Contacts of the helix formed by residues 14 - 24 (chain D) in PDB entry 1TU8
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 ALA 14 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D LEU* 4.1 11.2 - - + -
7D TYR* 3.2 43.4 - - + -
11D ARG 3.3 1.4 + - - -
13D LEU* 1.3 78.5 - - - +
15D GLU* 1.3 64.8 + - - +
16D PRO 3.4 0.2 - - - -
17D ILE* 3.0 20.0 + - - +
18D ARG* 3.0 25.6 + - - +
51D PRO* 4.3 10.1 - - + -
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Residues in contact with GLU 15 (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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11D ARG* 3.1 28.3 + - + +
12D GLY 4.0 0.9 - - - +
13D LEU 3.3 0.2 - - - -
14D ALA* 1.3 76.8 - - - +
16D PRO* 1.3 62.8 - - + +
18D ARG* 2.9 32.4 + - - +
19D LEU* 2.9 35.5 + - + +
32D ARG* 5.0 1.6 + - - -
156D GLU* 3.4 36.6 - - - +
191D TYR* 2.6 28.3 + - - -
195D ARG* 2.9 26.0 + - - +
200D VAL* 5.6 0.2 - - - +
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Residues in contact with PRO 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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12D GLY 4.0 7.2 - - - +
13D LEU* 3.7 11.9 - - - +
14D ALA 3.6 2.7 - - - -
15D GLU* 1.3 93.0 - - + +
17D ILE* 1.3 56.7 + - + +
19D LEU* 3.4 13.0 + - + +
20D PHE* 3.0 27.0 + - - +
67D LEU* 4.3 13.8 - - + +
98D HIS* 6.4 1.1 - - + -
152D TYR* 3.6 8.0 - - + +
153D ALA* 4.0 34.3 - - + +
156D GLU* 4.2 13.9 - - + -
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Residues in contact with ILE 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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5D LEU* 4.0 20.4 - - + -
13D LEU 4.2 9.4 - - - +
14D ALA* 3.0 8.7 + - - +
16D PRO* 1.3 75.4 - - + +
18D ARG* 1.3 67.4 + - - +
20D PHE* 3.2 6.9 + - - +
21D LEU* 3.0 33.6 + - + +
51D PRO* 4.2 8.5 - - + -
53D LEU* 5.3 0.4 - - + -
63D SER* 3.9 31.2 - - - +
66D ILE* 3.8 29.6 - - + -
67D LEU* 4.3 14.8 - - + -
70D LEU* 3.9 23.3 - - + -
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Residues in contact with ARG 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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5D LEU* 3.6 17.5 + - + +
7D TYR* 3.7 15.4 - - - +
8D PHE 3.2 24.4 + - - -
10D ILE 2.8 22.4 + - - -
11D ARG 3.5 7.9 + - - -
14D ALA* 3.0 18.9 + - - +
15D GLU* 2.9 31.5 + - - +
17D ILE* 1.3 75.1 - - - +
19D LEU* 1.3 57.5 + - - +
21D LEU* 3.3 3.3 + - - +
22D VAL* 2.9 36.0 + - - +
28D PHE* 4.2 15.7 - - + -
30D ASP* 2.9 29.7 + - - +
31D ASP 5.5 0.2 + - - -
32D ARG* 3.4 24.7 - - - +
191D TYR* 3.7 20.9 - - + +
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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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15D GLU* 2.9 26.1 + - + +
16D PRO 3.6 4.3 - - - +
17D ILE 3.2 0.2 - - - -
18D ARG* 1.3 73.5 - - - +
20D PHE* 1.3 65.3 + - - +
22D VAL* 4.6 1.3 - - - -
23D ASP* 2.9 28.1 + - - +
152D TYR* 3.8 36.1 - - + +
155D PHE* 3.9 23.3 - - + -
156D GLU* 3.8 26.7 - - + +
188D LEU* 3.7 22.1 - - + +
191D TYR* 3.8 25.8 - - + -
192D CYS* 4.7 1.3 - - - -
195D ARG* 4.0 8.5 - - - +
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Residues in contact with PHE 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 PRO 3.0 14.7 + - - +
17D ILE* 3.4 8.7 - - - +
19D LEU* 1.3 75.8 - - - +
21D LEU* 1.3 67.3 + - - +
23D ASP* 3.9 0.3 - - - -
24D GLN* 3.0 31.6 + - + +
26D ILE* 3.8 22.2 - - + -
67D LEU* 3.8 19.7 - - + -
70D LEU* 3.5 41.7 - - + -
71D ALA* 4.0 13.2 - - - -
74D TYR* 4.2 7.4 - - + -
76D LEU* 3.6 28.9 - - + -
149D TYR* 4.0 7.6 - - + -
152D TYR* 3.7 32.4 - + + -
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Residues in contact with LEU 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 TYR* 5.1 5.2 - - + -
5D LEU* 4.8 5.8 - - + -
17D ILE* 3.0 35.2 + - + +
18D ARG* 3.7 0.9 - - - +
20D PHE* 1.3 78.7 - - + +
22D VAL* 1.3 62.9 + - - +
24D GLN 3.7 0.2 - - - -
25D ASP* 3.1 3.6 + - - -
26D ILE* 2.9 65.1 + - + +
28D PHE* 3.7 50.0 - - + -
53D LEU* 4.9 5.8 - - + -
70D LEU* 4.1 26.2 - - + -
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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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18D ARG 2.9 21.7 + - - +
19D LEU* 4.0 3.4 - - - +
21D LEU* 1.3 76.1 - - - +
23D ASP* 1.3 63.2 + - - +
25D ASP* 3.1 15.2 + - - +
26D ILE 5.2 0.4 - - - -
28D PHE* 4.2 16.4 - - + -
187D LYS* 3.6 38.4 - - + +
188D LEU* 4.2 6.1 - - + -
191D TYR* 3.8 38.4 - - + -
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Residues in contact with ASP 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 2.9 19.3 + - - +
22D VAL* 1.3 77.7 - - - +
24D GLN* 1.3 62.0 + - - +
25D ASP 3.2 0.4 - - - -
152D TYR* 2.5 35.3 + - + +
185D ARG* 3.0 48.9 + - - +
187D LYS* 3.5 25.0 + - - +
188D LEU* 3.7 20.9 + - + +
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Residues in contact with GLN 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 PHE* 3.0 37.5 + - + +
21D LEU 4.2 0.2 - - - +
23D ASP* 1.3 82.5 + - - +
25D ASP* 1.3 69.7 + - - +
26D ILE* 3.3 23.8 + - + +
74D TYR* 4.6 14.8 - - + +
76D LEU* 3.7 28.7 - - + +
147D ILE* 4.0 9.5 - - - +
152D TYR* 3.0 23.2 + - - +
185D ARG* 4.7 3.0 - - - +
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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