Contacts of the helix formed by residues 44 - 60 (chain D) in PDB entry 2POZ
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 GLY 44 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D HIS* 4.9 0.4 + - - -
39D ILE* 3.7 15.1 - - - +
42D GLY 4.0 0.8 + - - -
43D VAL* 1.3 79.2 - - - +
45D GLY* 1.3 69.3 + - - +
46D THR 3.3 0.2 - - - -
47D ALA* 3.0 7.4 + - - +
48D ALA 2.9 18.7 + - - -
88D ILE* 4.1 4.5 - - - +
51E MSE 3.8 15.9 - - - -
54E ASP* 3.2 14.4 + - - +
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Residues in contact with GLY 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 4.0 8.9 - - - +
19D HIS* 3.6 32.7 - - - -
21D VAL* 3.6 10.6 - - - +
39D ILE* 4.0 7.6 - - - -
44D GLY* 1.3 76.8 - - - +
46D THR* 1.3 62.6 + - - +
48D ALA* 3.1 14.1 + - - +
49D ALA* 3.2 10.9 + - - +
54E ASP* 3.2 3.2 + - - -
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Residues in contact with THR 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 4.0 17.5 - - + +
45D GLY* 1.3 72.8 - - - -
47D ALA* 1.3 63.4 + - - +
49D ALA* 3.3 2.8 + - - +
50D GLY* 3.0 19.8 + - - -
380D TRP* 4.0 21.2 - - + +
50E GLY* 3.8 21.1 - - - -
53E LYS* 4.5 16.0 + - + +
54E ASP* 2.7 33.0 + - - -
380E TRP* 3.9 16.2 - - + -
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Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D GLY* 3.0 16.5 + - - +
46D THR* 1.3 80.4 - - - +
48D ALA* 1.3 57.1 + - - +
50D GLY 3.2 0.7 + - - -
51D MSE 2.9 25.5 + - - +
88D ILE* 3.9 18.4 - - + -
47E ALA* 3.2 35.1 - - - +
50E GLY 4.0 1.2 - - - -
51E MSE 3.9 20.0 - - + +
54E ASP* 3.6 2.2 + - - -
88E ILE* 4.2 2.7 - - + -
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Residues in contact with ALA 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D VAL* 4.1 14.6 - - + -
37D ALA* 4.4 8.3 - - + -
39D ILE* 3.9 28.7 - - + -
44D GLY 2.9 11.0 + - - +
45D GLY 3.1 8.7 + - - +
47D ALA* 1.3 77.8 - - - +
49D ALA* 1.3 60.8 + - - +
51D MSE 3.3 2.8 + - - +
52D ILE* 3.1 29.1 + - - +
88D ILE* 4.2 10.7 - - - +
91D ALA* 5.1 2.9 - - + -
92D GLY* 4.9 0.8 - - - +
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Residues in contact with ALA 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ILE* 3.9 20.0 - - + +
12D LEU* 4.8 7.2 - - + -
21D VAL* 4.1 8.6 - - + +
45D GLY 3.2 9.0 + - - +
46D THR* 3.6 10.3 - - - +
47D ALA 3.3 0.2 - - - -
48D ALA* 1.3 75.1 - - - +
50D GLY* 1.3 67.3 + - - +
52D ILE* 3.2 4.2 + - - +
53D LYS* 2.9 23.4 + - - +
380D TRP* 3.5 34.5 - - + -
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Residues in contact with GLY 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D THR 3.0 13.3 + - - -
47D ALA 3.7 3.1 - - - -
49D ALA* 1.3 76.8 - - - +
51D MSE 1.3 56.3 + - - +
53D LYS* 3.4 2.0 + - - +
54D ASP* 2.8 38.0 + - - +
380D TRP* 3.7 19.6 - - - -
46E THR* 3.7 14.5 - - - -
47E ALA 3.9 5.6 - - - -
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Residues in contact with MSE 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ALA 2.9 16.9 + - - +
48D ALA 3.6 4.9 - - - +
49D ALA 3.2 0.2 - - - -
50D GLY* 1.3 74.4 - - - +
52D ILE* 1.3 60.2 + - - +
54D ASP* 3.2 1.6 + - - -
55D LEU* 2.9 72.6 + - + +
88D ILE* 3.6 28.0 - - + +
89D ILE* 3.2 43.1 - - + -
92D GLY* 4.4 2.7 - - - -
43E VAL* 3.8 24.2 - - + +
44E GLY* 3.8 12.3 - - - -
47E ALA* 3.6 11.1 - - + +
88E ILE* 5.5 3.4 - - - -
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Residues in contact with ILE 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ILE* 3.5 23.8 - - + -
21D VAL* 3.8 24.5 - - + +
22D LEU 4.9 0.4 - - - +
23D VAL* 3.7 25.8 - - + -
37D ALA* 4.0 6.5 - - + +
