Contacts of the helix formed by residues 37 - 47 (chain A) in PDB entry 2G3T
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 THR 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.0 8.7 - - - -
35A ILE 3.8 9.4 - - - +
36A LEU* 1.3 78.9 - - - +
38A GLU* 1.3 63.3 + - - +
39A LYS* 3.5 12.3 + - - +
40A ASP* 2.8 42.2 + - - +
41A LEU* 3.2 14.4 + - - +
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Residues in contact with GLU 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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12A ALA 5.4 1.6 - - - +
14A CYS* 4.0 18.6 + - + +
15A SER* 3.5 35.5 + - - +
18A LEU* 3.6 18.6 - - + +
37A THR* 1.3 73.5 - - - +
39A LYS* 1.3 63.1 + - - +
41A LEU* 3.3 8.9 + - - +
42A LEU* 2.9 41.9 + - + +
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Residues in contact with LYS 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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37A THR* 3.5 11.4 + - - +
38A GLU* 1.3 78.9 - - - +
40A ASP* 1.3 65.5 + - - +
42A LEU* 3.3 11.2 + - + +
43A GLU* 2.5 62.7 + - - +
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Residues in contact with ASP 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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35A ILE 4.2 2.3 - - - +
36A LEU* 3.5 27.9 - - + +
37A THR* 2.8 37.0 + - - +
39A LYS* 1.3 84.1 - - - +
41A LEU* 1.3 55.2 + - - +
43A GLU* 3.3 2.8 + - - -
44A ASP* 2.7 49.1 + - - +
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Residues in contact with LEU 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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14A CYS* 3.6 32.3 - - + +
17A ILE* 4.0 11.9 - - + -
18A LEU* 3.8 30.5 - - + +
21A ILE* 4.4 6.1 - - + -
36A LEU* 3.6 26.5 - - + -
37A THR 3.2 6.8 + - - +
38A GLU* 3.3 8.0 + - - +
40A ASP* 1.3 79.0 - - - +
42A LEU* 1.3 57.4 + - - +
45A GLY* 3.0 16.6 + - - -
46A PHE* 3.8 1.9 - - - -
52A TYR* 2.5 48.4 + - + +
76A MET* 4.4 13.9 - - + -
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Residues in contact with LEU 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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11A ALA* 3.5 42.0 - - + +
14A CYS* 3.6 13.5 - - + -
38A GLU* 2.9 38.3 + - + +
39A LYS* 3.6 9.2 - - + +
41A LEU* 1.3 74.0 - - - +
43A GLU* 1.3 59.7 + - - +
46A PHE* 2.7 39.7 + - + +
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Residues in contact with GLU 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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39A LYS* 2.5 55.8 + - + +
40A ASP* 3.9 2.9 - - - +
42A LEU* 1.3 78.4 - - - +
44A ASP* 1.3 67.5 + - - +
47A GLY* 3.3 25.0 + - - +
49A HIS 4.6 3.1 - - - +
51A PHE* 5.3 1.2 - - - -
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Residues in contact with ASP 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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36A LEU* 4.8 5.9 - - - +
40A ASP* 2.7 38.9 + - - +
43A GLU* 1.3 80.1 - - - +
45A GLY* 1.3 56.6 + - - +
49A HIS 3.4 6.6 - - - +
51A PHE* 2.8 50.4 + - + +
52A TYR* 3.8 14.8 - - + -
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Residues in contact with GLY 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 LEU 3.0 12.3 + - - -
44A ASP* 1.3 80.3 - - - +
46A PHE* 1.3 72.1 + - - +
47A GLY 3.6 1.8 - - - -
50A PRO* 3.6 19.8 - - - +
52A TYR* 3.4 31.8 - - - +
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Residues in contact with PHE 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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9A ALA* 3.7 20.6 - - + -
10A THR* 3.5 22.7 - - - -
11A ALA* 3.4 32.8 - - + -
14A CYS* 3.5 26.9 - - - -
17A ILE* 5.7 1.3 - - + -
41A LEU 3.8 9.0 - - - -
42A LEU* 2.7 20.9 + - + +
45A GLY* 1.3 79.9 - - - +
47A GLY* 1.3 65.3 + - - +
52A TYR* 3.7 15.7 - + - -
54A CYS 6.3 1.1 - - - -
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Residues in contact with GLY 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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42A LEU 4.3 0.4 - - - -
43A GLU* 3.3 25.6 + - - -
44A ASP 4.7 0.4 - - - -
45A GLY 3.6 1.4 - - - -
46A PHE* 1.3 84.9 - - - +
48A GLU* 1.3 66.0 + - - +
49A HIS* 3.4 5.3 + - - -
50A PRO* 5.1 1.2 - - - +
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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