Contacts of the helix formed by residues 13 - 24 (chain D) in PDB entry 3O9Z
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 ILE 13 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D GLY 5.4 0.2 - - - +
11D GLY 2.6 7.2 + - - -
12D TYR* 1.3 75.5 - - + +
14D ALA* 1.3 65.8 + - - +
15D PRO* 3.2 5.6 - - - -
16D ARG* 3.3 54.0 + - - +
17D HIS* 3.8 5.4 - - + -
77D ALA* 3.6 24.2 - - + +
100D GLU* 3.9 17.7 - - + +
264D HIS* 4.3 4.3 - - + +
311D NAD 3.3 68.6 + - + +
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Residues in contact with ALA 14 (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 LEU* 4.4 9.8 - - + +
8D GLY 3.5 16.8 - - - +
9D LEU* 3.2 35.4 - - + +
11D GLY 3.2 2.2 + - - +
13D ILE* 1.3 82.4 - - - +
15D PRO* 1.3 66.7 - - + +
17D HIS* 2.9 21.8 + - - +
18D LEU* 3.0 15.8 + - + +
77D ALA* 4.7 3.1 - - + -
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Residues in contact with PRO 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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9D LEU 5.1 1.6 - - - +
11D GLY 3.8 4.5 - - - +
12D TYR 3.6 13.7 - - - +
13D ILE 3.3 5.2 - - - -
14D ALA* 1.3 93.7 - - + +
16D ARG* 1.3 62.4 + - + +
18D LEU* 3.3 14.4 + - + +
19D LYS* 3.0 26.5 + - - +
40D LEU* 3.6 28.0 - - + -
44D PHE* 4.6 4.3 - - + -
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Residues in contact with ARG 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 TYR* 3.8 28.9 + - - +
13D ILE* 3.5 32.7 - - - +
14D ALA 3.2 0.8 - - - -
15D PRO* 1.3 78.5 - - + +
17D HIS* 1.3 58.8 + - - +
19D LYS* 3.6 9.4 + - - +
20D ALA* 3.0 27.5 + - - +
260D PHE* 3.5 10.5 + - - -
261D THR* 2.5 67.4 + - - +
262D ASP 4.1 0.9 - - - +
264D HIS* 3.8 42.5 - - + +
265D THR* 5.1 0.5 + - - -
311D NAD 4.0 11.5 + - - -
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Residues in contact with HIS 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 4.1 19.0 - - + +
13D ILE 3.8 15.7 - - - -
14D ALA* 2.9 8.2 + - - +
16D ARG* 1.3 77.1 - - - +
18D LEU* 1.3 60.9 + - - +
20D ALA* 3.9 3.2 - - - +
21D ILE* 2.9 38.0 + - + +
75D SER* 4.1 5.9 - - - -
76D ILE 4.5 7.6 - - - -
77D ALA* 4.1 14.5 - - + +
98D LEU 4.7 7.4 - - - -
100D GLU* 2.7 39.5 + - + +
127D VAL* 4.1 18.8 - - + -
264D HIS* 3.7 10.0 - + - -
268D TYR* 2.7 29.3 + + - +
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Residues in contact with LEU 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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6D LEU* 3.8 22.2 - - + -
9D LEU* 3.9 20.0 - - + -
14D ALA* 3.0 17.0 + - + +
15D PRO* 3.3 13.7 + - + +
17D HIS* 1.3 76.6 - - - +
19D LYS* 1.3 56.6 + - - +
21D ILE* 3.4 6.6 + - + +
22D LYS* 3.0 29.5 + - - +
28D LEU* 3.8 24.9 - - + -
40D LEU* 4.4 7.6 - - + -
41D VAL* 4.1 17.7 - - + +
44D PHE* 3.8 39.0 - - + -
45D PHE* 4.0 8.5 - - + -
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Residues in contact with LYS 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 PRO 3.0 15.0 + - - +
16D ARG* 3.6 12.1 - - - +
18D LEU* 1.3 73.6 - - - +
20D ALA* 1.3 55.7 + - - +
22D LYS* 3.2 1.9 + - - +
23D GLU* 2.7 63.0 + - + +
44D PHE* 3.8 21.2 - - + -
265D THR* 4.8 3.4 - - - +
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Residues in contact with ALA 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 ARG 3.0 18.0 + - - +
17D HIS 3.9 0.9 - - - +
19D LYS* 1.3 76.0 - - - +
21D ILE* 1.3 64.2 + - - +
23D GLU 4.4 0.2 - - - +
24D VAL* 2.9 31.2 + - - +
264D HIS 4.0 1.3 - - - +
265D THR* 3.7 27.6 + - - +
268D TYR* 3.2 39.5 - - + -
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Residues in contact with ILE 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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4D PHE* 3.6 44.0 - - + -
6D LEU* 4.9 5.8 - - + -
17D HIS* 2.9 32.5 + - + +
18D LEU* 3.8 8.3 - - + +
20D ALA* 1.3 78.5 - - - +
22D LYS* 1.3 59.4 + - - +
24D VAL* 3.6 6.2 - - - +
25D GLY 3.5 1.2 + - - -
26D GLY* 2.8 37.6 + - - -
27D VAL 4.0 6.3 - - - +
28D LEU* 4.2 16.4 - - + +
45D PHE* 3.8 19.3 - - + -
75D SER* 4.4 7.2 - - - +
268D TYR* 3.7 22.9 - - + +
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Residues in contact with LYS 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 LEU 3.0 18.2 + - - +
19D LYS* 3.4 5.8 - - - +
21D ILE* 1.3 76.0 - - - +
23D GLU* 1.3 66.9 + - + +
25D GLY* 3.1 15.6 + - - -
26D GLY 4.7 2.8 - - - +
43D SER 5.4 1.3 - - - +
44D PHE* 2.7 52.1 + - + +
45D PHE* 3.6 21.9 - - + -
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Residues in contact with GLU 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 LYS* 2.7 52.0 + - + +
22D LYS* 1.3 80.1 - - + +
24D VAL* 1.3 58.4 + - - +
25D GLY 3.1 3.6 + - - -
265D THR* 2.8 40.6 + - + +
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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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2D THR* 5.6 1.8 + - - -
4D PHE* 4.6 5.6 - - + -
20D ALA 2.9 27.2 + - - +
21D ILE* 3.6 13.2 - - - +
23D GLU* 1.3 76.5 - - - +
25D GLY* 1.3 59.6 + - - +
26D GLY* 4.0 4.7 - - - +
265D THR* 4.1 18.2 - - + +
268D TYR* 3.9 26.7 - - + -
269D ARG* 4.2 12.1 - - + +
272D LEU* 3.7 28.4 - - + +
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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