Contacts of the helix formed by residues 45 - 59 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C GLY* 3.5 5.3 + - - -
44C LEU* 1.3 79.4 - - - +
46C GLY* 1.3 71.0 + - - +
47C LEU 3.3 2.7 - - - +
48C GLY 3.1 2.0 + - - +
49C ALA* 2.8 21.3 + - - +
67C ASP* 5.0 1.2 + - - -
69C GLU* 3.3 11.8 + - - -
75C ASP* 6.5 0.2 - - - -
79C GLN* 4.2 10.1 - - - -
91C ARG* 2.9 45.1 - - - +
132C THR* 5.1 0.6 - - + +
133C CYS* 3.8 34.2 - - - +
298C GLU* 3.2 26.5 - - - +
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Residues in contact with GLY 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LYS* 1.3 78.4 - - - +
47C LEU* 1.3 60.4 + - - +
49C ALA* 3.5 5.1 + - - +
50C GLU* 3.4 24.8 + - - +
78C ALA 5.4 6.7 - - - -
79C GLN* 4.5 5.3 - - - +
80C PHE* 5.4 0.5 - - - -
298C GLU* 3.0 17.4 + - - -
303C CYS* 3.5 16.7 - - - +
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C LYS* 3.3 1.4 - - - +
46C GLY* 1.3 72.4 - - - +
48C GLY* 1.3 66.2 + - - +
50C GLU* 3.3 2.6 + - - +
51C ILE* 3.1 34.3 + - + +
132C THR* 3.7 12.1 - - + +
133C CYS* 6.3 0.9 - - - -
156C GLY* 3.6 10.8 - - - +
157C ASP* 3.5 42.4 - - - +
158C VAL* 4.7 8.3 - - + +
298C GLU* 4.5 3.2 + - - +
303C CYS* 3.5 19.5 - - - +
306C VAL* 3.7 16.2 - - + +
307C GLY* 3.2 39.9 - - - +
310C LEU* 4.8 0.9 - - + -
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Residues in contact with GLY 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 3.2 16.0 - - - +
43C GLY 3.3 24.1 + - - -
44C LEU* 3.9 7.0 - - - -
45C LYS 3.1 5.6 + - - +
47C LEU* 1.3 78.4 - - - +
49C ALA* 1.3 57.1 + - - +
51C ILE* 3.3 7.6 + - - -
52C ALA* 2.9 26.2 + - - +
132C THR* 4.2 8.2 + - - +
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Residues in contact with ALA 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LEU* 3.9 5.6 - - - +
45C LYS 2.8 21.6 + - - +
46C GLY* 3.7 5.6 - - - +
48C GLY* 1.3 73.6 - - - +
50C GLU* 1.3 60.7 + - - +
52C ALA* 3.6 1.9 - - - +
53C LYS* 3.1 24.3 + - - +
79C GLN* 3.5 32.3 - - + +
80C PHE* 3.7 19.9 - - + -
81C LEU* 3.8 13.1 - - + +
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Residues in contact with GLU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C GLY 3.4 15.0 + - - +
47C LEU 3.3 7.8 + - - +
48C GLY 3.2 0.6 - - - -
49C ALA* 1.3 75.1 - - - +
51C ILE* 1.3 59.6 + - - +
53C LYS* 3.4 25.9 + - - +
54C ASN* 2.9 37.0 + - - +
80C PHE* 3.3 19.7 - - + -
300C ALA 5.3 1.1 - - - +
303C CYS* 3.7 28.3 - - + +
304C ALA* 3.6 18.9 - - - +
307C GLY* 4.2 6.1 - - - -
31D GLU* 4.2 0.5 - - - +
34D LYS* 3.1 26.6 + - - +
35D ASN* 4.6 0.9 - - - +
38D LEU* 5.2 3.5 - - - +
392D ALA* 4.8 2.1 - - - +
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Residues in contact with ILE 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 4.2 15.5 - - + -
47C LEU* 3.1 37.3 + - + +
48C GLY* 3.3 5.8 + - - +
50C GLU* 1.3 73.2 - - - +
52C ALA* 1.3 66.7 + - - +
54C ASN* 3.3 5.9 + - - +
55C LEU* 2.9 47.9 + - + +
130C CYS* 4.2 6.1 - - - -
132C THR* 4.2 9.6 - - - +
307C GLY* 3.9 19.7 - - - +
310C LEU* 3.8 26.0 - - + -
311C ALA* 4.4 4.7 - - + -
314C ILE* 4.4 13.7 - - + -
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Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 3.7 13.9 - - + +
44C LEU* 4.4 0.9 - - + -
48C GLY 2.9 18.1 + - - +
49C ALA 3.6 5.2 - - - +
51C ILE* 1.3 78.0 - - - +
53C LYS* 1.3 58.0 + - - +
55C LEU* 3.7 1.4 - - - +
56C ILE* 2.8 40.5 + - + +
