Contacts of the helix formed by residues 17 - 28 (chain R) in PDB entry 5A0Q
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 PHE 17 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Q ARG* 6.1 1.1 - - - -
7R ILE 5.6 0.4 - - - -
8R THR* 4.5 3.2 - - - +
9R VAL* 3.9 23.0 + - + -
10R PHE 4.8 1.1 - - - -
11R SER* 3.3 38.4 - - - -
12R PRO* 4.3 8.7 - - + -
13R ASP* 4.3 6.1 - - - -
16R LEU* 1.3 69.8 - - - +
18R GLN* 1.3 81.7 + - + +
20R GLU* 3.1 22.3 - - - +
21R TYR* 3.0 54.1 + - + -
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Residues in contact with GLN 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Q ARG* 3.3 19.0 - - - +
11Q ILE* 3.6 9.2 - - - +
12Q PHE* 3.0 43.6 + - + +
7R ILE* 3.3 33.5 + - + +
8R THR* 3.6 22.9 - - + +
17R PHE* 1.3 92.0 - - - +
19R VAL* 1.3 57.4 + - - +
21R TYR* 3.5 8.8 + - - +
22R ALA* 3.0 28.2 + - - +
125R ARG* 5.2 1.1 - - + -
126R PRO* 3.5 25.6 - - + +
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Residues in contact with VAL 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8R THR* 3.8 7.4 - - + -
16R LEU* 3.7 34.8 - - + +
17R PHE 3.2 0.2 - - - -
18R GLN* 1.3 74.9 - - - +
20R GLU* 1.4 60.3 + - - +
22R ALA* 3.2 5.5 + - - +
23R GLN* 3.0 30.4 + - + +
119R THR* 3.8 28.0 - - + -
126R PRO* 4.1 5.8 - - + -
149R PRO* 4.7 3.1 - - + -
150R SER* 3.3 38.6 - - - +
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Residues in contact with GLU 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13R ASP* 4.8 3.5 - - - +
15R HIS* 3.4 33.6 - - + +
16R LEU 3.3 12.3 + - - +
17R PHE* 3.1 42.6 - - - +
19R VAL* 1.4 77.2 - - - +
21R TYR* 1.4 73.6 + - + +
23R GLN* 3.1 23.4 + - + +
24R GLU* 3.2 18.3 + - - +
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Residues in contact with TYR 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Q ILE* 5.8 1.8 - - + -
12Q PHE* 2.8 58.1 - - + -
13Q SER 3.3 8.1 - - - +
14Q PRO* 3.5 42.1 - - + +
16Q GLY* 4.1 3.0 - - - -
17R PHE* 3.0 50.5 + + + +
18R GLN* 3.6 9.2 - - - +
20R GLU* 1.4 90.1 - - + +
22R ALA* 1.3 55.8 + - - +
24R GLU* 3.3 11.7 + - + +
25R ALA* 3.1 16.8 + - - -
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Residues in contact with ALA 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Q PHE* 3.4 13.0 - - + -
18R GLN 3.0 15.0 + - - +
19R VAL 3.2 9.6 + - - +
21R TYR* 1.3 73.9 - - - +
23R GLN* 1.4 57.6 + - - +
25R ALA* 3.1 15.4 + - - +
26R VAL* 3.2 15.1 + - - +
126R PRO* 4.2 13.5 - - + +
128R GLY* 4.0 14.3 - - - +
149R PRO* 3.8 25.5 - - + +
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Residues in contact with GLN 23 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19R VAL* 3.0 26.5 + - + +
20R GLU* 3.1 15.8 + - + +
22R ALA* 1.4 74.4 - - - +
24R GLU* 1.3 65.8 + - - +
26R VAL* 3.1 24.4 - - - +
27R LYS* 3.4 23.6 + - - +
148R ASP* 4.2 16.7 - - - +
149R PRO* 3.6 24.3 - - - +
150R SER* 3.1 25.9 + - - -
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Residues in contact with GLU 24 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Q PRO 5.7 5.8 - - - +
15Q GLU 5.6 0.2 - - - +
16Q GLY* 5.2 2.7 - - - -
20R GLU* 3.2 13.8 + - + +
21R TYR* 3.6 11.0 - - + +
22R ALA 3.2 0.2 - - - -
23R GLN* 1.3 82.5 - - - +
25R ALA* 1.3 59.6 + - - +
26R VAL 3.5 0.2 - - - -
27R LYS* 3.6 44.7 + - - +
28R LYS* 3.0 29.4 + - - +
163R ARG* 5.0 0.2 + - - -
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Residues in contact with ALA 25 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Q PHE* 3.1 37.9 - - + -
16Q GLY 3.8 11.7 - - - +
21R TYR 3.1 3.0 + - - -
22R ALA* 3.1 9.5 + - - +
24R GLU* 1.3 75.0 - - - +
26R VAL* 1.3 63.4 + - - +
27R LYS 3.2 0.2 - - - -
28R LYS* 3.2 21.2 + - - +
29R GLY 3.7 2.9 + - - -
75R GLY* 4.5 5.3 - - - -
76R LEU* 4.9 13.1 - - + +
128R GLY* 4.4 9.6 - - - +
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Residues in contact with VAL 26 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22R ALA 3.2 9.5 + - - +
23R GLN* 3.1 27.8 - - - +
25R ALA* 1.3 77.3 - - - +
27R LYS* 1.3 59.3 + - + +
29R GLY* 3.0 18.9 + - - -
74R ALA* 4.0 18.6 - - + +
75R GLY* 3.9 9.0 - - - -
128R GLY 3.7 12.2 + - - +
130R SER* 3.4 28.5 - - - +
149R PRO* 4.9 2.2 - - + -
161R ILE* 3.5 30.3 - - + -
162R GLY* 3.9 7.1 - - - -
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Residues in contact with LYS 27 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23R GLN* 3.4 26.0 + - - +
24R GLU* 3.6 41.2 + - - +
25R ALA 3.2 0.8 - - - -
26R VAL* 1.3 78.8 - - + +
28R LYS* 1.3 56.1 - - - +
29R GLY 3.3 0.7 - - - -
161R ILE* 6.2 1.6 - - + -
162R GLY 4.4 9.0 - - - +
163R ARG* 3.0 50.0 + - - +
166R LYS* 4.1 35.8 - - + +
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Residues in contact with LYS 28 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Q GLU 3.0 29.4 + - - -
16Q GLY* 3.7 21.3 - - - +
17Q ARG* 3.8 19.1 - - + +
24R GLU* 3.0 33.1 + - - +
25R ALA* 3.2 9.4 + - + +
26R VAL 3.1 0.8 - - - -
27R LYS* 1.3 72.3 - - - +
29R GLY* 1.4 65.2 + - - +
30R SER* 5.3 0.3 + - - -
76R LEU* 5.4 11.9 - - + -
163R ARG* 3.6 24.2 + - - +
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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