Contacts of the helix formed by residues 22 - 36 (chain W) 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 THR 22 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20W PRO 4.6 3.8 - - - +
21W LEU* 1.3 77.2 - - - +
23W ASP* 1.3 59.8 + - - +
24W GLU* 3.5 9.7 + - - +
25W GLN* 2.8 46.9 + - - +
26W ILE* 2.9 27.5 + - - +
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Residues in contact with ASP 23 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21W LEU 5.3 0.3 - - - +
22W THR* 1.3 73.3 - - - +
24W GLU* 1.3 55.6 + - - +
26W ILE* 3.3 17.6 + - - +
27W ALA* 2.9 30.8 + - - +
90W LEU* 5.7 1.0 - - - +
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Residues in contact with GLU 24 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22W THR* 3.2 9.5 + - - +
23W ASP* 1.3 79.6 - - - +
25W GLN* 1.3 57.5 + - + +
27W ALA* 3.5 6.3 + - - +
28W ALA* 3.0 27.7 + - - +
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Residues in contact with GLN 25 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429V GLN* 3.6 20.2 + - - +
433V GLU* 3.9 16.1 - - - +
19W PRO* 5.0 2.2 + - - +
20W PRO 3.9 4.2 + - - -
21W LEU* 3.3 23.8 - - + +
22W THR* 2.8 54.0 + - - +
24W GLU* 1.3 75.5 - - + +
26W ILE* 1.3 66.2 + - - +
28W ALA* 3.4 7.8 + - - +
29W GLN* 3.2 28.4 + - - +
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Residues in contact with ILE 26 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21W LEU* 3.8 31.6 - - + +
22W THR 2.9 19.7 + - - +
23W ASP* 3.6 17.0 - - - +
25W GLN* 1.3 74.1 - - - +
27W ALA* 1.3 65.5 + - - +
29W GLN* 3.1 10.7 + - - +
30W VAL* 3.0 26.4 + - + +
90W LEU* 4.3 16.8 - - + -
93W ILE* 4.5 12.1 - - + -
121W PHE* 4.2 15.5 - - + -
122W LEU 5.8 0.7 - - - +
123W VAL* 4.8 20.4 - - + +
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Residues in contact with ALA 27 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23W ASP 2.9 17.2 + - - +
24W GLU* 3.7 9.0 - - - +
26W ILE* 1.3 75.7 - - - +
28W ALA* 1.3 57.1 + - - +
30W VAL* 3.2 9.2 + - - +
31W ASP* 2.9 35.4 + - - +
86W PRO* 5.5 0.5 - - - +
90W LEU* 4.4 23.3 - - + +
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Residues in contact with ALA 28 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432V ASN 4.1 6.4 - - - +
433V GLU* 3.9 29.1 - - + +
24W GLU 3.0 18.3 + - - +
25W GLN* 3.6 8.1 - - - +
26W ILE 3.2 0.2 - - - -
27W ALA* 1.3 75.4 - - - +
29W GLN* 1.3 63.6 + - - +
31W ASP* 3.4 13.4 + - - +
32W TYR* 3.1 19.9 + - - +
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Residues in contact with GLN 29 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429V GLN* 3.9 22.6 + - - +
432V ASN* 2.9 43.2 + - - +
433V GLU* 4.4 5.5 - - - +
15W PHE* 3.6 20.1 - - + -
21W LEU* 4.5 6.3 - - + -
25W GLN 3.2 15.9 + - - +
26W ILE 3.1 7.9 + - - +
28W ALA* 1.3 73.4 - - - +
30W VAL* 1.3 65.4 + - - +
32W TYR* 3.2 7.7 - - - +
33W ILE* 3.1 26.2 + - - +
119W MET* 4.1 11.9 - - + +
121W PHE* 3.6 30.7 - - + -
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Residues in contact with VAL 30 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26W ILE* 3.0 20.1 + - + +
27W ALA* 3.2 9.6 + - - +
29W GLN* 1.3 73.6 - - - +
31W ASP* 1.3 64.0 + - - +
33W ILE* 3.1 11.9 + - + +
34W VAL* 3.1 21.7 + - + +
86W PRO* 3.7 38.6 - - + +
89W VAL* 3.8 20.6 - - + -
90W LEU* 4.1 19.1 - - + -
93W ILE* 4.8 0.7 - - + -
107W LEU* 3.8 25.4 - - + -
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Residues in contact with ASP 31 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27W ALA* 2.9 20.4 + - - +
28W ALA* 3.5 14.1 - - - +
29W GLN 3.3 0.2 - - - -
30W VAL* 1.3 74.4 - - - +
32W TYR* 1.3 57.9 + - - +
34W VAL* 3.3 5.0 + - - +
35W ALA* 2.8 32.9 + - - +
86W PRO* 3.5 25.3 - - - +
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Residues in contact with TYR 32 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431V ARG* 3.3 31.6 + - + -
432V ASN* 3.1 64.4 + - + +
28W ALA 3.1 8.7 + - - +
29W GLN* 3.2 15.4 + - - +
31W ASP* 1.3 73.1 - - - +
33W ILE* 1.3 65.7 + - - +
35W ALA* 3.8 4.9 - - + +
36W ASN* 2.9 50.1 + - - +
38W TRP* 3.6 27.3 - + - -
119W MET* 5.3 8.3 - - + -
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Residues in contact with ILE 33 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29W GLN 3.1 12.2 + - - +
30W VAL* 3.4 12.6 - - + +
32W TYR* 1.3 78.9 - - - +
34W VAL* 1.3 63.6 + - + +
36W ASN* 3.3 1.4 + - - -
37W GLY 3.2 3.1 + - - -
38W TRP* 3.1 52.5 + - + +
40W PRO* 4.0 19.1 - - + -
89W VAL* 5.4 0.7 - - + -
107W LEU* 3.8 27.6 - - + -
108W VAL 4.7 0.4 - - - +
109W ALA* 3.9 21.8 - - + -
119W MET* 3.6 40.6 - - + -
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Residues in contact with VAL 34 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30W VAL* 3.1 18.4 + - + +
31W ASP 3.9 2.9 - - - +
33W ILE* 1.3 77.6 - - + +
35W ALA* 1.3 67.5 + - - +
37W GLY* 2.9 16.0 + - - +
38W TRP 5.2 1.8 - - - +
40W PRO* 5.6 1.6 - - + -
83W CYS* 4.8 7.2 - - - +
84W ARG* 3.5 35.7 - - + +
85W ASP 4.4 3.8 - - - +
86W PRO* 4.0 34.1 - - + -
89W VAL* 5.1 5.4 - - + -
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Residues in contact with ALA 35 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31W ASP 2.8 23.2 + - - +
32W TYR* 3.8 7.9 - - + +
34W VAL* 1.3 74.2 - - - +
36W ASN* 1.3 64.5 + - - +
37W GLY 3.7 0.2 + - - -
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Residues in contact with ASN 36 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32W TYR* 2.9 55.9 + - - +
33W ILE 3.3 0.2 + - - -
34W VAL 3.1 0.6 - - - -
35W ALA* 1.3 82.1 - - - +
37W GLY* 1.3 62.2 + - - +
38W TRP* 3.3 44.0 + - + -
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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