Contacts of the helix formed by residues 64 - 81 (chain D) in PDB entry 2PY9
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 PRO 64 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D THR* 4.3 17.7 - - + -
44D GLY 4.2 7.0 - - - +
63D GLY* 1.4 86.3 - - - +
65D THR* 1.3 56.4 + - - +
66D ASN* 3.2 14.8 - - - +
67D ALA* 2.7 43.4 + - + +
68D ILE 3.2 3.6 + - - -
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Residues in contact with THR 65 (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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76C ILE* 2.9 35.1 - - + +
77C ASP* 4.8 8.5 - - - +
80C GLU* 3.1 32.8 + - - +
13D THR* 5.4 1.4 - - - +
14D LEU* 4.8 6.3 - - - +
63D GLY 3.5 2.9 + - - -
64D PRO* 1.3 70.4 - - - +
66D ASN* 1.3 59.8 + - - +
67D ALA 3.1 0.2 - - - -
68D ILE* 3.2 11.8 + - - +
69D PHE* 2.9 25.0 + - + +
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Residues in contact with ASN 66 (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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64D PRO* 2.9 19.2 + - - +
65D THR* 1.3 73.9 + - - +
67D ALA* 1.3 63.7 + - - +
68D ILE 3.2 0.7 - - - -
69D PHE* 3.7 9.5 - - + +
70D LYS* 3.1 40.9 + - - +
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Residues in contact with ALA 67 (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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43D SER* 3.4 18.8 - - - +
44D GLY* 3.3 28.3 - - - +
45D ALA* 3.6 9.9 - - + +
63D GLY 4.6 0.4 - - - -
64D PRO* 2.7 26.6 + - + +
66D ASN* 1.3 85.1 - - - +
68D ILE* 1.3 55.6 + - - +
70D LYS* 3.4 2.9 + - - +
71D ALA* 2.9 29.6 + - - +
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Residues in contact with ILE 68 (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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72C PHE* 4.1 2.0 - - + -
76C ILE* 4.0 23.8 - - + -
14D LEU* 3.5 34.1 - - + +
16D ILE* 4.0 22.9 - - + -
45D ALA* 4.5 0.7 - - + -
61D LEU* 4.0 10.2 - - + +
62D ALA* 4.0 23.3 - - - +
63D GLY 3.4 24.9 - - - +
64D PRO 3.2 4.4 + - - +
65D THR* 3.5 8.7 - - - +
67D ALA* 1.3 77.4 - - - +
69D PHE* 1.3 67.8 + - - +
71D ALA* 3.4 6.6 + - - +
72D PHE* 3.0 23.4 + - - +
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Residues in contact with PHE 69 (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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69C PHE* 3.8 38.8 - + + -
72C PHE* 3.7 27.6 - + - -
73C ALA* 3.7 26.2 - - + -
76C ILE* 5.1 4.3 - - + -
65D THR* 2.9 14.9 + - + +
66D ASN* 3.7 13.0 - - - +
68D ILE* 1.3 82.4 - - - +
70D LYS* 1.3 58.6 + - - +
72D PHE* 3.3 3.4 + - - +
73D ALA* 2.9 31.3 + - + +
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Residues in contact with LYS 70 (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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42D GLU 3.5 18.6 - - - +
43D SER* 3.4 25.2 + - - +
66D ASN* 3.1 33.5 + - - +
67D ALA* 3.4 5.8 + - - +
69D PHE* 1.3 79.6 - - - +
71D ALA* 1.3 60.2 + - - +
73D ALA* 3.5 6.9 + - - +
74D MSE 3.3 48.9 + - + +
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Residues in contact with ALA 71 (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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39D MSE 3.4 6.6 - - - +
43D SER* 3.9 19.0 - - - +
45D ALA* 4.2 7.2 - - + -
47D ILE* 4.4 6.5 - - + -
61D LEU* 4.0 24.2 - - + -
67D ALA 2.9 18.1 + - - +
68D ILE* 3.7 5.6 - - - +
69D PHE 3.1 0.2 - - - -
70D LYS* 1.3 73.4 - - - +
72D PHE* 1.3 61.3 - - - +
74D MSE 3.4 3.2 + - - +
75D ILE* 3.1 31.4 + - - +
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Residues in contact with PHE 72 (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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16C ILE* 3.9 26.7 - - + -
68C ILE* 3.9 16.2 - - + -
69C PHE* 3.5 31.2 - + - -
72C PHE* 3.5 55.6 - + + -
18D LEU* 4.2 18.8 - - + -
61D LEU* 4.2 6.9 - - + +
68D ILE 3.0 16.1 + - - +
69D PHE* 3.3 4.7 - + - +
71D ALA* 1.3 78.2 - - - +
73D ALA* 1.3 59.9 + - - +
