Contacts of the helix formed by residues 45 - 59 (chain A) in PDB entry 1Y8Q
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A GLY 3.3 5.4 + - - -
44A LEU* 1.3 78.8 - - - +
46A GLY* 1.3 62.0 + - - +
47A LEU 3.5 1.8 - - - +
48A GLY 4.0 1.3 - - - +
49A ALA* 2.8 29.2 + - - +
67A ASP* 4.6 4.7 - - - +
69A GLU* 4.4 10.3 + - - +
75A ASP* 5.8 3.1 - - - +
79A GLN* 4.5 7.4 - - - -
91A ARG* 3.6 36.3 - - - +
132A THR* 5.4 0.9 - - + -
133A CYS* 3.2 33.5 - - + +
256A ASP* 4.8 10.1 + - - -
298A GLU* 3.6 26.0 + - - +
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Residues in contact with GLY 46 (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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45A LYS* 1.3 79.2 - - - +
47A LEU* 1.3 64.2 + - - +
49A ALA* 3.2 12.2 + - - +
50A GLU* 3.3 15.2 + - - +
78A ALA 5.6 4.9 - - - -
79A GLN* 4.8 4.5 - - - +
298A GLU* 3.3 15.9 + - - -
303A CYS* 3.8 15.9 - - - +
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Residues in contact with LEU 47 (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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45A LYS* 3.5 1.0 - - - +
46A GLY* 1.3 72.2 - - - +
48A GLY* 1.3 64.0 + - - +
50A GLU* 3.1 13.2 + - - +
51A ILE* 3.1 26.4 + - + +
132A THR* 4.0 15.3 - - + +
156A GLY* 3.4 37.9 - - - +
157A ASP* 3.5 14.4 - - - +
158A VAL* 4.2 13.7 - - + +
298A GLU* 4.6 4.1 + - - +
303A CYS* 3.7 17.0 - - - +
306A VAL* 3.8 16.2 - - + -
307A GLY* 3.4 38.1 - - - +
310A LEU* 4.7 0.7 - - + -
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Residues in contact with GLY 48 (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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41A LEU* 3.2 20.6 - - - +
43A GLY 3.3 24.2 + - - -
44A LEU* 3.9 6.3 - - - -
45A LYS 3.3 4.5 + - - -
46A GLY 3.3 0.8 - - - -
47A LEU* 1.3 78.5 - - - +
49A ALA* 1.3 56.8 + - - +
51A ILE* 3.5 1.1 + - - -
52A ALA* 2.9 25.3 + - - +
132A THR* 4.3 10.8 - - - +
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Residues in contact with ALA 49 (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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44A LEU* 3.9 3.5 - - - +
45A LYS 2.8 21.7 + - - +
46A GLY* 3.4 6.7 - - - +
48A GLY* 1.3 74.9 - - - +
50A GLU* 1.3 60.8 + - - +
52A ALA* 3.4 2.8 + - - +
53A LYS* 3.1 23.0 + - - +
79A GLN* 3.6 32.3 - - + +
80A PHE* 3.9 13.4 - - + -
81A LEU* 3.8 17.7 - - + +
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Residues in contact with GLU 50 (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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46A GLY 3.3 10.3 + - - +
47A LEU 3.1 7.4 + - - +
49A ALA* 1.3 74.4 - - - +
51A ILE* 1.3 60.7 + - - +
53A LYS* 2.6 38.9 + - - +
54A ASN* 2.8 37.8 + - - +
80A PHE* 4.2 8.4 - - + -
300A ALA 4.7 2.4 - - - +
303A CYS* 3.5 30.6 - - + +
304A ALA* 3.8 15.8 + - - +
307A GLY* 4.2 6.7 - - - -
31B GLU* 4.0 0.3 - - - +
34B LYS* 2.5 33.1 + - - +
35B ASN* 4.0 1.6 - - - +
38B LEU* 5.4 1.6 - - - +
392B ALA* 4.8 1.4 - - - +
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Residues in contact with ILE 51 (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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41A LEU* 4.1 17.0 - - + -
47A LEU* 3.1 29.1 + - + +
48A GLY 3.8 5.4 - - - +
50A GLU* 1.3 76.2 - - - +
52A ALA* 1.3 62.1 + - - +
54A ASN* 3.8 6.6 - - - +
55A LEU* 2.9 46.6 + - + +
130A CYS* 3.9 9.2 - - - -
132A THR* 4.3 6.3 - - - +
307A GLY* 3.9 20.0 - - - +
310A LEU* 3.6 32.3 - - + -
311A ALA* 4.4 5.4 - - + -
314A ILE* 4.3 13.9 - - + -
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Residues in contact with ALA 52 (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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41A LEU* 3.7 13.4 - - + +
44A LEU* 4.2 4.0 - - + -
48A GLY 2.9 18.8 + - - +
49A ALA 3.5 6.1 - - - +
50A GLU 3.2 0.2 - - - -
