Contacts of the helix formed by residues 35 - 46 (chain D) in PDB entry 1UDY
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 ILE 35 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D PHE* 3.3 39.4 + - + -
31D ALA* 3.4 25.5 + - + +
34D GLU* 1.3 75.3 - - - +
36D ILE* 1.3 67.6 + - - +
38D VAL* 3.0 7.1 + - - +
39D ALA* 2.9 20.9 + - + -
52D LEU* 4.4 13.5 - - + -
87D LEU* 4.4 18.8 - - + +
90D GLY 3.7 25.1 - - - -
91D CYS* 3.8 14.6 - - + +
94D VAL* 4.2 23.1 - - + -
95D GLN 5.9 0.2 - - - +
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Residues in contact with ILE 36 (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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31D ALA 3.0 12.9 + - - +
32D ARG* 3.8 25.8 - - + +
35D ILE* 1.3 79.5 - - - +
37D PRO* 1.3 72.8 - - + +
38D VAL 3.1 1.0 + - - -
39D ALA* 3.4 16.6 + - - +
40D ALA* 4.6 2.8 + - - +
89D TYR* 3.7 30.5 - - + -
90D GLY* 3.6 16.4 - - - -
269D ARG* 3.9 26.7 + - - +
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Residues in contact with PRO 37 (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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32D ARG 3.9 5.6 - - - +
33D GLU* 3.6 25.1 - - - +
34D GLU* 3.7 13.2 - - - +
35D ILE 3.5 3.6 - - - -
36D ILE* 1.3 97.5 - - + +
38D VAL* 1.3 62.8 + - + +
40D ALA* 5.4 1.8 + - - +
41D GLU* 5.9 0.2 - - - +
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Residues in contact with VAL 38 (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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34D GLU 3.5 16.2 - - - +
35D ILE 3.4 10.5 - - - +
37D PRO* 1.3 83.8 - - + +
39D ALA* 1.3 65.2 - - - +
40D ALA 3.3 2.7 - - - -
41D GLU* 3.1 20.6 + - + +
42D TYR* 3.2 41.3 + - + -
52D LEU* 3.8 15.3 - - + -
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Residues in contact with ALA 39 (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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35D ILE* 2.9 15.2 + - + +
36D ILE* 3.4 9.5 + - - +
38D VAL* 1.3 79.2 - - - +
40D ALA* 1.3 62.7 + - - +
42D TYR* 3.5 5.9 + - - +
43D ASP* 3.2 24.1 + - - +
90D GLY 3.7 22.4 - - - +
91D CYS* 3.9 19.7 - - + -
94D VAL* 5.8 2.5 - - - -
269D ARG* 5.8 2.0 - - - +
364D LYS* 3.9 10.5 - - + +
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Residues in contact with ALA 40 (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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36D ILE 4.6 2.7 + - - +
37D PRO 5.4 1.5 - - - +
38D VAL 3.3 1.2 - - - -
39D ALA* 1.3 79.1 - - - +
41D GLU* 1.3 58.4 + - - +
43D ASP* 3.6 7.7 - - - +
44D ARG* 3.1 56.1 + - - +
364D LYS* 4.9 6.7 - - + +
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Residues in contact with GLU 41 (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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38D VAL* 3.1 16.6 + - + +
40D ALA* 1.3 77.6 - - - +
42D TYR* 1.3 61.2 + - + +
43D ASP 3.1 1.6 - - - -
44D ARG* 3.3 29.1 + - - +
45D THR* 3.0 49.8 + - + +
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Residues in contact with TYR 42 (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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38D VAL* 3.2 47.9 + - + +
39D ALA* 4.1 5.6 - - - +
41D GLU* 1.3 79.4 - - + +
43D ASP* 1.3 54.5 + - - +
45D THR* 3.8 4.0 - - - -
46D GLY* 2.6 33.4 + - - -
47D GLU* 3.1 34.5 + - + -
48D TYR 4.0 5.2 - - - -
49D PRO* 3.5 26.2 - - + -
51D PRO* 3.6 30.4 - - + +
52D LEU* 4.0 15.9 - - + +
91D CYS* 6.3 0.7 - - - -
94D VAL* 5.5 2.7 - - + -
219D CYS* 3.6 20.1 - - + +
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Residues in contact with ASP 43 (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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39D ALA 3.2 18.8 + - - +
40D ALA* 3.6 6.9 - - - +
41D GLU 3.1 0.2 - - - -
42D TYR* 1.3 79.7 - - - +
44D ARG* 1.3 67.2 + - - +
45D THR 3.4 0.5 + - - -
46D GLY 3.7 4.0 + - - -
217D GLN 5.4 0.2 + - - -
218D ARG* 3.1 61.4 + - - +
219D CYS* 4.8 2.7 - - - +
358D THR* 5.8 0.3 + - - -
363D GLU* 4.7 0.7 - - - +
364D LYS* 3.5 29.3 - - + +
367D ARG* 3.1 31.0 + - - -
368D ASP* 5.0 1.9 - - - +
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Residues in contact with ARG 44 (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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40D ALA* 3.1 40.0 + - - +
41D GLU* 3.3 35.1 + - - +
43D ASP* 1.3 82.9 - - - +
45D THR* 1.3 59.7 + - + +
218D ARG* 4.2 11.5 + - - +
358D THR* 4.1 26.5 + - - +
359D GLU* 4.0 19.8 + - - +
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Residues in contact with THR 45 (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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41D GLU* 3.0 33.4 + - + +
42D TYR* 3.7 3.8 + - - -
43D ASP 4.3 0.2 - - - -
44D ARG* 1.3 79.4 - - + +
46D GLY* 1.3 65.5 + - - +
47D GLU* 3.0 31.9 + - - +
211D LYS* 4.8 0.7 + - - -
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Residues in contact with GLY 46 (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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42D TYR 2.6 21.8 + - - -
43D ASP 3.7 5.3 + - - -
45D THR* 1.3 74.7 - - - +
47D GLU* 1.3 63.9 + - - +
48D TYR 3.5 1.7 + - - -
211D LYS* 2.5 28.2 + - - +
218D ARG* 3.4 23.0 - - - +
219D CYS* 3.8 3.9 - - - +
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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