Contacts of the helix formed by residues 55 - 77 (chain D) in PDB entry 2Q6W
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 GLU 55 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D LYS 5.5 0.5 - - - +
53D SER* 4.2 0.8 + - - -
54D PHE* 1.3 86.4 - - + +
56D ALA* 1.3 72.9 + - - +
57D GLN* 3.2 25.4 + - + +
58D GLY* 3.0 20.7 + - - +
24F ALA* 5.5 4.1 - - + +
25F TRP 4.8 1.6 + - - -
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Residues in contact with ALA 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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34D VAL* 3.6 15.3 - - + -
39D LYS* 3.3 36.3 - - - +
40D GLU 3.7 1.3 - - - +
41D THR* 3.9 13.0 - - + -
54D PHE* 3.2 15.8 + - - -
55D GLU* 1.3 73.9 + - - +
57D GLN* 1.3 64.8 + - - +
58D GLY 3.1 0.2 - - - -
59D ALA* 3.0 8.1 + - - +
60D LEU* 3.0 24.1 + - - +
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Residues in contact with GLN 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LYS* 4.8 12.4 - - - +
55D GLU* 3.2 22.6 + - + +
56D ALA* 1.3 76.6 - - - +
58D GLY* 1.3 55.4 + - - +
60D LEU* 3.7 20.2 - - - +
61D ALA* 2.8 48.5 + - + +
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Residues in contact with GLY 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D PHE* 4.6 0.4 - - - -
55D GLU* 3.0 16.2 + - - +
57D GLN* 1.3 76.8 - - - +
59D ALA* 1.3 60.0 + - - +
61D ALA* 3.8 4.0 - - - +
62D ASN* 3.1 31.3 + - - +
27F SER* 3.9 10.1 - - - -
29F GLU* 3.6 16.9 - - - +
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Residues in contact with ALA 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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22D PHE* 3.3 39.3 - - + -
34D VAL* 3.3 27.8 - - + -
36D MET* 4.7 0.7 - - + -
54D PHE* 4.0 5.2 - - + -
56D ALA 3.0 11.0 + - - +
58D GLY* 1.3 73.2 - - - +
60D LEU* 1.3 55.0 - - - +
62D ASN* 3.0 4.0 + - - +
63D ILE* 2.8 39.5 + - - +
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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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34D VAL* 3.9 7.0 - - + -
36D MET* 3.7 38.6 - - + +
39D LYS* 4.1 42.6 - - + +
56D ALA 3.0 12.4 + - - +
57D GLN* 3.5 28.3 - - - +
59D ALA* 1.3 79.8 - - - +
61D ALA* 1.3 62.5 + - - +
63D ILE* 3.3 7.0 + - - +
64D ALA* 3.1 20.3 + - - +
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Residues in contact with ALA 61 (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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57D GLN* 2.8 33.7 + - + +
58D GLY* 3.8 5.8 - - - +
60D LEU* 1.3 72.8 - - - +
62D ASN* 1.3 59.0 - - - +
64D ALA* 3.0 22.9 + - - +
65D VAL* 3.0 18.1 + - + +
29F GLU* 4.2 10.5 - - - +
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Residues in contact with ASN 62 (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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9D GLN* 3.1 4.0 + - - -
11D GLU* 2.8 27.7 - - - +
22D PHE* 3.7 5.4 - - + -
58D GLY 3.1 9.9 + - - +
59D ALA 3.0 10.2 + - - +
61D ALA* 1.3 79.3 - - - +
63D ILE* 1.3 54.3 + - - +
65D VAL* 3.2 4.8 + - - +
66D ASP* 2.7 37.8 + - - +
28F ASP 2.6 24.8 - - - +
29F GLU* 2.6 33.8 + - - +
30F ALA* 2.9 25.0 + - - +
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Residues in contact with ILE 63 (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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11D GLU* 3.7 7.9 - - + -
12D PHE 3.6 13.5 - - - +
13D TYR* 3.5 27.2 - - + -
20D GLY* 4.4 4.5 - - - -
21D GLU 3.4 30.3 - - - +
22D PHE* 4.4 4.3 - - + -
36D MET* 4.2 25.8 - - - -
59D ALA 2.8 17.5 + - - +
60D LEU* 3.7 5.8 - - - +
62D ASN* 1.3 74.4 - - - +
64D ALA* 1.3 61.3 + - - +
66D ASP* 3.3 17.7 - - + +
67D LYS* 3.0 26.4 + - + +
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Residues in contact with ALA 64 (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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60D LEU 3.1 11.9 + - - +
61D ALA* 3.0 14.6 + - - +
63D ILE* 1.3 75.6 - - - +
65D VAL* 1.3 59.4 + - + +
67D LYS* 3.6 11.0 - - - +
68D ALA* 3.1 27.9 + - - +
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Residues in contact with VAL 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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61D ALA* 3.0 15.8 + - + +
62D ASN* 3.3 8.3 - - - +
64D ALA* 1.3 75.1 - - + +
66D ASP* 1.3 55.7 + - - +
67D LYS 3.1 1.3 - - - -
68D ALA* 3.0 8.1 + - - +
69D ASN* 2.6 38.9 + - - +
30F ALA* 3.4 29.2 - - + +
31F LEU 3.4 32.5 - - - +
32F PRO* 3.7 15.9 - - + -
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Residues in contact with ASP 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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11D GLU* 2.6 35.8 - - - +
13D TYR* 4.1 17.7 - - + +
62D ASN 2.7 25.8 + - - +
63D ILE* 3.3 17.0 - - - +
65D VAL* 1.3 73.4 - - - +
67D LYS* 1.3 52.8 + - - +
69D ASN* 4.1 9.7 + - - +
70D LEU* 2.7 33.6 + - - +
9E GLU* 3.3 16.7 - - + +
11E ARG* 3.9 16.0 - - - +
30E TYR* 5.5 0.9 - - - -