63C LEU* 3.8 21.5 - - + -
65C MET* 4.1 14.6 - - - -
81C LEU* 4.4 8.1 - - + -
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Residues in contact with LYS 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ALA 3.1 14.5 + - - +
50C GLU* 3.5 21.4 + - - +
52C ALA* 1.3 79.2 - - - +
54C ASN* 1.3 76.0 + - - +
56C ILE* 3.4 1.2 + - - +
57C LEU* 3.0 57.2 + - + +
80C PHE* 3.9 22.7 - - + -
81C LEU* 5.0 1.0 - - + +
102C LEU* 3.7 28.4 - - + +
31D GLU* 2.5 37.3 + - - +
34D LYS* 4.4 5.2 - - - +
61D PHE* 4.2 12.1 - - + -
392D ALA* 4.0 2.4 - - - +
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Residues in contact with ASN 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C GLU* 2.9 24.5 + - - +
51C ILE 3.9 0.2 - - - +
53C LYS* 1.3 102.6 + - - +
55C LEU* 1.3 58.5 + - - +
57C LEU* 3.5 5.0 + - - +
58C ALA* 3.0 27.5 + - - +
307C GLY 3.2 30.7 + - - -
308C GLY* 3.7 7.9 - - - -
311C ALA* 3.4 18.6 - - + +
315C VAL* 5.3 0.7 - - - +
388D ALA* 4.2 12.9 - - - +
389D THR* 3.9 16.6 - - + +
392D ALA* 4.2 8.6 - - - +
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C VAL* 3.9 30.3 - - + -
41C LEU* 5.7 0.7 - - + -
51C ILE* 2.9 40.0 + - + +
52C ALA* 3.8 2.9 - - - +
54C ASN* 1.3 74.7 - - - +
56C ILE* 1.3 66.4 + - + +
58C ALA* 3.4 2.9 + - - +
59C GLY 3.3 15.9 + - - -
60C VAL* 3.6 29.6 + - + +
63C LEU* 4.3 13.2 - - + -
130C CYS* 6.0 0.4 - - + -
311C ALA* 3.9 12.6 - - + +
314C ILE* 3.9 24.5 - - + -
315C VAL* 3.7 26.9 - - + -
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Residues in contact with ILE 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ALA* 2.8 27.4 + - + +
53C LYS* 3.9 4.7 - - - +
55C LEU* 1.3 76.5 - - - +
57C LEU* 1.3 61.4 + - - +
59C GLY 3.4 4.2 + - - -
60C VAL* 5.0 0.2 - - - -
63C LEU* 3.7 26.7 - - + -
99C ALA* 3.6 46.9 - - + +
102C LEU* 4.0 8.5 - - + -
103C ASN* 2.9 45.7 + - + +
106C VAL* 3.5 23.0 - - + +
108C VAL* 4.1 13.0 - - + -
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Residues in contact with LEU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C TYR* 3.7 14.7 - - - -
22C GLN* 4.3 1.0 - - - +
53C LYS* 3.0 46.5 + - + +
54C ASN 3.9 3.8 - - - +
56C ILE* 1.3 78.7 - - - +
58C ALA* 1.3 61.1 + - - +
59C GLY 3.3 0.5 + - - -
102C LEU* 3.8 24.2 - - + +
103C ASN* 4.0 3.9 + - + +
31D GLU* 5.2 1.3 - - - +
57D LEU 3.6 23.7 - - - +
58D ASN* 3.6 25.1 - - - +
59D ARG* 4.5 6.3 - - - +
61D PHE* 3.9 25.4 - - + +
388D ALA* 4.0 21.3 - - + -
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Residues in contact with ALA 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C TYR* 3.7 1.3 - - - -
22C GLN* 2.8 31.6 + - - +
26C TRP* 4.9 4.9 - - + -
31C GLN* 3.0 9.7 - - - +
34C LEU* 3.6 19.1 - - + +
54C ASN 3.0 17.5 + - - +
55C LEU 3.8 5.4 - - - +
56C ILE 3.3 0.4 - - - -
57C LEU* 1.3 78.6 - - - +
59C GLY* 1.3 59.6 + - - +
60C VAL* 5.1 0.7 - - + +
315C VAL* 4.0 20.6 - - + -
388D ALA* 5.8 1.1 - - + +
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Residues in contact with GLY 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C TYR* 3.3 25.6 + - - -
31C GLN* 4.3 3.8 - - - +
34C LEU* 3.7 3.0 - - - +
35C ARG* 3.4 23.6 + - - +
55C LEU 3.3 3.4 + - - -
56C ILE 3.4 7.4 + - - -
57C LEU 3.2 4.0 - - - -
58C ALA* 1.3 81.8 - - - +
60C VAL* 1.3 69.1 + - - +
103C ASN* 4.1 1.3 - - - -
106C VAL* 4.2 1.1 - - - -
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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