Contacts of the helix formed by residues 44 - 56 (chain A) in PDB entry 2DJ0
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 PHE 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLU* 3.4 38.8 - - - +
40A ASP 3.9 2.6 + - - +
41A CYS* 2.7 22.2 + - - +
43A SER* 1.3 72.4 - - - +
45A ALA* 1.3 64.7 + - - +
46A PRO* 3.2 2.9 - - - -
47A ILE* 2.8 36.6 + - + -
48A TYR* 2.8 44.5 + + + +
51A LEU* 4.5 7.0 - - + -
89A PRO* 5.0 10.5 - - + -
91A LEU* 4.5 12.1 - - + -
117A PHE* 4.8 23.1 - + + -
118A SER 4.8 6.1 - - - -
122A VAL* 4.3 26.2 - - + -
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Residues in contact with ALA 45 (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 CYS* 2.8 12.8 + - - +
42A GLN* 3.2 17.3 - - - +
44A PHE* 1.3 78.6 - - - +
46A PRO* 1.3 68.2 - - + +
48A TYR* 4.1 3.4 - - - +
49A ALA* 3.3 19.9 + - - +
64A LYS* 5.4 9.1 + - - +
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Residues in contact with PRO 46 (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 GLN 3.3 10.8 - - - +
43A SER* 3.8 10.3 - - - +
44A PHE 3.3 1.8 - - - -
45A ALA* 1.3 97.8 - - + +
47A ILE* 1.3 67.9 + - + +
49A ALA* 3.4 6.5 + - + +
50A ASP* 3.0 35.4 + - - +
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Residues in contact with ILE 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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43A SER* 3.2 28.3 - - - +
44A PHE* 2.8 45.9 + - + +
46A PRO* 1.3 76.3 - - + +
48A TYR* 1.3 62.5 + - - +
50A ASP* 3.2 6.3 + - - +
51A LEU* 3.1 30.6 + - + +
117A PHE 4.9 8.5 - - - +
118A SER* 5.3 4.0 - - - -
119A GLU* 4.3 22.3 - - + +
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Residues in contact with TYR 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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9A ILE* 3.6 20.6 - - + -
30A ILE* 3.1 20.5 + - + +
32A GLU* 2.8 29.8 - - + +
44A PHE* 2.8 34.6 + + + +
45A ALA* 4.1 3.6 - - - +
47A ILE* 1.3 73.1 - - - +
49A ALA* 1.3 62.6 + - - +
51A LEU* 2.9 11.9 + - + +
52A SER* 2.8 24.0 + - - -
62A PHE* 3.3 33.7 - + - -
63A GLY 3.0 20.1 + - - -
64A LYS* 3.5 35.9 - - + +
91A LEU* 4.2 15.5 - - + -
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Residues in contact with ALA 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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7A GLY* 4.8 15.9 - - - -
9A ILE* 4.9 10.3 - - + +
45A ALA 3.3 16.9 + - - +
46A PRO* 3.6 8.3 - - + +
48A TYR* 1.3 77.7 - - - +
50A ASP* 1.3 62.7 + - - +
52A SER* 2.6 23.0 + - - -
53A LEU* 3.1 20.4 + - + +
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Residues in contact with ASP 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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46A PRO* 3.0 26.5 + - - +
47A ILE* 3.5 9.8 - - - +
49A ALA* 1.3 76.9 - - - +
51A LEU* 1.3 65.9 + - - +
53A LEU* 3.6 13.0 + - - +
54A LYS* 3.2 20.2 + - - +
119A GLU* 5.0 10.5 - - - +
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Residues in contact with LEU 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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44A PHE* 4.5 9.9 - - + -
47A ILE* 3.1 22.5 + - + +
48A TYR* 2.9 13.1 + - + +
50A ASP* 1.3 73.8 - - - +
52A SER* 1.3 68.3 + - - +
54A LYS* 2.7 20.3 + - + +
55A TYR* 3.0 33.2 + - + -
62A PHE* 4.2 9.0 - - + -
119A GLU* 3.5 35.9 + - + +
122A VAL* 4.5 17.9 - - + -
123A ILE* 3.6 28.5 - - + -
128A LEU* 3.8 7.2 - - + -
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Residues in contact with SER 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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7A GLY* 5.7 0.2 - - - -
8A TYR 4.8 1.2 + - - -
9A ILE* 4.2 14.5 - - - +
48A TYR* 2.8 15.0 + - - -
49A ALA* 2.6 28.8 + - - -
51A LEU* 1.3 70.4 - - - +
53A LEU* 1.3 54.7 + - - +
54A LYS 2.8 0.9 + - - -
55A TYR 2.8 2.4 + - - -
56A ASN* 2.5 56.3 + - - +
62A PHE* 3.4 35.9 - - - -
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Residues in contact with LEU 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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5A SER 4.4 5.4 - - - +
6A SER* 3.9 9.6 - - - +
7A GLY* 3.0 41.1 - - - +
8A TYR* 4.1 18.2 - - + +
49A ALA* 3.1 25.0 + - + +
50A ASP* 3.7 11.7 - - - +
52A SER* 1.3 81.9 + - - +
54A LYS* 1.3 63.3 + - - +
56A ASN* 3.3 20.5 + - - +
57A CYS* 5.6 0.7 - - - -
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Residues in contact with LYS 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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50A ASP 3.2 10.8 + - - +
51A LEU* 2.7 20.6 + - - +
53A LEU* 1.3 77.8 - - - +
55A TYR* 1.3 78.3 + - + +
56A ASN 3.2 5.4 + - - -
57A CYS* 4.8 8.0 - - - +
119A GLU* 4.4 16.8 - - - -
123A ILE* 5.6 2.9 - - - -
129A ASN* 5.3 0.7 - - - +
135A SER* 4.1 22.9 + - - +
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Residues in contact with TYR 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 LEU* 3.0 40.1 + - + -
52A SER 2.8 7.0 + - - -
54A LYS* 1.3 90.6 - - + +
56A ASN* 1.3 59.1 + - - +
57A CYS* 3.1 5.9 + - - +
60A LEU* 3.0 33.3 - - + +
62A PHE* 3.4 27.8 - + + -
123A ILE* 3.4 12.0 - - - +
128A LEU* 3.2 38.2 - - + +
129A ASN* 2.8 36.3 + - - -
132A SER* 3.8 26.5 + - - -
133A GLY 5.0 2.7 - - - -
135A SER* 5.7 0.7 - - - -
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Residues in contact with ASN 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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8A TYR* 3.3 56.7 + - + +
52A SER* 2.5 37.8 + - - +
53A LEU* 3.3 29.5 - - - +
54A LYS 3.0 3.8 - - - -
55A TYR* 1.3 68.7 - - - +
57A CYS* 1.3 68.9 + - - +
60A LEU 4.5 2.0 - - - -
61A ASN* 5.4 0.6 - - - +
62A PHE* 3.8 18.0 + - - +
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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