30F ALA* 3.6 9.4 - - - +
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Residues in contact with LYS 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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13D TYR* 3.4 54.6 + - + +
15D ASN* 4.9 4.5 + - - +
18D GLN* 5.1 6.3 - - - +
63D ILE* 3.0 20.9 + - + +
64D ALA* 3.6 9.4 - - - +
66D ASP* 1.3 75.0 - - - +
68D ALA* 1.3 58.9 + - - +
70D LEU* 3.1 5.7 - - - +
71D GLU* 3.1 26.0 + - - +
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Residues in contact with ALA 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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64D ALA 3.1 15.1 + - - +
65D VAL* 3.0 7.3 + - - +
67D LYS* 1.3 79.9 - - - +
69D ASN* 1.3 63.2 + - - +
71D GLU* 3.3 11.2 - - - +
72D ILE* 3.2 29.3 + - + +
32F PRO* 5.9 4.9 - - + -
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Residues in contact with ASN 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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65D VAL* 2.6 28.8 + - - +
66D ASP* 3.7 8.4 + - - +
68D ALA* 1.3 70.4 - - - +
70D LEU* 1.3 61.0 + - - +
72D ILE* 3.8 6.5 - - - +
73D MET* 2.8 34.5 + - - +
9E GLU* 3.8 10.5 - - + +
30E TYR* 4.4 9.9 - - + -
30F ALA* 5.5 0.2 - - - +
31F LEU 2.8 25.2 + - - -
32F PRO* 3.3 6.7 - - - +
33F LEU* 2.7 50.2 + - + +
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Residues in contact with LEU 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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13D TYR* 3.3 31.2 - - + +
15D ASN* 3.0 34.5 - - - +
66D ASP 2.7 17.5 + - - +
67D LYS* 3.1 11.0 - - - +
69D ASN* 1.3 69.9 - - - +
71D GLU* 1.3 55.8 + - - +
72D ILE 3.1 0.3 + - - -
73D MET 3.1 0.5 + - - -
74D THR* 2.6 58.4 + - - +
7E PHE* 3.4 19.3 - - + +
9E GLU* 3.4 30.9 - - + +
32E HIS* 3.5 9.4 - - - +
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Residues in contact with GLU 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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15D ASN* 4.8 5.2 - - - +
67D LYS 3.1 8.1 + - - +
68D ALA* 3.3 15.1 - - - +
70D LEU* 1.3 77.2 - - - +
72D ILE* 1.3 68.6 + - + +
74D THR* 3.7 4.7 - - - -
75D LYS* 3.2 52.3 + - + +
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Residues in contact with ILE 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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68D ALA* 3.2 19.3 + - + +
69D ASN* 3.9 11.7 - - - +
70D LEU 3.1 1.0 - - - -
71D GLU* 1.3 83.7 - - + +
73D MET* 1.3 65.0 + - - +
74D THR 3.3 0.3 + - - -
75D LYS* 3.3 7.6 + - - +
76D ARG* 2.8 69.0 + - + +
32F PRO* 6.0 0.9 - - + -
33F LEU* 4.4 4.0 - - + -
34F GLY* 3.6 32.8 - - - +
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Residues in contact with MET 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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69D ASN 2.8 25.5 + - - +
72D ILE* 1.3 72.1 - - - +
74D THR* 1.3 52.8 + - - +
76D ARG* 3.8 17.3 - - - -
77D SER* 2.7 38.5 + - - -
9E GLU* 3.2 25.4 - - - +
32E HIS* 3.5 9.8 - - + -
37E PHE* 3.5 22.4 - - + -
53E LEU* 2.8 64.3 - - + +
57E VAL* 5.2 0.4 - - - -
33F LEU* 3.2 22.9 - - + -
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Residues in contact with THR 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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15D ASN* 5.1 1.4 + - - -
70D LEU* 2.6 43.3 + - - +
71D GLU* 3.7 7.3 + - - -
73D MET* 1.3 76.7 - - - +
75D LYS* 1.3 61.7 + - - +
77D SER* 3.0 6.8 + - - -
79D TYR* 2.9 50.5 + - + -
7E PHE* 3.5 36.2 - - + +
32E HIS* 3.4 10.4 + - - -
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Residues in contact with LYS 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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71D GLU* 3.2 44.3 + - + +
72D ILE* 3.7 8.3 - - - +
74D THR* 1.3 76.3 - - - +
76D ARG* 1.3 63.8 + - + +
78D ASN* 2.9 19.6 + - - +
79D TYR* 3.1 41.7 + - + +
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Residues in contact with ARG 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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72D ILE* 2.8 48.2 + - + +
73D MET* 4.2 10.2 - - - -
75D LYS* 1.3 73.0 - - + +
77D SER* 1.3 57.9 + - - +
78D ASN* 3.3 5.0 + - - -
53E LEU* 3.2 31.8 + - + +
56E PRO* 4.1 17.6 - - - +
57E VAL* 3.5 29.3 - - - +
33F LEU 3.8 14.8 + - - -
34F GLY* 4.2 8.9 - - - -
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Residues in contact with SER 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 MET 2.7 21.1 + - - -
74D THR 3.4 5.4 - - - -
75D LYS 3.0 0.6 - - - -
76D ARG* 1.3 78.3 - - - +
78D ASN* 1.3 66.1 + - - +
79D TYR 4.4 1.6 - - - -
80D THR* 2.6 40.0 + - - -
32E HIS* 3.4 21.8 + - - -
33E ASN* 5.1 0.7 + - - -
53E LEU* 3.8 14.7 - - - +
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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
------------------------------------------------------------
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