Contacts of the helix formed by residues 14 - 24 (chain D) in PDB entry 2RD9
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 ARG 14 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C VAL* 3.8 13.5 + - + +
22C PHE* 3.4 26.7 - - + +
24C GLU 3.1 27.5 + - - -
25C GLY* 3.7 18.6 + - - -
26C LEU* 3.6 14.3 - - - +
10D GLN* 3.0 24.1 + - - +
11D LEU* 3.0 10.4 + - - +
13D GLU* 1.3 109.7 + - + +
15D THR* 1.3 59.0 + - - +
16D PRO* 3.4 3.1 - - - -
17D LYS* 3.3 8.1 + - - +
18D THR* 2.6 37.0 + - - +
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Residues in contact with THR 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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22C PHE* 5.2 2.1 - - - -
11D LEU* 3.3 16.6 + - - +
13D GLU 3.7 0.2 - - - -
14D ARG* 1.3 75.5 - - - +
16D PRO* 1.3 71.0 - - - +
18D THR* 3.7 5.7 - - - -
19D LEU* 3.0 32.4 + - + +
49D LEU* 4.7 3.1 - - + -
97D PHE* 3.9 16.8 - - + -
101D ARG* 3.8 2.9 - - - -
143D ASP* 2.6 40.8 + - + +
147D ILE* 4.0 25.1 - - + +
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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 LEU 3.6 11.4 - - - +
13D GLU 4.0 5.8 - - - +
14D ARG 3.5 3.6 - - - -
15D THR* 1.3 96.5 - - - +
17D LYS* 1.3 59.8 + - - +
19D LEU* 3.5 1.9 + - - +
20D GLU* 3.1 26.0 + - - +
94D PHE* 5.0 5.6 - - - +
97D PHE* 3.8 24.7 - - + -
98D GLN* 3.7 36.8 - - + +
101D ARG* 3.6 30.3 - - + -
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Residues in contact with LYS 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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17C LYS* 6.3 0.4 - - - +
21C VAL* 3.8 20.2 - - + -
13D GLU 5.3 1.8 - - - +
14D ARG* 3.3 11.1 + - - +
15D THR 3.3 0.4 - - - -
16D PRO* 1.3 76.9 - - - +
18D THR* 1.3 59.7 + - - +
20D GLU* 3.5 32.3 + - - +
21D VAL* 2.9 47.2 + - + +
98D GLN* 4.2 12.0 + - - +
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Residues in contact with THR 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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18C THR* 4.1 17.7 - - + +
21C VAL* 3.5 16.7 - - - +
22C PHE* 3.6 45.7 - - + -
14D ARG* 2.6 25.1 + - - +
15D THR* 3.7 6.1 - - - -
17D LYS* 1.3 77.5 - - - +
19D LEU* 1.3 60.3 + - + +
21D VAL* 4.0 1.9 - - - +
22D PHE* 3.0 32.6 + - + +
147D ILE* 5.5 9.4 - - + -
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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 THR* 3.0 24.5 + - + +
16D PRO* 4.0 3.8 - - + +
18D THR* 1.3 79.6 - - + +
20D GLU* 1.3 53.8 + - - +
22D PHE* 4.3 11.2 - - + -
23D LEU* 2.8 51.9 + - + +
46D VAL* 4.6 10.8 - - + -
49D LEU* 3.6 30.3 - - + -
94D PHE* 4.0 10.3 - - + -
97D PHE* 4.2 14.4 - - + -
147D ILE* 4.1 23.8 - - + -
150D ILE* 3.9 28.3 - - + -
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Residues in contact with GLU 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 3.1 18.3 + - - +
17D LYS* 3.6 35.4 + - - +
19D LEU* 1.3 75.1 - - - +
21D VAL* 1.3 61.7 + - + +
24D GLU* 2.8 63.2 + - + +
94D PHE* 4.1 29.0 - - + +
98D GLN* 5.4 7.1 - - - +
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Residues in contact with VAL 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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14C ARG* 3.6 22.8 + - + +
17C LYS* 3.6 33.4 - - + +
18C THR* 3.8 20.4 - - - +
21C VAL* 3.8 15.0 - - + -
17D LYS* 2.9 50.6 + - - +
18D THR* 4.0 2.9 - - - +
20D GLU* 1.3 73.0 - - + +
22D PHE* 1.3 59.5 + - - +
24D GLU 4.8 0.5 - - - +
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Residues in contact with PHE 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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11C LEU* 4.6 7.7 - - + +
14C ARG* 3.3 26.7 - - + +
15C THR* 5.4 4.3 - - - -
18C THR* 3.4 31.4 - - + +
144C LEU* 3.8 27.4 - - + -
147C ILE* 4.1 20.2 - - + -
18D THR* 3.0 19.7 + - + +
19D LEU* 3.8 10.1 - - + +
21D VAL* 1.3 78.7 - - - +
23D LEU* 1.3 73.7 + - + +
26D LEU* 3.7 8.8 - - - +
147D ILE* 6.0 2.0 - - + -
150D ILE* 4.2 6.3 - - + -
151D VAL* 3.8 23.1 - - + -
154D MSE 3.7 27.6 - - + -
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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* 2.8 39.3 + - + +
22D PHE* 1.3 96.0 - - + +
24D GLU* 1.3 64.2 + - - +
26D LEU* 3.3 18.7 + - + +
30D TRP 5.8 0.4 - - - +
31D HIS* 2.7 33.3 + - + +
42D VAL* 4.0 26.9 - - + -
46D VAL* 4.2 14.4 - - + -
90D ILE* 4.8 1.1 - - + -
94D PHE* 3.7 19.3 - - + -
150D ILE* 4.2 3.8 - - + -
154D MSE 3.8 22.4 - - - -
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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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14C ARG* 2.7 26.3 + - - -
20D GLU* 2.8 43.2 + - + +
21D VAL 4.8 0.5 - - - +
22D PHE 3.8 0.4 - - - -
23D LEU* 1.3 72.4 - - - +
25D GLY* 1.3 61.6 + - - +
26D LEU 3.0 3.2 + - - -
31D HIS* 4.9 0.7 - - - -
90D ILE* 5.4 1.6 - - + -
91D SER* 3.8 25.8 - - - +
94D PHE* 3.1 33.8 - - + +
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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