51A ILE* 1.3 77.8 - - - +
53A LYS* 1.3 62.6 + - - +
55A LEU* 5.0 0.4 - - - -
56A ILE* 3.0 34.5 + - + +
63A LEU* 3.9 19.9 - - + +
65A MET* 4.2 16.2 - - - -
81A LEU* 4.3 6.1 - - + -
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Residues in contact with LYS 53 (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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49A ALA 3.1 13.1 + - - +
50A GLU* 2.6 37.3 + - - +
52A ALA* 1.3 76.8 - - - +
54A ASN* 1.3 80.4 + - - +
56A ILE* 4.0 0.3 - - - +
57A LEU* 2.9 48.4 + - + +
80A PHE* 3.9 16.4 - - + -
81A LEU* 5.2 1.1 - - + +
102A LEU* 3.7 27.8 - - + -
31B GLU* 2.8 36.8 + - - +
34B LYS* 3.8 1.8 - - - +
61B PHE* 3.9 22.2 - - + -
392B ALA* 4.2 2.8 - - - +
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Residues in contact with ASN 54 (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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50A GLU* 2.8 27.5 + - - +
51A ILE 3.8 0.4 - - - +
53A LYS* 1.3 96.8 + - - +
55A LEU* 1.3 59.2 + - - +
57A LEU* 3.8 4.1 - - - +
58A ALA* 2.8 29.2 + - - +
307A GLY 3.2 30.3 + - - -
308A GLY* 3.8 7.5 - - - +
311A ALA* 3.5 17.9 - - + -
315A VAL* 6.0 0.4 - - - -
388B ALA* 3.9 19.6 - - + +
389B THR* 4.2 14.0 + - - -
392B ALA* 4.2 6.2 - - - +
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Residues in contact with LEU 55 (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 VAL* 3.8 33.4 - - + -
41A LEU* 5.8 0.9 - - + -
51A ILE* 2.9 37.6 + - + +
52A ALA 4.1 2.2 - - - +
54A ASN* 1.3 75.9 - - - +
56A ILE* 1.3 62.7 + - - +
58A ALA* 3.2 6.8 + - - +
59A GLY 3.1 17.5 + - - -
60A VAL* 3.5 27.3 + - + +
63A LEU* 4.3 13.0 - - + -
130A CYS* 5.9 0.2 - - + -
311A ALA* 3.9 28.9 - - + +
314A ILE* 4.1 20.2 - - + -
315A VAL* 4.1 13.0 - - + -
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Residues in contact with ILE 56 (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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52A ALA* 3.0 29.9 + - + +
53A LYS 4.0 2.7 - - - +
55A LEU* 1.3 74.0 - - - +
57A LEU* 1.3 64.1 + - - +
59A GLY 3.2 4.5 + - - -
60A VAL* 4.8 0.4 - - - -
63A LEU* 3.6 24.2 - - + -
99A ALA* 3.4 44.0 - - + +
102A LEU* 3.9 9.4 - - + -
103A ASN* 2.8 44.9 + - + +
106A VAL* 3.5 19.9 - - + +
108A VAL* 3.6 21.3 - - + -
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Residues in contact with LEU 57 (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 GLN* 4.9 0.3 + - - -
19A TYR* 3.7 14.4 - - - -
53A LYS* 2.9 45.4 + - + +
54A ASN 3.8 3.1 - - - +
56A ILE* 1.3 78.1 - - - +
58A ALA* 1.3 63.4 + - - +
59A GLY 3.2 1.0 + - - -
102A LEU* 3.5 35.0 - - + +
103A ASN* 3.8 4.5 + - - +
31B GLU* 5.1 0.9 - - - +
57B LEU 3.6 19.5 - - - +
58B ASN* 3.6 26.4 - - - +
59B ARG* 4.4 7.2 - - - +
61B PHE* 3.8 20.2 - - + -
388B ALA* 4.0 21.8 - - + -
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Residues in contact with ALA 58 (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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19A TYR* 3.6 0.9 - - - -
22A GLN* 3.0 31.8 + - - +
26A TRP* 5.2 5.4 - - + -
31A GLN* 3.1 10.4 + - - -
34A LEU* 3.8 10.3 - - + +
54A ASN 2.8 18.6 + - - +
55A LEU* 3.3 11.9 - - - +
57A LEU* 1.3 77.5 - - - +
59A GLY* 1.3 59.0 + - - +
60A VAL* 4.9 1.6 - - + +
315A VAL* 4.0 23.6 - - + -
388B ALA* 5.7 1.1 - - - +
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Residues in contact with GLY 59 (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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19A TYR* 3.2 26.6 + - - -
31A GLN* 4.3 5.4 + - - -
34A LEU* 3.7 10.0 - - - +
35A ARG* 3.7 13.5 + - - +
55A LEU 3.1 4.2 + - - -
56A ILE 3.2 8.5 + - - -
57A LEU 3.1 3.8 - - - -
58A ALA* 1.3 81.4 - - - +
60A VAL* 1.3 69.9 + - - +
103A ASN* 3.9 1.6 - - - -
106A VAL* 4.0 1.8 - - - -
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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