Contacts of the helix formed by residues 13 - 25 (chain D) in PDB entry 5BOU
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 LEU 13 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D VAL 5.9 1.3 - - - +
5D SER* 3.9 7.9 - - - +
6D THR 3.6 12.6 - - - +
7D PHE* 3.6 28.9 - - + -
12D ARG* 1.3 70.6 - - - +
14D PHE* 1.3 67.3 + - - +
15D GLN* 3.3 1.3 - - + +
16D VAL* 3.1 30.2 + - + +
17D GLU* 3.1 24.4 + - - +
113D LEU* 4.2 14.1 - - + -
115D PHE* 4.6 9.2 - - + -
76E LEU* 4.4 14.5 - - + +
125E ARG* 3.6 41.1 - - - +
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Residues in contact with PHE 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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2D ARG* 3.5 45.8 - - - +
4D VAL 5.8 0.6 + - - +
6D THR* 3.4 31.1 + - + +
7D PHE 3.5 19.5 - - - -
8D SER* 3.5 28.0 - - - -
9D PRO* 4.3 7.4 - - + -
12D ARG 3.4 2.4 + - - -
13D LEU* 1.3 70.4 - - - +
15D GLN* 1.3 61.9 + - + +
17D GLU* 3.3 5.4 + - + +
18D TYR* 2.9 65.1 + + + -
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Residues in contact with GLN 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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8C ILE* 3.7 22.5 - - - +
9C PHE* 3.1 57.5 + - - +
4D VAL* 3.3 39.0 + - + +
13D LEU* 3.3 1.7 - - + +
14D PHE* 1.3 79.3 - - + +
16D VAL* 1.3 60.4 + - - +
18D TYR* 3.4 11.2 + - - +
19D SER* 3.0 29.1 + - - -
115D PHE* 4.2 4.0 - - + -
128D ARG* 4.2 1.4 - - - +
129D PRO* 3.8 25.4 - - + +
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Residues in contact with VAL 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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13D LEU* 3.1 36.1 + - + +
15D GLN* 1.3 76.0 - - - +
17D GLU* 1.3 73.7 + - - +
19D SER* 2.7 23.1 + - - +
20D LEU* 3.2 16.8 + - + +
113D LEU* 4.1 12.3 - - + -
115D PHE* 4.0 17.9 - - + -
129D PRO* 4.5 3.4 - - + -
152D PRO 4.3 6.7 - - - +
153D SER* 3.6 33.9 - - - +
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Residues in contact with GLU 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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12D ARG* 3.5 43.8 - - + +
13D LEU 3.1 15.2 + - - +
14D PHE* 3.6 8.7 - - - +
16D VAL* 1.3 83.0 - - - +
18D TYR* 1.3 67.9 + - + +
20D LEU* 3.5 34.1 - - - +
21D GLU* 3.6 13.2 + - - +
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Residues in contact with TYR 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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9C PHE* 3.6 25.1 - - + -
10C SER 3.4 24.5 - - - +
11C PRO* 3.6 43.6 - - + +
13C GLY* 3.3 20.4 - - - -
2D ARG* 3.7 13.0 + - - -
14D PHE* 2.9 56.6 + + + +
15D GLN* 3.8 11.4 - - - +
17D GLU* 1.3 81.5 - - + +
19D SER* 1.3 63.6 + - - +
21D GLU* 3.1 14.9 + - + +
22D ALA 3.4 0.2 + - - -
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Residues in contact with SER 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C PHE* 3.6 27.5 - - - -
15D GLN 3.0 13.8 + - - -
16D VAL* 2.7 22.0 + - - -
18D TYR* 1.3 76.5 - - - +
20D LEU* 1.3 60.9 + - - +
22D ALA* 3.1 14.3 + - - +
23D ILE* 3.2 16.8 + - - +
129D PRO* 4.4 3.0 - - - +
130D PHE 3.5 20.2 - - - -
131D GLY* 4.6 0.9 - - - -
152D PRO* 3.6 19.4 - - - +
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Residues in contact with LEU 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 VAL* 3.2 24.1 + - + +
17D GLU* 3.5 32.3 - - - +
18D TYR 3.2 0.4 - - - -
19D SER* 1.3 87.9 + - - +
21D GLU* 1.3 60.1 + - + +
23D ILE* 3.5 11.4 + - + +
24D LYS* 3.3 32.3 + - - +
151D GLU* 4.6 20.2 - - + +
152D PRO* 3.9 23.8 - - + -
153D SER* 5.1 3.6 - - - +
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Residues in contact with GLU 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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11C PRO 3.6 18.4 - - - +
12C ASP* 4.0 7.0 - - - +
13C GLY* 3.8 14.6 - - - +
17D GLU 3.7 14.4 - - - +
18D TYR* 3.1 11.2 + - + +
20D LEU* 1.3 76.8 - - - +
22D ALA* 1.3 63.6 + - - +
24D LYS* 3.1 49.7 + - - +
25D LEU* 3.6 13.2 + - - +
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Residues in contact with ALA 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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9C PHE* 4.0 19.1 - - + -
13C GLY* 3.3 25.2 - - - +
18D TYR 3.4 2.6 + - - -
19D SER 3.1 10.9 + - - +
21D GLU* 1.3 78.3 - - - +
23D ILE* 1.3 62.5 + - - +
25D LEU* 3.2 22.5 + - + +
26D GLY 3.6 4.2 + - - -
72D GLY* 4.2 6.4 - - - -
73D LEU* 4.5 11.6 + - + +
131D GLY 4.4 10.5 - - - +
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Residues in contact with ILE 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 SER 3.2 13.5 + - - +
20D LEU* 3.7 16.8 - - + +
21D GLU 3.3 0.2 - - - -
22D ALA* 1.3 74.5 - - - +
24D LYS* 1.3 63.4 + - + +
26D GLY* 3.1 12.1 + - - -
71D SER* 3.8 11.8 + - - +
72D GLY* 4.1 6.5 - - - -
131D GLY 3.8 15.7 - - - +
132D VAL* 3.8 9.9 - - - +
133D ALA* 3.7 27.1 - - + +
151D GLU* 6.1 0.2 - - + -
152D PRO* 3.5 38.4 - - + -
164D ILE* 5.2 2.2 - - + -
165D GLY* 3.7 20.0 - - - +
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Residues in contact with LYS 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 LEU* 3.3 18.9 + - - +
21D GLU* 3.1 44.1 + - - +
22D ALA 3.3 0.6 - - - -
23D ILE* 1.3 78.8 - - + +
25D LEU* 1.3 58.3 + - + +
26D GLY 3.3 0.2 - - - -
165D GLY 4.5 9.6 - - - +
166D SER* 3.1 29.2 - - - -
168D SER* 6.0 1.3 - - - +
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Residues in contact with LEU 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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12C ASP 4.4 9.2 - - - +
13C GLY 4.8 0.4 - - - +
14C HIS* 3.8 30.5 - - + +
21D GLU 3.8 13.2 - - - +
22D ALA* 3.2 15.1 + - - +
23D ILE 3.2 0.6 - - - -
24D LYS* 1.3 76.9 - - + +
26D GLY* 1.3 60.5 + - - +
45D ARG* 3.2 21.3 + - - -
166D SER* 4.6 3.1 - - - -
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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