Contacts of the helix formed by residues 33 - 50 (chain A) in PDB entry 1MGT
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 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LEU* 6.3 0.2 - - - +
4A VAL* 4.4 18.5 - - + +
15A TRP* 3.6 53.1 - - + +
32A ASP* 1.3 73.9 - - - +
34A GLY* 1.3 58.0 + - - +
36A LEU* 3.3 3.9 + - + +
37A MET* 2.9 59.1 + - + +
58A VAL* 5.3 11.1 - - - +
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Residues in contact with GLY 34 (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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32A ASP* 3.2 7.4 + - - -
33A ARG* 1.3 77.2 - - - +
35A THR* 1.3 62.2 + - - +
37A MET* 3.3 7.2 + - - +
38A LYS* 3.2 21.3 + - - +
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Residues in contact with THR 35 (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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30A ALA* 3.8 9.2 - - + -
31A PHE 5.5 0.4 - - - +
32A ASP* 2.8 34.2 + - - -
34A GLY* 1.3 72.6 - - - +
36A LEU* 1.3 66.6 + - - +
38A LYS* 3.2 12.0 + - + +
39A ARG* 3.0 56.9 + - + +
159A GLU* 5.1 1.1 - - - +
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Residues in contact with LEU 36 (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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4A VAL* 3.6 42.2 - - + -
15A TRP* 3.8 15.3 - - + +
16A ILE 4.0 2.9 - - - -
17A GLY* 3.7 13.7 - - - +
28A ALA* 3.4 38.8 - - + +
29A PHE* 3.7 11.0 - - - +
30A ALA* 3.6 8.4 - - + +
32A ASP 3.1 14.3 + - - +
33A ARG* 3.4 10.5 - - + +
35A THR* 1.3 77.1 - - - +
37A MET* 1.3 61.6 + - - +
39A ARG* 3.1 6.0 + - - +
40A ILE* 2.9 31.2 + - + +
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Residues in contact with MET 37 (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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2A LEU* 4.2 19.3 - - + -
4A VAL* 4.4 19.3 - - - -
33A ARG* 2.9 54.8 + - + +
34A GLY* 3.8 6.3 - - - +
35A THR 3.2 0.2 - - - -
36A LEU* 1.3 82.2 - - + +
38A LYS* 1.3 60.7 + - - +
40A ILE* 3.4 10.4 + - + +
41A HIS* 2.8 55.6 + - + +
56A LEU* 5.8 0.9 - - + -
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Residues in contact with LYS 38 (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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34A GLY 3.2 12.3 + - - +
35A THR* 3.2 14.1 + - + +
37A MET* 1.3 74.8 - - - +
39A ARG* 1.3 63.3 + - + +
41A HIS* 3.3 8.7 + - + +
42A ASP* 2.9 53.3 + - - +
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Residues in contact with ARG 39 (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 ALA* 4.0 15.6 - - + +
29A PHE 2.9 30.0 + - - +
30A ALA* 3.6 9.4 - - - +
35A THR* 3.0 32.0 + - + +
36A LEU* 3.6 6.3 - - - +
38A LYS* 1.3 79.4 - - + +
40A ILE* 1.3 59.4 + - - +
42A ASP* 3.3 10.2 + - - +
43A LEU* 2.9 30.5 + - - +
154A SER 5.4 0.4 + - - -
155A SER* 3.2 41.8 + - - +
156A GLY* 4.4 2.2 - - - +
159A GLU* 2.8 32.5 + - - +
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Residues in contact with ILE 40 (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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2A LEU* 4.0 24.7 - - + -
17A GLY* 4.1 15.5 - - - +
19A ILE* 4.0 24.2 - - + +
27A ILE 5.0 0.2 - - - -
28A ALA* 3.8 22.0 - - + +
36A LEU* 2.9 30.0 + - + +
37A MET* 3.7 16.6 - - + +
39A ARG* 1.3 75.3 - - - +
41A HIS* 1.3 58.1 + - + +
43A LEU* 3.3 7.1 + - + +
44A ALA* 2.9 27.5 + - - +
56A LEU* 4.2 29.2 - - + -
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Residues in contact with HIS 41 (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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37A MET* 2.8 52.5 + - + +
38A LYS* 3.7 6.5 - - - +
40A ILE* 1.3 73.4 - - - +
