Contacts of the helix formed by residues 45 - 59 (chain D) in PDB entry 1Y8R
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 LYS 45 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D GLY 3.6 5.5 + - - -
44D LEU* 1.3 74.6 - - - +
46D GLY* 1.3 70.4 + - - +
47D LEU 3.5 1.8 - - - +
48D GLY* 3.6 1.5 - - - +
49D ALA* 2.8 24.1 + - - +
75D ASP* 4.9 8.3 - - - +
79D GLN* 4.0 12.0 - - - +
91D ARG* 3.1 47.9 - - - +
132D THR* 5.8 0.4 - - + -
133D CYS* 3.2 34.4 - - - +
298D GLU* 3.2 26.5 - - - +
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Residues in contact with GLY 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LYS* 1.3 82.2 - - - +
47D LEU* 1.3 61.8 + - - +
49D ALA* 3.5 2.6 + - - +
50D GLU* 3.4 23.0 + - - +
78D ALA* 4.3 18.4 + - - +
79D GLN* 4.8 0.2 - - - +
80D PHE* 5.6 0.3 - - - -
298D GLU* 2.9 18.9 + - - -
303D CYS* 3.6 16.8 - - - -
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Residues in contact with LEU 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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45D LYS* 4.9 0.4 - - - +
46D GLY* 1.3 74.3 - - - +
48D GLY* 1.3 63.7 + - - +
50D GLU* 3.4 1.9 + - - +
51D ILE* 3.1 37.5 + - + +
132D THR* 4.2 12.3 - - + +
156D GLY* 3.4 38.4 - - - +
157D ASP* 3.5 16.2 - - - +
158D VAL* 4.6 6.1 - - + +
298D GLU* 4.5 3.1 + - - +
303D CYS* 3.5 20.6 - - - +
306D VAL* 3.8 15.0 - - + -
307D GLY* 3.3 38.6 - - - +
310D LEU* 4.8 1.6 - - + -
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Residues in contact with GLY 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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41D LEU* 3.3 16.8 - - - +
43D GLY 3.2 27.0 + - - -
44D LEU* 4.0 7.0 - - - -
45D LYS 3.1 9.4 + - - +
47D LEU* 1.3 79.6 - - - +
49D ALA* 1.3 60.8 + - - +
51D ILE 3.4 0.2 + - - -
52D ALA* 3.1 17.7 + - - +
132D THR* 4.5 9.0 - - - +
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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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44D LEU* 4.0 3.8 - - - +
45D LYS 2.8 16.8 + - - +
46D GLY 4.1 2.0 - - - +
48D GLY* 1.3 72.7 - - - -
50D GLU* 1.3 64.3 + - - +
52D ALA* 3.0 4.5 + - - +
53D LYS* 2.8 25.1 + - - +
79D GLN* 3.4 28.9 - - + +
80D PHE* 4.0 17.7 - - + -
81D LEU* 3.5 21.1 - - + +
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Residues in contact with GLU 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 GLY 3.4 13.1 + - - +
47D LEU 3.6 8.7 - - - +
48D GLY 3.3 0.2 - - - -
49D ALA* 1.3 79.6 - - - +
51D ILE* 1.3 64.5 + - - +
53D LYS* 3.2 26.8 + - - +
54D ASN* 3.0 31.4 + - - +
80D PHE* 3.4 16.1 - - + -
300D ALA 5.3 0.9 - - - +
303D CYS* 3.8 12.6 - - + +
304D ALA* 3.7 36.2 - - - +
307D GLY* 4.3 7.2 - - - -
34E LYS* 2.7 27.5 + - - -
35E ASN* 4.5 0.5 - - - +
38E LEU* 5.4 2.4 - - - +
392E ALA* 4.7 0.9 - - - +
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Residues in contact with ILE 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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41D LEU* 4.3 16.6 - - + -
47D LEU* 3.1 29.3 + - + +
48D GLY 3.9 3.6 - - - +
50D GLU* 1.3 75.3 - - - +
52D ALA* 1.3 65.5 + - - +
54D ASN* 3.1 9.6 + - - +
55D LEU* 2.9 44.8 + - + +
130D CYS* 4.1 8.3 - - - -
132D THR* 4.7 6.3 - - - +
307D GLY* 3.8 20.2 - - - +
310D LEU* 3.4 36.8 - - + -
311D ALA* 4.5 3.4 - - + +
314D ILE* 4.3 11.9 - - + -
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Residues in contact with ALA 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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41D LEU* 3.8 15.4 - - + +
44D LEU* 4.7 0.7 - - + -
48D GLY 3.1 13.9 + - - +
49D ALA* 3.0 13.4 + - - +
51D ILE* 1.3 79.1 - - - +
53D LYS* 1.3 64.0 + - - +
55D LEU* 3.2 2.4 + - - +
56D ILE* 2.9 34.9 + - + +
