Contacts of the helix formed by residues 65 - 80 (chain A) 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 THR 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL* 3.5 11.7 + - - +
14A LEU* 3.7 17.8 - - + +
63A GLY 3.4 3.2 + - - -
64A PRO* 1.3 70.6 - - - +
66A ASN* 1.3 59.5 + - + +
68A ILE* 3.2 6.4 - - - +
69A PHE* 3.0 27.9 + - + +
76B ILE* 3.7 26.6 - - + +
77B ASP* 5.6 1.3 - - - +
80B GLU* 2.6 29.0 + - - +
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Residues in contact with ASN 66 (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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64A PRO* 2.8 6.8 + - + +
65A THR* 1.3 77.2 - - + +
67A ALA* 1.3 66.6 + - - +
69A PHE* 3.3 12.0 + - - +
70A LYS* 2.9 48.7 + - - +
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Residues in contact with ALA 67 (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 SER* 3.3 27.7 - - - +
44A GLY* 3.7 21.1 - - - +
45A ALA* 3.6 13.6 - - + +
63A GLY 4.8 0.2 - - - -
64A PRO* 2.9 24.5 + - + +
66A ASN* 1.3 76.3 - - - +
68A ILE* 1.3 69.0 + - - +
70A LYS* 3.3 2.3 + - - -
71A ALA* 3.0 16.5 + - - +
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Residues in contact with ILE 68 (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 LEU* 4.1 16.8 - - + +
16A ILE* 4.2 15.0 - - + -
45A ALA* 4.5 2.9 - - + -
61A LEU* 3.8 13.8 - - + +
62A ALA* 3.5 44.2 - - - +
63A GLY 3.6 11.2 - - - +
64A PRO 3.0 12.5 + - - +
65A THR* 3.2 10.8 - - - +
66A ASN 3.2 0.2 - - - -
67A ALA* 1.3 79.7 - - - +
69A PHE* 1.3 57.9 + - - +
71A ALA* 3.0 3.6 + - - +
72A PHE* 2.9 23.9 + - - +
72B PHE* 3.6 28.7 - - + -
76B ILE* 4.3 8.7 - - + -
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Residues in contact with PHE 69 (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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65A THR* 3.0 11.4 + - + +
66A ASN* 3.5 19.3 - - - +
68A ILE* 1.3 81.6 - - + +
70A LYS* 1.3 65.6 + - + +
72A PHE* 3.5 5.2 + - - +
73A ALA* 2.9 32.3 + - + +
69B PHE* 4.5 29.4 - + + -
72B PHE* 4.1 25.1 - + - -
73B ALA* 4.3 23.8 - - + -
76B ILE* 5.8 5.4 - - + -
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Residues in contact with LYS 70 (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 GLU 3.8 19.6 + - - -
43A SER* 3.8 24.9 + - - +
66A ASN* 2.9 45.3 + - - +
67A ALA* 4.7 0.4 - - - -
69A PHE* 1.3 73.6 - - + +
71A ALA* 1.3 68.3 + - - +
73A ALA* 3.0 7.8 + - - +
74A MSE 2.9 38.2 + - + +
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Residues in contact with ALA 71 (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 MSE 4.7 1.6 - - - +
43A SER* 3.6 22.8 - - - +
45A ALA* 4.2 5.8 - - + -
47A ILE* 4.0 20.0 - - + -
61A LEU* 4.1 15.5 - - + -
67A ALA 3.0 8.6 + - - +
68A ILE 3.0 8.7 + - - +
70A LYS* 1.3 78.1 - - - +
72A PHE* 1.3 61.3 + - - +
74A MSE 3.4 7.9 + - - +
75A ILE* 3.0 27.5 + - + +
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Residues in contact with PHE 72 (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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18A LEU* 4.0 23.1 - - + -
61A LEU* 3.9 7.7 - - + +
68A ILE 2.9 8.6 + - - +
69A PHE* 3.5 8.7 - + - +
71A ALA* 1.3 73.6 - - - +
73A ALA* 1.3 67.4 + - - +
75A ILE* 3.0 5.3 + - + +
76A ILE* 2.9 45.7 + - + +
16B ILE* 3.4 35.7 - - + -
68B ILE* 3.9 13.2 - - + -
69B PHE* 3.9 19.5 - + - -
72B PHE* 3.4 62.1 - + + -
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Residues in contact with ALA 73 (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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69A PHE* 2.9 27.6 + - + +
