Contacts of the helix formed by residues 41 - 59 (chain A) in PDB entry 2DIN
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 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ALA* 3.4 4.5 - - - -
39A GLY 5.8 0.2 - - - +
40A ARG* 1.3 78.0 - - - +
42A ALA* 1.3 55.9 + - - +
43A ALA* 4.0 6.2 + - - +
44A GLN* 3.0 39.6 + - - +
45A CYS* 2.8 32.4 + - - -
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Residues in contact with ALA 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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31A TRP* 3.8 35.0 - - + +
32A ARG* 4.1 14.1 - - + +
35A ALA* 3.2 13.5 - - + +
41A THR* 1.3 72.5 - - - +
43A ALA* 1.3 59.2 + - - +
45A CYS* 3.3 3.1 + - - +
46A LEU* 2.9 31.8 + - - +
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Residues in contact with ALA 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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41A THR* 3.2 7.0 + - - +
42A ALA* 1.3 77.9 - - - +
44A GLN* 1.3 55.2 + - + +
46A LEU* 4.0 7.2 - - - +
47A GLU* 2.7 41.3 + - + +
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Residues in contact with GLN 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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10A THR* 3.7 28.5 + - - +
12A TRP* 3.5 8.7 + - + +
40A ARG* 3.8 21.1 - - + +
41A THR* 3.0 47.2 + - - +
43A ALA* 1.3 79.8 - - + +
45A CYS* 1.3 57.4 + - - +
47A GLU* 3.9 8.5 - - - +
48A HIS* 2.9 33.8 + - - +
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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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12A TRP* 3.7 15.5 - - - -
20A LEU* 3.7 12.4 - - + +
31A TRP* 4.2 11.9 - - + +
34A ILE* 4.4 6.7 - - + -
35A ALA* 3.7 26.5 - - - +
38A ILE* 4.5 11.2 - - - -
40A ARG* 3.7 17.0 - - - -
41A THR 2.8 22.0 + - - +
42A ALA* 3.6 5.4 - - - +
44A GLN* 1.3 73.7 - - - +
46A LEU* 1.3 53.3 + - - +
49A TYR* 2.8 39.2 + - - +
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Residues in contact with LEU 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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31A TRP* 3.5 50.6 - - + +
42A ALA 2.9 15.9 + - - +
43A ALA* 4.0 6.7 - - - +
45A CYS* 1.3 73.7 - - - +
47A GLU* 1.3 68.4 + - - +
50A GLU* 2.9 64.8 + - + +
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Residues in contact with GLU 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 ALA* 2.7 25.3 + - + +
44A GLN* 3.9 7.9 - - - +
46A LEU* 1.3 76.5 - - - +
48A HIS* 1.3 61.3 + - - +
50A GLU* 3.8 3.3 + - - +
51A PHE* 3.2 22.9 + - - +
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Residues in contact with HIS 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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12A TRP* 3.0 72.4 - + + +
17A GLU* 3.7 15.5 - - + +
20A LEU* 3.6 12.3 - - + -
44A GLN 2.9 20.7 + - - +
45A CYS 3.9 0.2 - - - +
47A GLU* 1.3 71.8 + - - +
49A TYR* 1.3 71.3 + - - +
51A PHE* 3.0 22.8 + + - +
52A LEU* 3.0 37.5 + - + +
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Residues in contact with TYR 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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20A LEU* 3.5 18.3 - - + +
21A LEU* 4.1 34.2 + - + -
24A ALA* 3.6 29.9 - - + +
25A LYS* 4.8 8.3 + - - +
28A PRO* 6.1 2.0 - - + -
31A TRP* 3.4 24.9 - + + -
45A CYS 2.8 24.4 + - - +
46A LEU* 3.6 2.5 - - - +
48A HIS* 1.3 71.7 - - - +
50A GLU* 1.3 69.5 + - + +
52A LEU* 2.7 29.2 + - - +
53A LEU* 2.9 43.1 - - + +
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Residues in contact with GLU 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 LEU* 2.9 50.6 + - + +
47A GLU* 4.0 4.2 - - - +
49A TYR* 1.3 82.7 - - + +
51A PHE* 1.3 63.8 + - - +
53A LEU* 3.1 27.7 + - - +
54A ASP* 3.4 7.1 + - - +
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Residues in contact with PHE 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 GLU 3.2 12.9 + - - +
48A HIS* 3.0 28.8 + + - +
50A GLU* 1.3 78.1 - - - +
52A LEU* 1.3 67.1 + - + +
54A ASP* 3.4 7.5 + - + +
55A LYS* 2.9 61.6 + - + +
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Residues in contact with LEU 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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17A GLU* 4.1 21.8 - - + +
20A LEU* 3.7 12.8 - - + -
21A LEU* 3.3 36.6 - - + -
48A HIS* 3.0 33.1 + - + +
49A TYR* 2.7 30.5 + - - +
51A PHE* 1.3 78.0 - - + +
53A LEU* 1.3 66.4 + - + +
55A LYS* 2.9 23.9 + - - +
56A ALA* 2.8 27.1 + - - +
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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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21A LEU* 5.0 9.0 - - + -
49A TYR* 2.9 72.2 - - + +
50A GLU* 3.4 12.3 - - - +
52A LEU* 1.3 77.6 - - + +
54A ASP* 1.3 60.6 + - - +
56A ALA* 3.4 6.6 + - - +
57A ALA* 3.3 18.7 + - - +
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Residues in contact with ASP 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 GLU 3.4 6.3 + - - +
51A PHE* 3.7 9.2 - - + +
52A LEU 3.2 0.6 - - - -
53A LEU* 1.3 76.7 - - - +
55A LYS* 1.3 67.6 + - - +
57A ALA* 3.1 10.3 + - - +
58A GLN* 3.0 48.7 + - - +
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Residues in contact with LYS 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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17A GLU* 5.3 5.1 + - - -
51A PHE* 2.9 47.2 + - + +
52A LEU* 3.3 26.0 - - - +
54A ASP* 1.3 75.8 + - - +
56A ALA* 1.3 66.5 + - - +
58A GLN* 3.4 9.6 + - - +
59A ARG* 3.2 38.3 + - - +
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Residues in contact with ALA 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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52A LEU 2.8 15.4 + - - +
53A LEU* 3.6 11.7 - - - +
55A LYS* 1.3 78.2 - - - +
57A ALA* 1.3 63.6 + - - +
59A ARG* 2.9 25.3 - - - +
61A SER 5.1 1.6 - - - +
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Residues in contact with ALA 57 (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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53A LEU 3.3 8.7 + - - +
54A ASP* 3.1 12.9 + - - +
56A ALA* 1.3 78.1 - - - +
58A GLN* 1.3 70.2 + - - +
59A ARG 3.2 9.5 + - - +
61A SER 4.5 2.9 - - - +
63A PRO* 5.8 2.6 - - - +
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Residues in contact with GLN 58 (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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54A ASP* 3.0 38.8 + - - +
55A LYS* 3.5 9.6 - - - +
57A ALA* 1.3 78.6 - - - +
59A ARG* 1.3 66.6 + - - +
60A ASP* 3.1 4.7 + - - +
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Residues in contact with ARG 59 (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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55A LYS* 3.2 24.5 + - - +
56A ALA* 2.9 22.8 + - - +
57A ALA 3.2 5.2 - - - +
58A GLN* 1.3 83.2 - - - +
60A ASP* 1.3 72.1 + - + +
61A SER* 2.9 32.8 + - - +
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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