Contacts of the helix formed by residues 43 - 55 (chain A) in PDB entry 2DMT
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 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A GLN* 4.3 7.0 + - - +
41A TYR 5.3 0.2 + - - -
42A LEU* 1.3 76.8 - - - +
44A THR* 1.3 68.8 + - - +
45A PRO* 3.4 13.0 - - - -
46A ASP* 3.6 22.0 + - - +
47A ARG* 2.9 28.0 + - - -
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Residues in contact with THR 44 (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* 1.3 75.8 - - - +
45A PRO* 1.3 77.7 - - + +
47A ARG* 3.9 10.6 + - - +
48A ILE* 3.3 27.6 + - + +
58A GLN* 5.2 0.3 + - - -
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Residues in contact with PRO 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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43A SER* 3.6 6.5 - - - -
44A THR* 1.3 103.3 - - + +
46A ASP* 1.3 80.4 + - - +
48A ILE* 2.9 23.4 + - + +
49A ASP* 3.0 12.3 + - - +
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Residues in contact with ASP 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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35A ARG* 5.6 0.6 + - - -
39A GLN* 4.1 12.5 + - - -
42A LEU* 4.3 10.2 - - + +
43A SER* 3.6 32.3 + - - +
45A PRO* 1.3 84.0 - - - +
47A ARG* 1.3 65.9 + - - +
48A ILE 2.8 2.3 + - - -
49A ASP* 2.8 20.4 + - - +
50A LEU* 3.1 12.2 + - - +
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Residues in contact with ARG 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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41A TYR* 4.9 2.8 - - - +
42A LEU* 3.3 45.1 + - + +
43A SER 2.9 24.6 + - - +
44A THR* 4.0 10.1 + - - +
46A ASP* 1.3 77.8 - - - +
48A ILE* 1.3 60.3 - - + +
50A LEU* 3.6 3.4 + - - +
51A ALA* 3.2 21.0 + - - +
58A GLN* 3.3 33.2 - - + +
61A VAL* 3.6 23.3 - - + +
62A LYS* 3.7 31.8 - - - +
65A TYR* 5.4 4.2 - - - -
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Residues in contact with ILE 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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44A THR* 3.3 26.0 - - + +
45A PRO* 2.9 15.5 + - + +
46A ASP 2.8 3.6 + - - -
47A ARG* 1.3 71.1 - - + +
49A ASP* 1.3 67.8 + - - +
50A LEU 3.0 2.4 + - - -
51A ALA* 3.0 13.3 + - + +
52A GLU* 3.0 24.7 + - + +
58A GLN* 3.3 42.4 - - + +
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Residues in contact with ASP 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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35A ARG* 4.9 8.5 + - - +
45A PRO 3.0 10.1 + - - +
46A ASP* 2.8 16.8 + - - +
48A ILE* 1.3 74.0 - - - +
50A LEU* 1.3 60.8 + - - +
52A GLU* 3.3 14.1 + - - +
53A SER* 3.1 25.1 + - - -
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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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31A GLY 4.9 0.7 - - - +
32A LEU* 4.3 10.3 - - + -
35A ARG* 3.8 52.2 - - + +
42A LEU* 3.9 18.6 - - + -
46A ASP 3.1 8.9 + - - +
47A ARG* 3.7 6.1 - - - +
48A ILE 3.0 0.6 - - - -
49A ASP* 1.3 72.6 - - - +
51A ALA* 1.3 55.9 + - - +
52A GLU 2.7 6.2 + - - -
53A SER* 2.6 27.7 + - - +
54A LEU* 2.9 48.0 + - + +
56A LEU* 6.0 0.4 - - + -
61A VAL* 3.5 29.2 - - + -
65A TYR* 4.6 0.4 - - - +
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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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47A ARG 3.2 11.2 + - - +
48A ILE* 3.0 11.1 + - + +
50A LEU* 1.3 81.4 - - - +
52A GLU* 1.3 58.1 + - + +
54A LEU* 5.3 0.4 - - - -
55A GLY* 2.9 6.6 + - - -
56A LEU* 2.7 59.4 + - + +
57A SER 4.0 1.1 - - - -
58A GLN* 3.8 21.5 - - + +
61A VAL* 4.9 3.4 - - + -
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Residues in contact with GLU 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 ILE* 3.0 21.5 + - + +
49A ASP* 3.4 18.8 - - - +
50A LEU 2.7 5.1 + - - -
51A ALA* 1.3 76.0 - - + +
53A SER* 1.3 63.0 + - - +
55A GLY* 3.8 7.0 + - - -
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Residues in contact with SER 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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35A ARG* 4.7 10.5 + - - -
49A ASP* 3.1 17.5 + - - -
50A LEU* 2.6 19.2 + - - -
52A GLU* 1.3 74.1 - - - +
54A LEU* 1.3 64.7 + - - +
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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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27A LEU* 4.2 25.3 - - + +
28A GLN* 3.9 35.5 + - + +
31A GLY* 4.0 16.6 - - - -
32A LEU* 3.9 12.6 - - + +
50A LEU* 2.9 41.4 + - + +
53A SER* 1.3 81.0 - - - +
55A GLY* 1.3 59.7 + - - +
56A LEU* 4.2 23.3 - - + +
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Residues in contact with GLY 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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28A GLN* 4.8 3.6 + - - -
51A ALA 2.9 12.9 + - - -
52A GLU* 3.8 5.8 + - - -
53A SER 3.4 2.4 - - - -
54A LEU* 1.3 80.4 - - - +
56A LEU* 1.3 63.8 + - - +
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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