Contacts of the helix formed by residues 42 - 53 (chain B) in PDB entry 1UTX
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 SER 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A SER* 6.1 0.7 - - - +
43A LEU 5.3 1.3 - - - +
41B PRO* 1.3 79.7 - - - +
43B LEU* 1.3 64.0 + - - +
44B GLN* 3.6 7.2 + - - +
45B LEU* 3.2 24.4 + - - +
46B ALA* 2.9 19.9 + - - +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ILE* 4.1 14.1 - - + -
40A ASN* 4.5 3.8 - - + -
41A PRO* 3.5 47.4 + - + +
42A SER* 5.3 0.2 - - - +
43A LEU* 4.2 25.3 - - + +
46A ALA* 3.8 23.1 - - + -
57A LEU* 4.4 11.0 - - + -
61A PHE* 4.0 17.7 - - + -
42B SER* 1.3 74.0 - - - +
44B GLN* 1.3 59.3 + - - +
46B ALA* 3.1 3.5 + - - +
47B LEU* 2.9 47.5 + - + +
57B LEU* 4.5 1.6 - - + -
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Residues in contact with GLN 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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1A MET* 2.8 37.7 + - - +
2A ILE* 3.8 20.8 + - + +
40A ASN* 5.5 4.9 + - - +
63A TRP* 3.4 23.8 - - + +
42B SER* 3.3 5.0 + - - +
43B LEU* 1.3 78.1 - - - +
45B LEU* 1.3 62.6 + - - +
47B LEU* 3.2 4.5 + - - +
48B LYS* 3.0 24.6 + - + +
1069B IOD 3.6 26.6 - - + +
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Residues in contact with LEU 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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24B LEU* 4.2 29.6 - - + +
26B VAL* 4.1 29.8 - - + -
30B THR* 4.6 7.6 - - + -
31B ILE* 6.0 0.2 - - + -
34B ILE* 4.1 15.0 - - + -
41B PRO* 3.7 22.7 - - + -
42B SER* 3.2 20.6 + - - +
44B GLN* 1.3 76.6 - - - +
46B ALA* 1.3 58.3 + - - +
48B LYS* 3.2 7.3 + - + -
49B ILE* 2.9 36.5 + - + +
1069B IOD 4.0 10.9 - - + +
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Residues in contact with ALA 46 (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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43A LEU* 3.8 18.2 - - + -
41B PRO* 4.0 16.7 - - + +
42B SER 2.9 17.7 + - - +
43B LEU 3.5 4.5 - - - +
45B LEU* 1.3 77.4 - - - +
47B LEU* 1.3 57.4 + - - +
49B ILE* 3.3 9.4 + - - +
50B ALA* 3.0 27.7 + - - +
57B LEU* 3.8 20.5 - - + +
61B PHE* 4.1 10.4 - - + -
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Residues in contact with LEU 47 (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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2A ILE* 3.7 34.8 - - + -
57A LEU* 3.7 26.9 - - + -
58A GLU* 4.1 13.5 - - + -
61A PHE* 3.8 24.2 - - + +
63A TRP* 3.9 23.7 - - + +
43B LEU* 2.9 29.3 + - + +
44B GLN 3.6 4.5 - - - +
46B ALA* 1.3 76.3 - - - +
48B LYS* 1.3 57.9 + - - +
50B ALA* 3.4 5.0 + - + +
51B TYR* 3.0 27.8 + - - +
57B LEU* 3.8 8.1 - - + -
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Residues in contact with LYS 48 (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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63A TRP* 3.6 45.8 - - + +
66A GLU 4.9 4.7 + - - -
23B LEU 4.9 1.1 + - - -
24B LEU* 3.5 41.9 + - + +
25B GLU* 4.5 11.7 + - - +
44B GLN* 3.0 16.8 + - + +
45B LEU* 3.2 10.9 + - + +
47B LEU* 1.3 74.5 - - - +
49B ILE* 1.3 64.2 + - - +
51B TYR* 3.3 6.6 + - - +
52B TYR* 3.0 37.2 + - + -
1069B IOD 4.3 17.5 - - + -
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Residues in contact with ILE 49 (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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6B LEU* 3.6 43.7 - - + -
20B LEU* 4.9 3.4 - - + -
24B LEU* 3.7 25.1 - - + -
31B ILE* 4.5 5.4 - - + -
34B ILE* 4.5 13.7 - - + -
41B PRO* 4.5 1.3 - - + -
45B LEU* 2.9 34.8 + - + +
46B ALA* 3.5 11.4 - - - +
48B LYS* 1.3 75.1 - - - +
50B ALA* 1.3 58.7 + - - +
52B TYR* 3.4 2.0 + - - +
53B LEU* 2.9 38.5 + - + +
60B ILE* 4.2 11.0 - - + -
61B PHE* 4.5 10.3 - - + -
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Residues in contact with ALA 50 (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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58A GLU* 4.4 4.9 - - + +
46B ALA 3.0 14.0 + - - +
47B LEU* 3.6 10.8 - - + +
49B ILE* 1.3 77.2 - - - +
51B TYR* 1.3 56.0 + - - +
53B LEU 3.4 0.6 + - - +
54B ASN* 3.0 23.9 + - - -
55B THR 3.1 30.3 + - - +
57B LEU* 3.9 25.1 - - + +
60B ILE* 3.7 11.2 - - + -
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Residues in contact with TYR 51 (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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63A TRP* 3.6 28.7 - + + -
65A PRO* 3.8 28.8 - - + +
1072A IOD 3.8 28.3 - - + -
47B LEU 3.0 16.4 + - - +
48B LYS 3.5 4.3 - - - +
49B ILE 3.2 0.2 - - - -
50B ALA* 1.3 77.3 - - - +
52B TYR* 1.3 98.9 + + - +
54B ASN* 3.2 22.9 + - - +
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Residues in contact with TYR 52 (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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63A TRP* 4.4 12.2 - + - -
66A GLU* 4.6 14.4 + - - -
15B ILE* 4.3 10.2 - - - +
20B LEU* 4.0 20.1 - - + +
23B LEU* 3.7 61.0 + - + +
24B LEU* 3.8 14.6 - - + -
48B LYS* 3.0 30.6 + - - +
51B TYR* 1.3 105.0 - + - +
53B LEU* 1.3 65.1 + - - +
54B ASN* 3.4 10.4 + - - +
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Residues in contact with LEU 53 (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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6B LEU* 3.5 32.1 - - + -
9B ILE* 4.1 17.0 - - + -
10B ARG* 4.2 20.2 - - + +
13B LYS* 3.2 22.4 - - + -
15B ILE* 3.9 26.0 - - + -
20B LEU* 4.4 19.7 - - + -
49B ILE* 2.9 25.3 + - + +
50B ALA 4.2 1.6 - - - +
52B TYR* 1.3 79.8 - - - +
54B ASN* 1.3 62.0 + - - +
55B THR* 2.8 30.0 + - - +
60B ILE* 4.4 5.8 - - + -
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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