48D ALA 3.1 17.7 + - - +
49D ALA 3.2 6.3 + - - +
51D MSE 1.3 76.0 - - - +
53D LYS* 1.3 55.1 + - - +
55D LEU* 3.5 7.8 + - - +
56D SER* 2.7 42.9 + - - +
92D GLY* 3.7 18.2 - - - +
95D ALA* 3.9 21.3 - - + -
96D ILE* 4.5 9.4 - - + -
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Residues in contact with LYS 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ILE* 4.2 13.2 - - + +
49D ALA 2.9 16.0 + - - +
50D GLY 3.5 5.2 - - - +
52D ILE* 1.3 76.6 - - - +
54D ASP* 1.3 64.2 + - - +
56D SER* 3.5 0.9 + - - -
57D GLU* 2.9 63.7 + - - +
380D TRP* 3.8 15.9 - - + -
381D ALA* 3.8 22.2 - - + -
382D SER 5.7 1.8 - - - -
383D CYS* 4.1 10.3 - - - -
46E THR* 4.5 18.1 + - + +
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Residues in contact with ASP 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D GLY 2.8 22.7 + - - +
51D MSE 3.2 2.9 + - - +
53D LYS* 1.3 73.7 + - - +
55D LEU* 1.3 64.7 + - - +
57D GLU* 4.1 11.6 - - - +
58D ARG* 3.2 26.3 + - - +
43E VAL* 3.5 20.8 - - + +
44E GLY* 3.4 18.6 - - - +
45E GLY* 4.2 1.5 + - - -
46E THR* 2.6 42.4 + - - -
47E ALA 3.4 1.4 + - - -
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D MSE 2.9 54.1 + - + +
52D ILE* 3.8 0.9 - - - +
54D ASP* 1.3 77.2 - - - +
56D SER* 1.3 53.4 + - - +
58D ARG 3.3 0.2 + - - -
59D PHE* 2.8 65.7 + - + +
60D LEU* 3.9 0.8 + - - -
75D MSE 4.1 13.0 - - + -
79D SER* 4.7 3.8 - - - -
92D GLY* 3.7 8.3 - - - -
93D ILE* 3.6 37.0 - - + +
96D ILE* 3.7 20.0 - - + -
43E VAL* 4.0 3.6 - - + -
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Residues in contact with SER 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D VAL* 3.2 42.4 - - - +
52D ILE* 2.7 26.2 + - - +
53D LYS 3.7 3.8 - - - -
55D LEU* 1.3 76.2 - - - +
57D GLU* 1.3 62.5 + - - +
60D LEU* 3.1 35.9 + - - +
61D ILE* 3.3 14.1 + - - +
96D ILE* 4.4 0.9 - - - +
383D CYS* 4.0 10.3 - - - -
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Residues in contact with GLU 57 (chain D).
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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53D LYS* 2.9 57.9 + - - +
54D ASP* 4.2 8.7 - - - +
56D SER* 1.3 75.3 - - - +
58D ARG* 1.3 59.0 + - - +
61D ILE* 4.6 9.2 - - - +
382D SER 4.8 3.1 - - - +
383D CYS* 3.4 21.9 - - + +
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Residues in contact with ARG 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ASP 3.2 17.9 + - - +
55D LEU 4.0 1.3 - - - +
56D SER 3.2 0.6 - - - -
57D GLU* 1.3 80.0 - - - +
59D PHE* 1.3 102.0 + - + +
63D LYS* 6.0 0.5 - - - -
74D THR* 5.4 1.6 - - - +
78D HIS* 4.6 14.3 + - - +
43E VAL* 4.0 14.3 - - + +
170E GLN* 4.8 10.7 + - - -
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Residues in contact with PHE 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LEU* 2.8 46.1 + - + +
58D ARG* 1.3 126.4 - - + +
60D LEU* 1.3 65.7 + - + +
63D LYS* 3.0 27.4 - - - +
71D LEU* 4.8 6.9 - - + +
74D THR* 3.7 34.1 - - + -
75D MSE 3.5 31.2 - - + -
78D HIS* 3.8 28.3 - - + -
79D SER* 4.0 3.1 - - - -
43E VAL* 3.9 9.9 - - + -
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Residues in contact with LEU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 4.0 23.7 - - + +
8D VAL* 3.9 14.8 - - + -
25D ILE* 4.2 11.2 - - + -
55D LEU 4.5 2.0 - - - +
56D SER* 3.1 37.4 + - - +
59D PHE* 1.3 86.4 - - + +
61D ILE* 1.3 74.4 + - + +
62D GLY 3.1 0.2 + - - -
63D LYS* 2.7 25.7 + - - +
71D LEU* 4.3 19.7 - - + -
75D MSE 5.1 4.5 - - - -
96D ILE* 3.8 38.1 - - + -
100D LEU* 5.1 0.7 - - + -
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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