63D LEU* 4.1 16.8 - - + -
65D MET* 4.6 8.1 - - - -
81D LEU* 4.4 10.1 - - + -
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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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49D ALA 2.8 15.8 + - - +
50D GLU* 3.3 26.1 + - - +
52D ALA* 1.3 71.7 - - - +
54D ASN* 1.3 86.1 + - - +
56D ILE* 3.3 1.6 + - - +
57D LEU* 2.9 48.8 + - + +
80D PHE* 4.1 17.3 - - + -
81D LEU* 5.2 1.3 - - + +
102D LEU* 3.5 30.5 - - + -
31E GLU* 2.6 41.2 + - - +
34E LYS* 4.1 5.6 - - - +
61E PHE* 4.3 15.9 - - + -
388E ALA* 5.3 0.2 - - + -
392E ALA* 3.8 4.6 - - - +
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Residues in contact with ASN 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 GLU* 3.0 13.9 + - - -
51D ILE 3.5 5.8 - - - +
53D LYS* 1.3 102.2 + - - +
55D LEU* 1.3 59.6 + - - +
57D LEU* 3.4 4.3 + - - +
58D ALA* 2.9 28.3 + - - +
307D GLY 3.1 31.9 + - - -
308D GLY* 3.7 8.9 - - - -
311D ALA* 3.5 16.0 - - + +
315D VAL* 6.2 0.2 - - - -
388E ALA* 4.3 12.4 - - + +
389E THR* 4.0 16.6 - - + +
392E ALA* 4.3 6.6 - - - +
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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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39D VAL* 3.8 32.3 - - + -
41D LEU* 5.9 0.7 - - + -
51D ILE* 2.9 36.7 + - + +
52D ALA 3.8 2.5 - - - +
54D ASN* 1.3 74.4 - - - +
56D ILE* 1.3 67.8 + - - +
58D ALA* 3.0 15.1 + - + +
59D GLY 3.2 9.0 + - - -
60D VAL* 3.6 25.8 - - + +
63D LEU* 3.8 17.5 - - + -
130D CYS* 6.2 0.2 - - + -
311D ALA* 4.1 9.4 - - + +
314D ILE* 3.9 26.7 - - + -
315D VAL* 4.0 22.2 - - + -
318D LEU* 5.4 0.2 - - + -
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Residues in contact with ILE 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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52D ALA* 2.9 25.9 + - + +
53D LYS* 3.7 5.4 - - - +
55D LEU* 1.3 77.2 - - - +
57D LEU* 1.3 63.9 + - - +
59D GLY 3.3 3.8 + - - -
60D VAL* 4.5 1.8 - - - -
63D LEU* 3.7 27.8 - - + -
99D ALA* 3.9 26.7 - - + +
100D GLN 5.2 0.2 - - - +
102D LEU* 3.6 25.4 - - + -
103D ASN* 3.1 37.1 + - + +
106D VAL* 3.4 19.8 - - + +
108D VAL* 4.1 17.3 - - + -
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Residues in contact with LEU 57 (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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19D TYR* 3.6 16.8 - - - -
22D GLN* 4.2 2.4 - - - +
53D LYS* 2.9 44.7 + - + +
54D ASN 3.8 3.8 - - - +
56D ILE* 1.3 77.7 - - - +
58D ALA* 1.3 63.1 + - - +
59D GLY 3.1 1.4 + - - -
102D LEU* 3.5 36.8 - - + +
103D ASN* 4.1 3.7 + - + +
57E LEU 3.7 18.4 - - - +
58E ASN* 3.4 27.7 - - - +
59E ARG* 4.2 13.9 - - - +
61E PHE* 4.0 17.7 - - + -
388E ALA* 4.3 8.3 - - + -
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Residues in contact with ALA 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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22D GLN* 2.8 32.0 + - - +
26D TRP* 4.7 6.3 - - + -
31D GLN* 3.2 6.6 - - - +
34D LEU* 3.5 22.1 - - + +
54D ASN 2.9 15.0 + - - +
55D LEU* 3.2 17.7 - - + +
57D LEU* 1.3 76.7 - - - +
59D GLY* 1.3 55.9 + - - +
60D VAL* 4.9 1.1 - - + +
315D VAL* 4.2 16.6 - - + -
388E ALA* 6.1 0.4 - - - +
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Residues in contact with GLY 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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19D TYR* 3.4 27.0 + - - -
31D GLN* 4.1 5.7 - - - +
34D LEU* 3.9 3.3 - - - -
35D ARG* 3.6 21.8 + - - +
55D LEU 3.2 2.4 + - - -
56D ILE 3.3 5.5 + - - -
57D LEU 3.1 4.4 + - - -
58D ALA* 1.3 81.2 - - - +
60D VAL* 1.3 69.3 + - - +
103D ASN* 4.3 1.3 - - - -
106D VAL* 4.5 0.4 - - - -
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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