70A LYS* 3.0 7.6 + - - +
72A PHE* 1.3 74.9 - - - +
74A MSE 1.3 52.9 + - + +
76A ILE* 3.1 3.8 + - - +
77A ASP* 2.7 37.1 + - - +
69B PHE* 3.9 29.0 - - + -
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Residues in contact with MSE 74 (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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38A LYS* 4.7 2.7 - - - +
39A MSE 3.8 47.5 - - + +
42A GLU* 3.5 46.4 - - + +
43A SER* 4.3 4.9 - - - +
70A LYS* 2.9 32.6 + - + +
71A ALA 3.7 3.6 - - - +
73A ALA* 1.3 76.9 - - + +
75A ILE* 1.3 60.5 + - - +
77A ASP* 3.3 11.9 - - + +
78A LYS* 3.3 21.3 + - - +
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Residues in contact with ILE 75 (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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18A LEU* 4.2 23.8 - - + -
20A MSE 4.8 3.1 - - - -
28A ILE* 3.9 26.2 - - + +
39A MSE 3.9 21.1 - - - -
47A ILE* 5.6 2.5 - - + -
59A ILE* 4.3 11.7 - - + -
61A LEU* 3.5 36.8 - - + -
71A ALA* 3.0 17.4 + - + +
72A PHE* 3.0 8.7 + - - +
74A MSE 1.3 71.2 - - - +
76A ILE* 1.3 71.4 + - + +
78A LYS* 3.0 16.3 + - - +
79A LEU* 3.1 26.0 + - + +
16B ILE* 6.1 0.2 - - + -
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Residues in contact with ILE 76 (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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72A PHE* 2.9 40.8 + - + +
73A ALA 3.4 8.7 - - - +
75A ILE* 1.3 73.3 - - + +
77A ASP* 1.3 64.2 + - - +
78A LYS 2.9 6.2 + - - -
79A LEU* 4.0 12.9 - - + +
80A GLU* 3.1 36.9 + - - +
14B LEU* 5.1 14.7 - - + +
16B ILE* 3.7 29.4 - - + -
65B THR* 4.2 19.3 - - + +
68B ILE* 4.7 6.5 - - + -
69B PHE* 4.4 10.3 - - + -
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Residues in contact with ASP 77 (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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73A ALA 2.7 21.7 + - - +
74A MSE 3.3 16.0 - - - +
76A ILE* 1.3 75.4 - - - +
78A LYS* 1.3 57.4 + - - +
80A GLU* 4.1 17.4 - - - +
81A GLU* 3.5 25.2 + - - +
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Residues in contact with LYS 78 (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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27A SER* 3.3 45.2 + - - +
28A ILE* 4.4 9.4 - - + -
35A SER* 3.4 16.7 + - - -
39A MSE 4.2 13.7 - - + +
74A MSE 3.6 8.5 - - - +
75A ILE* 3.3 10.8 - - - +
76A ILE 2.9 0.4 - - - -
77A ASP* 1.3 78.1 - - - +
79A LEU* 1.3 67.0 + - - +
80A GLU 3.1 1.3 - - - -
81A GLU* 3.0 52.2 + - - +
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Residues in contact with LEU 79 (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 MSE 4.3 8.1 - - + -
24A GLU* 3.4 46.4 - - + +
27A SER* 5.3 4.0 - - - +
28A ILE* 4.1 15.5 - - + -
75A ILE* 3.1 20.0 + - + +
76A ILE* 4.0 29.8 - - + +
78A LYS* 1.3 77.8 - - - +
80A GLU* 1.3 58.4 + - - +
81A GLU 5.0 1.0 - - - +
14B LEU* 4.7 17.1 - - + +
15B THR 5.5 2.5 - - - +
16B ILE* 4.3 13.0 - - + -
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Residues in contact with GLU 80 (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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76A ILE* 3.1 28.8 + - - +
77A ASP* 4.1 16.2 - - - +
79A LEU* 1.3 78.8 - - - +
81A GLU* 1.4 65.2 + - - +
14B LEU* 4.5 18.9 - - + +
65B THR* 3.2 33.1 + - - +
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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