Contacts of the helix formed by residues 42 - 53 (chain A) in PDB entry 2MT5
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 HIS 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A CYS* 3.5 21.0 - - + +
12A CYS* 3.3 23.6 - - - -
14A MET* 3.7 36.5 + - + +
15A ALA 4.5 2.4 + - - -
16A PHE* 4.2 14.7 - + - -
18A GLY 5.5 4.3 - - - -
20A CYS* 3.9 21.8 - - - -
31A PRO 4.8 3.8 - - - +
32A LEU* 4.1 16.8 - - + +
41A PHE* 1.3 74.6 - - - +
43A MET* 1.3 72.8 + - - +
45A CYS* 2.8 23.8 + - - -
46A ILE* 2.9 14.2 + - - +
101A ZN 2.9 15.8 - - - -
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Residues in contact with MET 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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31A PRO* 4.1 15.0 + - + +
32A LEU* 4.0 3.5 - - - +
33A VAL* 3.6 23.2 - - + +
41A PHE 3.3 4.6 + - - -
42A HIS* 1.3 72.1 - - - +
44A HIS* 1.3 83.6 + - + +
46A ILE* 3.8 8.1 - - - -
47A LEU* 2.6 53.0 + - + +
68A PHE* 4.2 19.7 - - + -
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Residues in contact with HIS 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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20A CYS* 3.6 11.2 - - - -
23A CYS* 5.2 0.7 - - - -
29A ASP 4.3 6.3 + - - -
30A CYS* 3.5 28.1 - - - -
31A PRO* 4.7 5.6 + - - +
42A HIS 3.5 0.2 - - - -
43A MET* 1.3 87.4 + - + +
45A CYS* 1.3 67.5 + - - +
47A LEU* 3.7 9.7 - - + +
48A LYS* 2.9 27.4 + - + +
102A ZN 2.8 34.4 - - - -
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Residues in contact with CYS 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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11A ILE* 4.5 12.3 - - + -
12A CYS* 3.6 12.3 - - - -
20A CYS* 4.5 10.3 - - - -
21A PRO* 4.6 6.3 - - - -
22A ASP* 6.2 0.7 - - - -
42A HIS* 2.8 29.3 + - - +
44A HIS* 1.3 79.1 - - - +
46A ILE* 1.3 65.4 + - - +
48A LYS* 2.8 11.2 + - - +
49A TRP* 3.0 9.9 + - - +
101A ZN 2.8 34.3 - - - -
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Residues in contact with ILE 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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11A ILE* 4.3 6.1 - - + +
33A VAL* 3.3 27.6 - - + -
39A HIS* 4.5 9.9 - - + +
41A PHE* 3.9 13.9 - - + +
42A HIS 2.9 13.9 + - - +
43A MET* 3.1 10.3 - - - +
45A CYS* 1.3 76.3 - - - +
47A LEU* 1.3 66.1 + - - +
49A TRP* 2.6 77.2 + - + +
50A LEU 3.0 10.0 + - - -
60A PRO* 3.7 21.5 - - + -
66A TRP* 3.9 19.7 - - + +
68A PHE* 4.5 3.8 - - + -
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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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43A MET* 2.6 54.1 + - + +
44A HIS* 3.7 9.2 - - + +
46A ILE* 1.3 76.1 - - - +
48A LYS* 1.3 69.5 + - + +
50A LEU* 3.4 0.8 + - - -
51A HIS* 2.5 82.7 + - + +
68A PHE* 4.1 14.6 - - + -
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Residues in contact with LYS 48 (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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44A HIS* 2.9 18.3 + - + +
45A CYS* 2.8 9.5 + - - +
47A LEU* 1.3 88.9 - - + +
49A TRP* 1.3 60.3 + - - +
51A HIS* 3.6 25.5 + - - +
52A ALA* 2.7 44.1 + - + +
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Residues in contact with TRP 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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11A ILE* 4.1 15.9 - - + -
45A CYS 3.0 7.2 + - - +
46A ILE* 2.6 53.7 + - + +
48A LYS* 1.3 73.0 - - - +
50A LEU* 1.3 88.7 + - + -
52A ALA* 5.0 0.2 - - - -
53A GLN* 3.5 38.3 + - - +
56A GLN 4.9 5.2 + - - +
57A GLN* 3.1 24.7 - - - -
58A HIS 3.2 21.5 + - - -
60A PRO* 3.3 39.2 - - + +
66A TRP* 3.3 22.0 - + + -
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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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46A ILE 3.0 4.6 + - - +
47A LEU 4.2 1.8 - - - +
49A TRP* 1.3 96.0 - - + +
51A HIS* 1.3 81.1 + - + +
52A ALA 3.2 5.6 - - - -
53A GLN 3.3 11.7 - - - +
54A GLN* 3.2 19.3 + - - -
56A GLN 5.3 0.7 - - - -
57A GLN* 3.8 39.5 - - + +
66A TRP* 3.3 28.7 - - + +
68A PHE* 4.0 4.9 - - + -
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Residues in contact with HIS 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 LEU* 2.5 71.3 + - + +
48A LYS* 3.6 22.2 + - - +
50A LEU* 1.3 95.8 - - + +
52A ALA* 1.3 58.7 + - - +
54A GLN* 3.5 13.2 + - - +
68A PHE* 4.1 11.2 - + - -
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Residues in contact with ALA 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 LYS* 2.7 26.5 + - + +
49A TRP* 4.7 1.3 - - - +
51A HIS* 1.3 80.5 - - - +
53A GLN* 1.3 67.7 + - + +
54A GLN* 3.6 10.6 + - - +
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Residues in contact with GLN 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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49A TRP* 3.5 35.4 + - + +
50A LEU* 3.3 13.7 - - - +
52A ALA* 1.3 84.8 - - + +
54A GLN* 1.3 63.2 + - - +
55A VAL* 3.4 18.4 - - + -
56A GLN* 3.3 20.1 - - + +
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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