Contacts of the helix formed by residues 47 - 58 (chain D) in PDB entry 1QK1
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 47 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D CYS 5.6 4.3 - - - +
40D LYS 4.4 6.7 - - - +
41D THR* 3.9 5.2 - - - +
45D GLY 3.6 6.1 - - - +
46D TRP* 1.3 79.4 - - - +
48D LEU* 1.3 64.6 + - - +
49D ASP* 3.7 8.3 + - - +
50D GLN* 3.0 33.9 + - - +
51D CYS* 3.1 23.6 + - - -
80D PHE* 3.8 9.4 - - - -
5E ARG* 3.5 36.6 - - + +
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Residues in contact with LEU 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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29D LEU* 4.9 3.4 - - + -
34D TYR* 3.7 40.4 - - + +
37D LEU* 3.8 31.0 - - + +
38D CYS* 4.0 14.5 + - - +
40D LYS 4.8 1.2 + - - -
47D THR* 1.3 72.6 - - - +
49D ASP* 1.3 65.1 + - - +
51D CYS* 3.0 19.8 + - + +
52D ILE* 3.1 19.7 + - + +
80D PHE* 3.5 35.1 - - + -
83D LEU* 4.0 27.8 - - + -
84D PHE* 6.1 0.2 - - + -
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Residues in contact with ASP 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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14D GLU* 5.2 5.9 - - - +
34D TYR* 2.7 35.4 + - - -
38D CYS* 6.0 1.2 - - - +
47D THR* 3.3 8.1 + - - +
48D LEU* 1.3 79.1 - - - +
50D GLN* 1.3 64.7 + - + +
52D ILE* 3.4 7.2 + - - +
53D GLN* 3.0 31.4 + - - +
142H THR* 6.0 2.3 - - - +
143H ARG* 3.3 23.1 + - - +
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Residues in contact with GLN 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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45D GLY 3.6 10.9 - - - +
46D TRP* 3.4 49.5 - - + -
47D THR* 3.0 39.4 + - - +
49D ASP* 1.3 77.6 - - + +
51D CYS* 1.3 66.6 + - - +
53D GLN* 3.8 13.3 + - - +
54D THR 5.2 0.5 + - - -
70D VAL* 4.5 3.8 - - - +
200D ALA* 6.0 1.4 - - - -
5E ARG* 4.6 7.5 + - - +
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Residues in contact with CYS 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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46D TRP* 3.3 29.8 - - - +
47D THR 3.1 13.9 + - - -
48D LEU* 3.0 12.4 + - + +
50D GLN* 1.3 78.8 - - - +
52D ILE* 1.3 65.7 + - + +
53D GLN 3.7 0.2 + - - -
54D THR* 4.4 2.3 + - - +
69D MET* 3.3 6.2 - - + -
70D VAL* 3.1 39.8 + - - +
76D THR* 3.8 19.1 - - - -
80D PHE* 4.0 11.0 - - - -
84D PHE* 3.8 15.0 - - + -
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Residues in contact with ILE 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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16D PRO* 4.3 7.0 - - + -
25D MET* 3.6 28.7 - - + -
29D LEU* 4.2 22.9 - - + -
34D TYR* 4.4 8.5 - - + -
48D LEU* 3.1 20.4 + - + +
49D ASP* 3.6 19.7 - - - +
51D CYS* 1.3 80.2 - - + +
53D GLN* 1.3 67.4 + - - +
54D THR 3.3 2.7 - - - -
55D GLY* 2.8 14.3 + - - -
56D VAL* 3.1 25.3 + - + +
68D GLY 4.0 6.7 - - - -
69D MET* 4.5 2.2 - - + -
83D LEU* 4.0 20.4 - - + -
143H ARG* 4.4 3.1 - - - +
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Residues in contact with GLN 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 ASP* 3.0 19.1 + - - +
50D GLN* 4.1 10.8 - - - +
51D CYS 3.5 1.8 - - - -
52D ILE* 1.3 76.3 - - - +
54D THR* 1.3 64.7 + - - +
56D VAL* 3.0 6.6 + - - +
57D ASP* 2.8 55.9 + - - +
199D ALA 4.2 14.1 - - - +
200D ALA* 5.9 0.7 - - - -
143H ARG* 4.1 10.2 + - - +
204H ARG* 3.9 22.1 + - + +
205H ASP* 3.1 28.6 + - - +
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Residues in contact with THR 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 GLN 5.2 0.2 + - - -
51D CYS 4.4 2.9 + - - +
53D GLN* 1.3 78.1 - - - +
55D GLY* 1.3 60.4 + - - +
57D ASP* 3.4 0.4 + - - -
58D ASN* 2.9 45.4 + - - +
68D GLY* 3.8 20.4 - - - +
69D MET* 3.9 10.5 - - - +
70D VAL* 4.3 17.5 - - + -
196D LEU* 2.7 31.5 + - - +
199D ALA* 4.0 12.3 + - - +
200D ALA* 4.0 14.7 - - + +
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Residues in contact with GLY 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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21D HIS* 3.1 22.7 - - - -
23D ASN* 3.1 12.2 + - - -
25D MET* 3.6 11.3 - - - +
52D ILE 2.8 6.7 + - - -
54D THR* 1.3 76.3 - - - +
56D VAL* 1.3 58.7 + - - +
58D ASN* 3.5 5.3 - - - +
68D GLY* 3.0 37.2 + - - -
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Residues in contact with VAL 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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16D PRO* 3.9 25.4 - - + -
17D ASP 5.4 2.9 - - - +
18D LEU* 4.3 4.7 - - + -
21D HIS* 2.9 27.6 + - + +
25D MET* 4.1 10.5 - - + -
52D ILE* 3.5 19.5 - - + +
53D GLN* 3.0 8.4 + - - +
55D GLY* 1.3 77.4 - - - +
57D ASP* 1.3 63.0 + - - +
59D PRO* 4.5 1.7 - - - +
143H ARG* 3.9 19.1 - - - +
205H ASP* 3.5 34.7 - - + +
206H TRP 4.7 6.4 - - - +
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Residues in contact with ASP 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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53D GLN* 2.8 36.0 + - - +
54D THR 3.9 3.8 - - - +
56D VAL* 1.3 76.6 - - - +
58D ASN* 1.3 65.0 - - - +
59D PRO* 3.4 8.4 - - - +
199D ALA* 3.8 19.9 - - + +
191H LYS* 3.5 25.4 + - - +
203H ALA 4.2 5.4 - - - +
204H ARG* 3.6 16.4 - - - +
205H ASP* 2.6 33.3 + - - +
206H TRP 4.8 7.7 - - - +
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Residues in contact with ASN 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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23D ASN* 3.3 16.3 + - - -
54D THR* 2.9 38.7 + - - +
55D GLY* 3.5 5.4 - - - +
56D VAL 3.3 0.2 - - - -
57D ASP* 1.3 84.1 - - - +
59D PRO* 1.3 67.0 - - - +
60D GLY* 3.4 3.6 + - - +
66D THR* 4.5 5.8 + - - +
195D PRO* 3.4 37.8 + - - +
196D LEU* 3.3 27.2 - - + +
199D ALA* 3.9 5.5 - - - +
191H LYS* 4.7 5.2 + - - -
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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