Contacts of the helix formed by residues 46 - 57 (chain A) in PDB entry 2J0Q
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 ARG 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A LEU* 1.3 73.2 - - - +
47A GLU* 1.3 67.3 + - - +
48A ASP* 3.1 13.5 - - - +
49A LEU* 2.7 32.2 + - + +
50A LEU* 3.0 7.8 + - - -
97A LEU 3.2 19.8 + - - -
98A GLN* 2.8 38.7 + - - +
100A LEU* 2.8 36.4 + - - +
102A ILE* 3.8 16.4 - - - +
133A MET* 3.3 26.4 - - - +
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Residues in contact with GLU 47 (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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45A LEU 3.6 3.9 + - - -
46A ARG* 1.3 70.1 - - - +
48A ASP* 1.3 63.0 + - + +
50A LEU* 3.6 6.8 - - - +
51A ARG* 3.2 22.9 + - - +
66G PRO* 4.2 25.6 - - + +
67G GLN* 6.1 0.2 - - - -
73G TRP* 5.2 11.0 - - + -
124G TYR* 4.0 9.7 + - - -
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Residues in contact with ASP 48 (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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46A ARG* 2.8 17.3 + - - +
47A GLU* 1.3 77.1 + - + +
49A LEU* 1.3 63.9 + - - +
51A ARG* 3.9 14.8 - - + +
52A GLY* 3.8 4.3 + - - -
129A LEU 4.7 1.4 - - - +
132A TYR* 3.3 48.9 + - + +
133A MET* 3.8 9.3 - - - +
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Residues in contact with LEU 49 (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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45A LEU* 3.3 26.2 - - + -
46A ARG* 2.7 26.4 + - + +
48A ASP* 1.3 72.5 + - - +
50A LEU* 1.3 58.0 + - - +
52A GLY* 2.9 21.3 + - - -
53A ILE* 2.9 20.5 + - + +
94A ILE* 3.3 27.1 - - - +
97A LEU* 3.4 34.8 - - + -
98A GLN* 3.4 25.4 - - - +
129A LEU* 4.4 11.0 - - + +
133A MET* 4.1 8.5 - - - +
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Residues in contact with LEU 50 (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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40A PHE* 3.6 43.1 - - + +
41A ASP* 3.5 31.6 - - - +
45A LEU* 3.8 29.5 - - + +
46A ARG 3.0 8.8 + - - +
47A GLU* 3.6 9.9 - - - +
49A LEU* 1.3 79.5 - - - +
51A ARG* 1.3 59.0 + - - +
53A ILE* 3.6 10.7 + - + +
54A TYR* 3.2 35.9 + - + -
73G TRP* 3.5 27.6 - - + -
124G TYR* 4.8 2.7 - - + -
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Residues in contact with ARG 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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47A GLU 3.2 17.5 + - - +
48A ASP* 3.9 12.7 - - - +
49A LEU 3.1 0.4 - - - -
50A LEU* 1.3 77.7 - - - +
52A GLY* 1.3 57.0 + - - +
54A TYR* 3.4 7.8 + - + +
55A ALA* 3.0 26.1 + - - +
132A TYR* 3.1 53.8 + - + +
124G TYR* 2.7 42.4 - - + +
128G GLN* 3.5 18.5 + - - +
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Residues in contact with GLY 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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48A ASP 3.8 1.5 + - - -
49A LEU 2.9 8.7 + - - -
51A ARG* 1.3 76.0 - - - +
53A ILE* 1.3 59.8 + - - +
55A ALA* 3.7 3.2 - - - +
56A TYR* 2.9 29.5 + - - +
128A ALA 4.5 3.6 - - - +
129A LEU* 3.7 23.1 - - - +
131A ASP* 5.4 1.1 - - - -
132A TYR* 3.5 23.1 - - - -
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Residues in contact with ILE 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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40A PHE* 3.8 42.6 - - + -
45A LEU* 4.0 24.7 - - + -
49A LEU* 2.9 20.0 + - + +
50A LEU* 3.6 14.1 - - + +
51A ARG 3.3 0.2 - - - -
52A GLY* 1.3 75.1 - - - +
54A TYR* 1.3 71.8 + - + +
56A TYR* 3.3 11.3 + - - +
57A GLY 3.5 0.3 + - - -
58A PHE* 3.4 25.8 + - + +
94A ILE* 3.5 37.5 - - + -
129A LEU* 4.3 13.0 - - + -
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Residues in contact with TYR 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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39A THR* 5.2 0.9 - - - -
40A PHE* 4.0 20.1 + + + +
41A ASP* 2.8 40.8 + - - -
50A LEU* 3.2 26.2 + - + -
51A ARG* 3.4 7.9 + - + +
53A ILE* 1.3 81.3 - - + +
55A ALA* 1.3 60.4 + - - +
57A GLY* 3.1 12.3 + - - -
58A PHE 3.5 15.5 - - - -
59A GLU* 3.7 24.8 + - - -
123G THR* 3.9 11.6 - - + +
124G TYR* 3.5 29.2 - + + -
125G LYS* 3.3 47.6 + - + +
128G GLN* 6.3 1.1 - - - +
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Residues in contact with ALA 55 (chain A).
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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51A ARG* 3.0 17.3 + - - +
52A GLY* 3.9 3.4 - - - +
53A ILE 3.3 0.6 - - - -
54A TYR* 1.3 76.5 - - - +
56A TYR* 1.3 61.9 + - - +
57A GLY* 3.3 1.6 + - - -
131A ASP* 6.4 0.7 - - + -
132A TYR* 3.7 30.7 - - + +
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Residues in contact with TYR 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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52A GLY 2.9 19.7 + - - +
53A ILE 3.6 6.1 - - - +
54A TYR 3.2 0.6 - - - -
55A ALA* 1.3 76.2 - - - +
57A GLY* 1.3 57.2 + - - +
58A PHE* 3.7 19.3 - + - -
125A GLY* 5.1 8.7 - - - -
128A ALA* 3.8 29.2 - - + +
129A LEU* 3.4 29.4 - - + -
1413A ANP 4.1 19.9 + - - -
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Residues in contact with GLY 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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54A TYR 3.1 10.7 + - - -
55A ALA 3.1 2.1 - - - -
56A TYR* 1.3 78.8 - - - +
58A PHE* 1.3 70.2 + - - +
59A GLU* 3.8 13.0 + - - +
1413A ANP 5.2 3.0 - - - -
125G LYS* 4.6 3.4 + - - -
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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