Contacts of the helix formed by residues 16 - 27 (chain V) in PDB entry 3HOU
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 ASP 16 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114O TYR* 6.6 0.2 - - - -
135O GLN* 5.2 7.6 + - - +
136O ASP* 4.4 23.7 + - + +
141O GLY* 4.1 9.7 - - - -
142O VAL* 3.5 27.4 + - - +
143O LEU* 4.7 1.8 - - - +
13V VAL* 4.4 13.9 - - - +
14V VAL 4.1 0.2 - - - -
15V GLY* 1.3 76.8 - - - +
17V LYS* 1.3 104.9 + - - +
18V TRP* 2.7 17.7 + - - +
19V GLU* 3.7 12.1 + - - +
20V SER* 4.1 7.6 + - - -
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Residues in contact with LYS 17 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135O GLN* 5.7 0.8 + - - -
12V LYS* 3.1 21.6 - - - +
13V VAL* 2.9 27.7 + - - +
14V VAL* 3.9 16.8 - - + +
15V GLY 3.6 0.6 - - - -
16V ASP* 1.3 106.8 + - - +
18V TRP* 1.3 64.1 + - - +
19V GLU 3.5 0.2 - - - -
20V SER* 3.8 9.8 - - - +
21V TYR* 3.0 25.6 + - - +
39V LEU* 3.7 45.5 - - + -
41V LEU* 4.2 11.9 - - + +
50V ILE* 4.7 10.8 - - + -
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Residues in contact with TRP 18 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143O LEU* 4.5 11.9 - - + -
146O LYS* 4.2 12.1 - - - +
3V VAL* 3.0 36.8 - - + -
14V VAL 4.1 3.6 + - - -
15V GLY 4.0 7.0 + - - +
16V ASP 2.7 8.9 + - - -
17V LYS* 1.3 74.5 - - - +
19V GLU* 1.3 70.4 + - + +
21V TYR* 3.5 16.0 - + - +
22V LEU* 3.0 59.2 + - + +
50V ILE* 4.0 34.1 - - + -
53V HIS* 4.2 23.6 - - + -
55V ASP* 3.3 38.6 + - + -
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Residues in contact with GLU 19 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112O ASN* 2.7 16.2 - - - +
114O TYR* 2.5 41.6 + - - -
140O ASN* 4.8 4.9 + - - -
143O LEU* 4.5 9.8 - - + +
146O LYS* 5.8 0.6 - - - +
16V ASP 3.7 7.4 + - - +
18V TRP* 1.3 88.5 - - + +
20V SER* 1.3 65.8 + - - +
22V LEU* 3.2 17.6 + - + +
23V ASN* 3.2 14.7 + - - +
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Residues in contact with SER 20 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136O ASP* 4.6 10.7 + - - -
137O LYS* 5.6 2.9 - - - +
138O GLU* 4.9 7.3 + - - -
16V ASP 4.1 9.6 + - - -
17V LYS* 3.5 7.0 + - - -
18V TRP 3.3 0.4 - - - -
19V GLU* 1.3 77.6 - - - +
21V TYR* 1.3 62.1 + - - +
23V ASN* 3.1 9.2 + - - +
24V LEU* 3.1 25.9 + - - +
39V LEU* 3.4 24.2 - - - -
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Residues in contact with TYR 21 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17V LYS 3.0 14.3 + - - +
18V TRP* 3.5 16.6 - + - +
20V SER* 1.3 72.2 - - - +
22V LEU* 1.3 82.3 + - + +
23V ASN 2.9 6.4 + - - -
24V LEU* 3.1 15.5 + - - +
25V LEU* 3.3 35.4 + - + +
32V GLU* 3.3 26.8 - - - +
35V ALA* 3.9 22.7 - - + -
36V LEU* 3.3 35.2 - - + -
39V LEU* 3.2 21.4 - - + +
50V ILE* 3.9 16.4 - - + -
51V LEU* 4.4 12.0 + - - +
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Residues in contact with LEU 22 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18V TRP* 3.0 56.8 + - + +
19V GLU* 3.2 10.7 + - - +
21V TYR* 1.3 99.6 - - + +
23V ASN* 1.3 58.2 + - - +
25V LEU* 3.7 10.2 - - + +
26V GLN* 3.2 27.0 + - - +
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Residues in contact with ASN 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19V GLU 3.2 9.6 + - - +
20V SER* 3.1 12.6 + - - +
21V TYR 2.9 0.8 - - - -
22V LEU* 1.3 75.3 - - - +
24V LEU* 1.3 57.5 - - + +
25V LEU 2.4 18.3 + - - -
26V GLN* 3.0 5.1 + - - +
27V GLU* 2.8 62.2 + - - +
28V ASP* 3.3 8.6 + - - +
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Residues in contact with LEU 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V SER* 3.1 13.4 + - - +
21V TYR 3.1 6.7 + - - +
23V ASN* 1.3 74.5 - - + +
25V LEU* 1.3 57.7 + - - +
28V ASP* 3.9 29.5 - - + +
30V LEU* 2.9 39.8 + - + +
35V ALA* 3.6 27.4 - - + +
38V ARG* 3.4 41.7 - - + -
39V LEU* 3.8 20.9 - - + -
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Residues in contact with LEU 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21V TYR* 3.5 40.8 - - + +
22V LEU* 3.7 12.6 - - + +
23V ASN 2.4 16.9 + - - -
24V LEU* 1.3 68.8 - - - +
26V GLN* 1.3 66.9 + - - +
29V GLU* 3.0 22.1 - - - +
30V LEU 3.7 13.8 + - - +
32V GLU* 3.8 39.5 - - + +
35V ALA* 4.0 15.3 - - + -
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Residues in contact with GLN 26 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V LEU 3.2 14.9 + - - +
23V ASN* 3.0 5.7 + - - +
25V LEU* 1.3 84.7 - - - +
27V GLU* 1.3 91.3 + - - +
29V GLU* 3.3 12.8 - - - +
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Residues in contact with GLU 27 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23V ASN* 2.8 44.5 + - - +
26V GLN* 1.3 86.5 + - - +
28V ASP* 1.3 64.9 + - - +
29V GLU* 2.5 28.9 + - - +
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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