Contacts of the helix formed by residues 20 - 25 (chain V) in PDB entry 1UW9
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 TYR 20 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18V LYS 3.5 2.9 + - - -
19V ASP* 1.3 71.2 - - - +
21V ARG* 1.3 57.2 + - - +
22V LEU 3.1 0.7 - - - -
23V THR 3.0 4.7 + - - -
24V TYR* 2.9 30.3 + + + +
52V GLU* 2.8 24.7 + - - +
55V ALA* 3.7 4.3 - - + +
56V ALA* 3.5 39.5 - - + +
59V ALA* 3.3 28.7 - - + -
60V GLU* 2.7 33.3 + - + +
64V GLY 5.0 0.2 - - - -
65V THR* 3.4 20.4 - - - -
66V TRP* 3.5 17.8 - - - +
127V PHE* 3.9 11.0 - + - -
1479V EDO 4.0 18.6 - - - -
1480V EDO 3.9 17.5 - - - -
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Residues in contact with ARG 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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19V ASP* 3.8 20.0 - - + -
20V TYR* 1.3 76.7 - - - +
22V LEU* 1.3 68.2 + - + +
23V THR 3.1 0.7 + - - -
25V TYR* 3.4 42.6 + - + +
49V PRO* 3.9 30.3 - - - +
51V GLU* 3.6 36.1 + - - +
52V GLU* 2.9 24.5 + - - +
55V ALA* 3.4 13.7 - - + -
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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 LYS* 4.0 30.7 - - + +
19V ASP* 3.6 27.1 - - + +
20V TYR 3.1 0.6 + - - -
21V ARG* 1.3 83.6 - - + +
23V THR* 1.3 62.2 + - - +
25V TYR 5.5 0.4 - - - +
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Residues in contact with THR 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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18V LYS* 4.1 23.0 + - - -
19V ASP 5.2 0.3 + - - -
20V TYR 3.0 2.5 + - - -
22V LEU* 1.3 83.1 - - - +
24V TYR* 1.3 88.0 + - + +
25V TYR 3.7 1.8 - - - -
26V THR* 3.9 5.9 - - - +
77V LEU* 4.0 23.3 - - + -
81V LYS* 2.8 44.7 + - + +
1478V EDO 4.5 4.4 - - - -
1479V EDO 4.6 2.3 + - - -
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Residues in contact with TYR 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 TYR* 2.9 21.1 + - - +
23V THR* 1.3 96.2 - - + +
25V TYR* 1.3 60.6 + - - +
26V THR* 3.9 2.5 - - - -
55V ALA* 3.4 22.7 - - + +
58V ALA* 4.1 1.1 - - + +
59V ALA* 3.4 38.1 - - + +
62V SER* 4.0 2.5 - - - -
63V THR* 2.9 30.5 + - - -
64V GLY* 3.3 7.0 - - - -
77V LEU* 4.1 4.9 - - - +
81V LYS* 3.6 14.6 - - + -
82V GLY 3.2 22.4 - - - +
83V ARG* 3.8 2.0 - - - +
84V CYS* 2.9 30.8 + - - +
1478V EDO 2.7 32.6 + - - -
1479V EDO 4.1 5.2 - - - -
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Residues in contact with TYR 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 ARG* 3.4 41.0 + - + +
22V LEU 5.5 0.3 - - - +
23V THR 5.0 0.5 - - - -
24V TYR* 1.3 77.2 + - - +
26V THR* 1.3 63.2 + - - +
27V PRO* 3.6 40.6 - - + +
51V GLU* 3.6 37.5 + - + +
55V ALA* 4.0 7.2 - - + +
84V CYS* 3.4 26.5 - - + -
86V ASP* 5.1 3.5 - - - -
87V ILE* 3.8 31.5 + - + +
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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