75D ILE* 3.0 9.5 + - + +
76D ILE* 2.9 53.7 + - + +
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Residues in contact with ALA 73 (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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69C PHE* 3.4 30.8 - - + -
69D PHE* 2.9 22.0 + - + +
70D LYS* 3.9 7.2 - - - +
71D ALA 3.4 0.2 - - - -
72D PHE* 1.3 76.6 - - - +
74D MSE 1.4 53.1 + - + +
76D ILE* 3.5 2.1 + - - +
77D ASP* 2.7 38.4 + - - +
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Residues in contact with MSE 74 (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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38D LYS 5.1 0.4 - - - -
39D MSE 3.6 45.0 - - + +
42D GLU* 3.9 31.2 - - + +
43D SER* 4.2 8.3 - - - -
70D LYS* 3.3 39.3 + - + +
71D ALA* 3.8 3.8 - - - +
72D PHE 3.2 0.4 - - - -
73D ALA* 1.4 73.7 - - + +
75D ILE* 1.3 69.2 + - - +
77D ASP* 3.3 12.2 - - - +
78D LYS* 3.1 22.2 + - - +
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Residues in contact with ILE 75 (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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18D LEU* 3.8 31.6 - - + -
20D MSE 5.0 1.8 - - - -
28D ILE* 4.0 24.6 - - + +
39D MSE 2.7 33.2 - - + -
59D ILE* 4.1 20.4 - - + -
61D LEU* 4.2 15.5 - - + -
71D ALA 3.1 13.6 + - - +
72D PHE* 3.0 11.0 + - + +
74D MSE 1.3 78.5 - - - +
76D ILE* 1.3 61.5 + - + +
78D LYS* 3.3 5.9 + - - +
79D LEU* 2.9 40.4 + - + +
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Residues in contact with ILE 76 (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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14C LEU* 4.4 14.1 - - + -
16C ILE* 3.9 22.7 - - + -
65C THR* 3.5 29.6 - - + -
68C ILE* 4.2 11.2 - - + -
69C PHE* 4.1 11.4 - - + -
72D PHE* 2.9 51.2 + - + +
73D ALA 3.7 3.4 - - - +
75D ILE* 1.3 75.9 - - + +
77D ASP* 1.3 71.0 + - - +
79D LEU* 3.2 8.6 + - + +
80D GLU* 3.0 23.4 + - - +
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Residues in contact with ASP 77 (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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73D ALA 2.7 20.5 + - - +
74D MSE 3.3 19.0 - - - +
76D ILE* 1.3 77.2 - - - +
78D LYS* 1.3 61.1 + - + +
80D GLU* 3.0 28.3 + - - +
81D GLU* 3.4 20.2 + - - +
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Residues in contact with LYS 78 (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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27D SER* 3.1 50.8 + - - +
28D ILE* 4.4 8.7 - - + -
30D GLY* 5.3 1.2 - - - -
35D SER* 3.3 26.8 + - - +
39D MSE 6.0 3.4 - - - -
74D MSE 3.1 8.8 + - - +
75D ILE* 3.5 9.4 - - - +
77D ASP* 1.3 78.5 - - + +
79D LEU* 1.3 66.6 + - - +
80D GLU 3.2 0.7 + - - -
81D GLU* 3.1 42.5 + - - +
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Residues in contact with LEU 79 (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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14C LEU* 4.8 18.2 - - + +
15C THR 5.6 1.3 - - - +
16C ILE* 4.9 18.4 - - + -
20D MSE 3.6 35.7 - - + -
24D GLU* 3.8 33.9 - - + +
27D SER* 5.2 3.6 - - - +
28D ILE* 4.7 4.0 - - + +
75D ILE* 2.9 31.4 + - + +
76D ILE* 3.2 11.9 + - + +
78D LYS* 1.3 76.5 - - - +
80D GLU* 1.3 60.7 + - - +
81D GLU 3.5 7.6 - - - +
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Residues in contact with GLU 80 (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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14C LEU* 4.1 19.4 - - + +
65C THR* 3.1 35.0 + - - +
76D ILE* 3.0 11.6 + - - +
77D ASP* 3.0 25.5 + - - +
79D LEU* 1.3 76.8 - - - +
81D GLU* 1.3 68.3 + - + +
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Residues in contact with GLU 81 (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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77D ASP* 3.4 19.3 + - - +
78D LYS* 3.1 40.9 + - - +
79D LEU 3.5 9.7 - - - +
80D GLU* 1.3 83.9 - - + +
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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