GLY* 1.3 71.9 - - - -
17D ALA* 1.3 60.9 + - - +
18D HIS 3.4 0.4 - - - -
19D ALA* 4.5 5.5 + - - +
20D ILE* 3.8 16.1 - - - +
63D LEU 4.8 4.3 - - - +
64D PRO* 4.4 11.7 - - + -
76D SER* 3.6 27.8 + - - +
80D LEU* 5.8 0.7 - - - +
108D MET* 5.9 2.2 - - + -
111D ARG* 3.6 44.6 - - - +
115D ILE* 5.1 9.2 - - + -
165D ASP* 5.6 1.1 - - - -
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Residues in contact with ALA 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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8D LEU* 4.8 8.1 - - + -
10D TYR* 3.4 35.9 - - + -
14D ARG 3.1 2.0 + - - +
16D LEU* 1.3 79.3 - - - +
18D HIS* 1.3 54.9 + - - +
19D ALA 3.4 0.4 - - - -
20D ILE* 2.8 32.6 + - - +
21D ARG* 2.8 37.7 + - + +
64D PRO* 4.9 3.6 - - + -
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Residues in contact with HIS 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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14D ARG* 3.0 48.8 + - + +
15D GLY 3.7 4.9 - - - +
16D LEU 3.4 1.0 - - - -
17D ALA* 1.3 75.6 - - - +
19D ALA* 1.3 62.7 + - - +
21D ARG* 3.3 10.2 + - - +
22D LEU* 3.1 62.5 + - + +
164D TYR* 3.9 9.1 - - - -
165D ASP* 3.2 34.1 - - + +
168D ASP* 4.5 0.8 + - - -
200D TYR* 4.6 4.6 + + - -
201D LEU* 4.7 0.7 - - + -
206D PHE* 3.2 38.4 - + - -
209D MET* 5.9 0.8 - - - +
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Residues in contact with ALA 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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16D LEU 4.5 5.0 + - - +
17D ALA 3.4 0.4 - - - -
18D HIS* 1.3 78.4 - - - +
20D ILE* 1.3 58.1 + - + +
22D LEU* 3.6 7.1 + - - +
23D LEU* 3.0 28.8 + - - +
80D LEU* 3.9 13.8 - - + +
111D ARG* 5.4 1.1 - - - +
161D PHE* 3.8 34.4 - - + +
162D LEU* 4.1 21.1 - - + -
165D ASP* 4.7 7.9 - - + +
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Residues in contact with ILE 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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8D LEU* 4.0 13.9 - - + -
16D LEU 3.8 18.8 - - - +
17D ALA* 2.8 12.3 + - - +
19D ALA* 1.3 74.9 - - - +
21D ARG* 1.3 66.3 + - - +
23D LEU* 3.2 2.7 + - - +
24D LEU* 2.9 37.9 + - + +
64D PRO* 3.8 26.7 - - + -
66D LEU* 5.6 0.2 - - + -
76D SER* 4.5 7.0 - - - -
79D ILE* 3.7 36.6 - - + -
80D LEU* 4.0 24.2 - - + -
83D ILE* 3.9 13.9 - - + -
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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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8D LEU* 4.1 10.0 - - + +
10D TYR* 4.2 3.2 - - - +
11D TRP 3.5 8.9 + - - -
13D ILE 2.9 29.5 + - - -
14D ARG* 3.3 24.5 + - - +
17D ALA* 2.8 30.0 + - - +
18D HIS* 3.3 12.1 + - - +
20D ILE* 1.3 75.3 - - - +
22D LEU* 1.3 58.6 - - - +
24D LEU* 3.2 10.7 + - - +
25D GLU* 2.9 35.1 + - - +
31D TYR* 4.2 8.6 + - - +
33D GLU* 3.1 32.8 + - - +
35D ARG* 3.0 20.4 - - - +
200D TYR* 3.5 28.7 - - + +
209D MET* 3.4 14.9 - - - +
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Residues in contact with LEU 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 HIS* 3.1 50.7 + - + +
19D ALA* 3.8 7.0 - - - +
21D ARG* 1.3 78.0 - - - +
23D LEU* 1.3 57.6 + - - +
25D GLU* 3.6 4.8 - - + +
26D PHE* 3.0 30.0 + - - +
161D PHE* 4.1 12.8 - - + +
164D TYR* 3.8 23.8 - - + -
191D PHE* 4.3 5.8 - - + -
197D ILE* 3.8 29.1 - - + +
200D TYR* 3.6 33.7 - - + -
201D LEU* 4.4 4.9 - - + -
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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 ALA 3.0 18.7 + - - +
20D ILE* 3.2 4.2 + - - +
22D LEU* 1.3 72.9 - - - +
24D LEU* 1.3 63.4 + - - +
26D PHE* 3.6 0.3 + - - +
27D THR* 2.8 35.0 + - + -
80D LEU* 3.7 40.6 - - + +
83D ILE* 4.1 16.4 - - + -
84D ALA* 4.0 18.2 - - + +
89D MET* 4.0 18.8 - - - -
158D PHE* 4.3 7.4 - - + -
161D PHE* 3.7 36.3 - - + -
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Residues in contact with LEU 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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6D MET* 4.1 12.1 - - - -
8D LEU* 3.9 27.4 - - + -
20D ILE* 2.9 25.5 + - + +
21D ARG* 3.4 6.1 - - - +
23D LEU* 1.3 77.7 - - - +
25D GLU* 1.3 58.9 + - - +
27D THR* 3.5 4.6 + - - -
28D ASP* 3.4 2.1 + - - -
29D THR* 2.8 59.8 + - + +
31D TYR* 3.6 38.4 - - + -
66D LEU* 5.0 2.5 - - + -
83D ILE* 3.7 24.9 - - + -
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Residues in contact with GLU 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 2.9 21.2 + - - +
22D LEU* 3.6 7.2 - - - +
24D LEU* 1.3 73.0 - - - +
26D PHE* 1.3 57.5 - - - +
28D ASP* 2.8 29.3 + - - +
29D THR 5.6 0.2 - - - -
31D TYR* 3.2 25.8 + - - +
196D LYS* 3.6 25.2 - - + +
197D ILE* 5.4 1.3 - - + -
200D TYR* 3.4 39.3 - - + +
205D GLN* 5.7 1.2 + - - -
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Residues in contact with PHE 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 LEU 3.0 15.8 + - - +
23D LEU 3.8 3.1 - - - +
25D GLU* 1.3 78.0 - - - +
27D THR* 1.3 70.8 - - + +
28D ASP* 3.2 8.3 + - - +
89D MET* 3.7 22.2 - - + -
156D LEU* 3.7 15.3 - - + -
161D PHE* 4.0 16.8 - + + -
194D LEU* 3.8 41.1 - - + -
196D LYS* 3.6 29.9 - - + +
197D ILE* 3.9 15.7 - - + +
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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