Contacts of the helix formed by residues 50 - 62 (chain A) in PDB entry 1JUO
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 ASP 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ILE* 1.3 74.0 - - - +
51A ALA* 1.3 53.5 + - - +
52A ASP* 2.9 13.1 + - - +
53A GLU* 2.7 58.4 + - - +
54A LEU* 2.7 33.3 + - - +
79A VAL* 4.2 4.0 - - - -
88A GLY 3.9 16.6 - - - +
89A THR* 4.5 6.4 - - + +
149B SER 6.0 1.3 - - - +
150B THR 4.6 9.8 - - - +
151B ASN* 4.3 13.5 - - - +
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Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASP* 1.3 75.8 - - - +
52A ASP* 1.3 57.1 + - - +
54A LEU* 4.1 1.8 - - - -
55A GLN* 2.9 29.3 + - - +
72A LEU* 3.9 7.7 - - + +
75A CYS* 3.4 6.7 - - - +
76A ARG* 3.6 46.9 - - + +
79A VAL* 3.6 18.3 - - + +
88A GLY 4.6 1.6 + - - -
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Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASP* 2.9 13.3 + - - +
51A ALA* 1.3 75.3 - - - +
53A GLU* 1.3 67.8 + - - +
55A GLN* 3.1 21.6 + - - +
56A ARG* 3.2 37.8 + - - +
72A LEU* 3.9 17.9 - - + +
150B THR 6.1 0.9 - - - +
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Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.3 36.1 - - + +
43A ALA 5.5 0.5 - - - -
48A GLN 3.8 5.1 - - - +
49A ILE* 3.2 17.9 - - + -
50A ASP* 2.7 50.9 + - - +
52A ASP* 1.3 71.2 - - - +
54A LEU* 1.3 66.2 + - - +
56A ARG* 3.1 32.4 + - - +
57A CYS 3.1 19.6 + - - -
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 3.8 22.2 - - + +
50A ASP 2.7 22.2 + - - +
51A ALA* 3.7 5.2 - - - +
53A GLU* 1.3 73.0 - - - +
55A GLN* 1.3 62.1 + - - +
57A CYS* 3.7 1.2 - - - -
58A LEU* 3.0 37.1 + - + +
75A CYS* 3.7 28.0 - - + +
78A MET* 3.8 20.0 - - + -
79A VAL* 3.7 12.8 - - + -
90A MET* 4.0 11.7 - - + -
95A PHE* 3.8 32.1 - - + -
98A LEU* 4.1 5.2 - - + -
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Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ALA 2.9 14.3 + - - +
52A ASP* 3.1 19.3 + - - +
54A LEU* 1.3 77.9 - - - +
56A ARG* 1.3 62.8 + - - +
58A LEU* 4.0 2.6 - - - +
59A THR* 2.6 46.4 + - - +
69A PRO* 4.9 5.3 - - - +
70A PHE* 3.4 26.4 + - + +
71A ASN 4.2 6.7 - - - +
72A LEU* 4.6 8.4 + - + +
75A CYS* 3.3 21.3 - - + -
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Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA 5.3 1.2 + - - -
42A VAL* 3.8 28.9 + - + +
52A ASP* 3.2 29.9 + - - +
53A GLU* 3.1 38.0 + - - +
55A GLN* 1.3 86.1 - - - +
57A CYS* 1.3 63.5 + - - +
59A THR* 3.0 22.7 + - - -
60A GLN* 3.2 13.5 + - + +
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Residues in contact with CYS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 3.5 29.5 - - - +
39A PHE* 4.7 3.4 - - - -
42A VAL* 3.7 20.4 - - + +
49A ILE* 4.5 5.2 - - - -
53A GLU 3.1 10.6 + - - -
54A LEU* 3.7 12.3 - - - -
56A ARG* 1.3 72.5 - - - +
58A LEU* 1.3 69.0 + - - +
60A GLN* 3.4 10.1 + - - +
61A SER* 3.0 23.6 + - - -
95A PHE* 3.5 35.8 - - - -
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.0 37.1 + - + +
55A GLN* 4.0 4.3 - - - +
57A CYS* 1.3 77.3 - - - +
59A THR* 1.3 62.9 + - - +
61A SER* 2.5 23.7 + - - +
62A GLY 3.2 4.0 + - - -
63A ILE* 3.7 26.8 + - + +
64A ALA* 5.1 0.9 + - - +
70A PHE* 3.9 19.7 - - + -
75A CYS* 4.6 4.7 - - - -
78A MET* 3.7 29.6 - - - -
95A PHE* 3.6 25.4 - - + -
98A LEU* 4.1 9.2 - - + -
99A TRP* 4.9 6.1 - - + -
102A LEU* 4.1 6.7 - - + -
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Residues in contact with THR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLN* 2.6 35.8 + - - +
56A ARG* 3.0 10.0 + - - -
58A LEU* 1.3 79.3 - - - +
60A GLN* 1.3 70.4 + - - +
62A GLY* 3.2 13.0 + - - -
64A ALA* 6.3 3.1 - - - -
69A PRO* 4.2 29.1 - - + +
70A PHE 5.4 1.0 + - - -
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 3.5 27.7 + - + +
56A ARG* 3.2 15.3 + - + +
57A CYS* 3.7 10.8 - - - +
58A LEU 3.3 0.2 - - - -
59A THR* 1.3 79.5 - - - +
61A SER* 1.3 62.3 - - - +
62A GLY* 2.9 8.0 + - - -
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 5.0 0.4 - - - -
38A TYR* 3.5 36.0 + - - -
57A CYS 3.0 14.5 + - - -
58A LEU* 2.5 27.9 + - - +
60A GLN* 1.3 76.5 - - - +
62A GLY* 1.3 59.7 + - - +
63A ILE* 3.3 10.6 + - - +
95A PHE* 5.0 2.7 - - - -
99A TRP* 3.3 34.5 - - - -
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Residues in contact with GLY 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU 3.2 0.6 + - - -
59A THR 3.2 13.4 + - - -
60A GLN 2.9 6.6 + - - -
61A SER* 1.3 81.1 + - - +
63A ILE* 1.3 65.1 + - - +
64A ALA* 3.1 3.8 - - - -
65A GLY* 3.1 18.5 + - - -
99A TRP* 5.0 0.4 - - - -
106A ARG* 4.3 4.0 + - - -
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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