Contacts of the helix formed by residues 34 - 45 (chain B) in PDB entry 1U31
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 ASN 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B ILE* 1.3 78.3 - - - +
35B LEU* 1.3 65.4 + - - +
36B ASP* 4.0 20.6 + - - +
37B ASN* 3.1 24.8 + - - +
38B ALA* 3.2 19.4 + - - +
186B LEU* 4.5 6.0 - - - +
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ASN* 1.3 76.6 - - - +
36B ASP* 1.3 58.0 + - - +
38B ALA* 3.2 8.0 + - - +
39B ILE* 3.0 33.3 + - + +
186B LEU* 4.1 19.0 - - + +
193B THR* 4.2 17.3 - - + +
196B ALA* 3.7 33.4 - - + -
197B LEU* 4.4 11.1 - - + +
200B LYS* 3.7 26.5 - - + +
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Residues in contact with ASP 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ASN* 3.4 17.4 + - - +
35B LEU* 1.3 75.6 - - - +
37B ASN* 1.3 62.1 + - - +
39B ILE* 3.4 9.2 + - - +
40B ASP* 3.2 30.5 + - - +
200B LYS* 2.8 34.1 + - - +
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Residues in contact with ASN 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ILE* 3.6 31.0 - - + +
34B ASN* 3.1 25.0 + - - +
36B ASP* 1.3 76.1 - - - +
38B ALA* 1.3 61.4 + - - +
40B ASP* 3.4 11.6 + - - +
41B MET* 3.2 37.8 + - - +
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ILE* 3.8 16.9 - - + +
34B ASN 3.2 3.8 + - - +
35B LEU 3.2 9.0 + - - +
37B ASN* 1.3 75.8 - - - +
39B ILE* 1.3 59.0 + - - +
41B MET* 3.3 2.9 + - - +
42B ILE* 3.0 36.1 + - + +
160B ILE* 4.0 13.3 - - + +
162B MET* 6.0 0.2 - - + -
186B LEU* 3.6 31.4 - - + -
197B LEU* 4.1 8.5 - - + -
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Residues in contact with ILE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 3.0 22.8 + - + +
36B ASP* 3.4 13.0 - - - +
38B ALA* 1.3 76.1 - - - +
40B ASP* 1.3 54.8 + - - +
42B ILE* 3.2 8.0 + - + +
43B ARG* 2.8 53.3 + - + +
197B LEU* 3.8 23.1 - - + +
200B LYS* 3.9 30.5 - - + +
201B VAL* 3.6 31.8 - - + +
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Residues in contact with ASP 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ASP* 3.2 18.1 + - - +
37B ASN* 3.6 11.8 - - - +
38B ALA 3.4 0.4 - - - -
39B ILE* 1.3 77.9 - - - +
41B MET* 1.3 57.4 + - + +
43B ARG* 3.4 20.0 + - - +
44B GLU* 2.9 31.9 + - - +
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Residues in contact with MET 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ILE* 4.2 11.0 - - + -
37B ASN* 3.2 31.7 + - - +
38B ALA 3.6 7.6 - - - +
39B ILE 3.3 0.2 - - - -
40B ASP* 1.3 75.6 - - + +
42B ILE* 1.3 62.5 + - - +
44B GLU* 3.6 4.8 + - - +
45B ALA* 3.2 25.1 + - - +
123B LEU* 3.7 10.7 - - + +
158B GLN* 3.8 37.9 - - + +
160B ILE* 3.7 30.1 - - + -
184B ALA* 4.3 10.8 - - + -
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Residues in contact with ILE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ALA* 3.0 22.1 + - + +
39B ILE* 3.2 11.4 + - + +
41B MET* 1.3 73.1 - - - +
43B ARG* 1.3 64.0 + - - +
45B ALA* 3.4 10.7 + - - +
48B ILE* 3.9 8.2 - - + +
68B LEU* 5.0 8.3 - - + -
72B LEU* 3.6 38.8 - - + -
77B LYS* 3.0 19.5 + - - +
123B LEU* 3.7 20.9 - - + -
125B LEU* 4.4 22.2 - - + -
160B ILE* 4.9 0.4 - - + -
162B MET* 5.7 0.2 - - + -
197B LEU* 4.1 26.7 - - + -
201B VAL* 5.2 7.6 - - + -
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Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ILE* 2.8 35.9 + - + +
40B ASP* 3.5 19.8 + - - +
42B ILE* 1.3 74.2 - - - +
44B GLU* 1.3 59.5 + - - +
46B ASN* 5.5 0.3 - - - +
75B GLN* 5.8 2.0 + - - -
77B LYS* 2.8 25.0 + - - +
204B SER* 4.1 23.4 + - - -
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ASP 2.9 17.5 + - - +
41B MET* 4.1 5.6 - - - +
42B ILE 3.3 0.2 - - - -
43B ARG* 1.3 78.4 - - - +
45B ALA* 1.3 61.0 + - - +
46B ASN* 3.7 11.8 + - - +
122B ASP* 4.9 0.7 - - - +
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B MET 3.2 17.7 + - - +
42B ILE 3.4 5.5 - - - +
43B ARG 3.3 1.0 - - - +
44B GLU* 1.3 77.4 - - - +
46B ASN* 1.3 61.5 + - - +
48B ILE* 4.0 9.1 - - + +
77B LYS* 2.8 33.6 + - - +
122B ASP* 3.8 16.4 - - + -
123B LEU* 3.6 27.4 - - + -
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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