42A ASP* 1.3 66.8 + - - +
44A ALA* 3.2 5.5 + - - +
45A GLU* 3.0 26.2 + - - +
56A LEU* 3.9 25.6 - - + +
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Residues in contact with ASP 42 (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 LYS* 2.9 50.0 + - - +
39A ARG* 3.3 10.4 + - - +
41A HIS* 1.3 78.2 - - - +
43A LEU* 1.3 63.1 + - - +
45A GLU* 3.5 5.8 + - - +
46A HIS* 3.1 23.0 + - - +
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Residues in contact with LEU 43 (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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19A ILE* 4.2 9.4 - - + -
26A GLY* 3.7 9.6 - - - -
27A ILE 3.5 42.2 - - - +
28A ALA* 4.9 5.2 - - + -
39A ARG 2.9 17.2 + - - +
40A ILE* 3.5 6.3 - - + +
42A ASP* 1.3 74.6 - - - +
44A ALA* 1.3 65.1 + - - +
46A HIS* 3.2 14.1 + - + +
47A LEU* 2.9 40.0 + - + +
132A ARG 5.6 0.2 - - - +
133A ASN 5.0 2.0 - - - +
134A PRO* 3.8 30.5 - - + +
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Residues in contact with ALA 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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19A ILE* 4.5 8.0 - - + +
40A ILE 2.9 17.6 + - - +
41A HIS* 3.7 6.5 - - - +
43A LEU* 1.3 77.7 - - - +
45A GLU* 1.3 55.4 + - - +
47A LEU* 3.9 4.9 - - - +
48A GLY* 2.9 26.9 + - - -
54A ILE* 4.3 22.2 - - + +
56A LEU* 4.2 21.3 - - + -
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Residues in contact with GLU 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 HIS 3.0 16.7 + - - +
42A ASP* 3.7 7.0 - - - +
44A ALA* 1.3 72.3 - - - +
46A HIS* 1.3 66.9 + - - +
48A GLY* 3.4 1.1 + - - -
49A LYS* 3.0 53.7 + - + +
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Residues in contact with HIS 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 ASP 3.1 14.3 + - - +
43A LEU* 3.6 16.6 - - + +
45A GLU* 1.3 76.6 - - - +
47A LEU* 1.3 79.5 + - + +
49A LYS* 3.3 16.1 + - - +
50A ARG* 3.4 37.6 + - - +
88A GLY 4.8 2.2 + - - -
132A ARG* 4.0 37.7 + - + +
134A PRO* 5.4 1.3 - - + +
303A SO4 3.6 24.9 + - - -
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Residues in contact with LEU 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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19A ILE* 4.9 3.6 - - + -
25A GLN* 3.3 28.9 - - + +
26A GLY* 4.6 0.4 - - - -
43A LEU* 2.9 39.5 + - + +
44A ALA* 4.0 4.3 - - - +
46A HIS* 1.3 83.8 - - + +
48A GLY* 1.3 65.6 + - - +
50A ARG* 2.9 15.5 + - - +
51A GLY 3.4 0.2 + - - -
52A VAL* 3.1 34.1 + - + +
54A ILE* 4.2 18.6 - - + -
87A GLU 3.9 21.8 - - - +
88A GLY* 4.6 8.7 - - - +
134A PRO* 4.3 12.1 - - + -
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Residues in contact with GLY 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 ALA 2.9 18.9 + - - -
45A GLU* 3.9 1.8 - - - -
47A LEU* 1.3 78.4 - - - +
49A LYS* 1.3 56.2 + - - +
51A GLY* 3.0 19.2 + - - -
52A VAL 3.6 15.5 + - - -
54A ILE* 4.9 1.5 - - - +
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Residues in contact with LYS 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 GLU* 3.0 42.7 + - + +
46A HIS* 3.6 9.0 - - - +
47A LEU 3.2 0.2 - - - -
48A GLY* 1.3 74.7 - - - +
50A ARG* 1.3 62.6 + - + +
51A GLY 3.3 1.5 + - - -
303A SO4 5.8 2.5 - - - +
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Residues in contact with ARG 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 HIS* 3.4 28.5 + - + +
47A LEU* 2.9 10.2 + - - +
49A LYS* 1.3 79.8 - - + +
51A GLY* 1.3 59.7 + - - +
52A VAL* 3.5 5.7 + - - +
88A GLY* 2.9 38.7 + - - -
90A THR* 3.8 17.0 - - - +
93A GLU* 2.7 44.1 + - - -
132A ARG* 3.7 8.5 - - - +
303A SO4 2.6 46.4 + - - +
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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