Contacts of the helix formed by residues 47 - 58 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D ARG* 4.0 24.2 - - + +
38E CYS 5.6 4.5 - - - +
40E LYS 4.4 7.0 - - - +
41E THR* 4.0 10.3 - - - +
45E GLY 3.6 11.7 - - - +
46E TRP* 1.3 78.7 - - - +
48E LEU* 1.3 64.0 + - - +
49E ASP* 3.7 8.0 + - - +
50E GLN* 3.1 34.7 + - - +
51E CYS* 3.1 24.3 + - - -
80E PHE* 3.7 9.2 - - - -
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Residues in contact with LEU 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E LEU* 4.8 3.4 - - + -
34E TYR* 3.7 40.2 - - + +
37E LEU* 3.9 31.9 - - + +
38E CYS* 4.1 14.2 + - - +
40E LYS 4.8 1.2 + - - -
47E THR* 1.3 73.3 - - - +
49E ASP* 1.3 65.7 + - - +
51E CYS* 3.0 19.0 + - + +
52E ILE* 3.1 19.3 + - + +
69E MET* 5.8 0.2 - - + -
80E PHE* 3.5 35.6 - - + -
83E LEU* 3.9 28.0 - - + -
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Residues in contact with ASP 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A THR* 5.9 3.5 - - - +
143A ARG* 3.5 22.1 + - - +
14E GLU* 5.2 6.2 - - - +
34E TYR* 2.7 35.6 + - - -
38E CYS* 6.0 1.0 - - - +
47E THR* 3.3 7.7 + - - +
48E LEU* 1.3 79.1 - - - +
50E GLN* 1.3 63.6 + - + +
52E ILE* 3.5 8.2 + - - +
53E GLN* 3.0 31.4 + - - +
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Residues in contact with GLN 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ARG* 3.9 11.3 + - - +
45E GLY 3.6 10.9 - - - +
46E TRP* 3.4 49.4 - - + -
47E THR* 3.1 38.3 + - - +
48E LEU 3.1 0.8 - - - -
49E ASP* 1.3 80.3 - - + +
51E CYS* 1.3 63.2 - - - +
53E GLN* 3.8 13.0 + - - +
54E THR 5.2 0.2 + - - -
70E VAL* 4.5 3.8 - - - +
200E ALA* 6.0 1.9 - - - -
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Residues in contact with CYS 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E TRP* 3.3 28.2 - - - +
47E THR 3.1 14.8 + - - -
48E LEU* 3.0 13.1 + - + +
50E GLN* 1.3 79.4 - - - +
52E ILE* 1.3 65.8 + - + +
53E GLN 3.7 0.2 + - - -
54E THR* 4.5 2.3 + - - +
69E MET* 3.3 6.2 - - + -
70E VAL* 3.1 40.1 + - - +
76E THR* 3.7 20.4 - - - -
80E PHE* 4.0 10.3 - - - -
84E PHE* 3.8 15.5 - - + -
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Residues in contact with ILE 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ARG* 4.4 2.5 - - - +
16E PRO* 4.4 7.2 - - + -
25E MET* 3.6 28.9 - - + -
29E LEU* 4.2 22.2 - - + -
34E TYR* 4.4 8.7 - - + -
48E LEU* 3.1 22.0 + - + +
49E ASP* 3.7 19.7 - - - +
51E CYS* 1.3 77.8 - - + +
53E GLN* 1.3 67.1 + - - +
54E THR 3.2 2.7 - - - -
55E GLY* 2.8 14.8 + - - -
56E VAL* 3.1 27.2 + - + +
68E GLY 4.0 5.6 - - - -
69E MET* 4.2 2.5 - - + -
83E LEU* 3.9 20.0 - - + -
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Residues in contact with GLN 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ARG* 4.0 9.6 + - - +
204A ARG* 3.9 22.7 + - + +
205A ASP* 3.0 28.7 + - - +
49E ASP* 3.0 20.0 + - - +
50E GLN* 3.8 10.3 + - - +
51E CYS 3.5 2.4 - - - -
52E ILE* 1.3 75.9 - - - +
54E THR* 1.3 64.2 + - - +
56E VAL* 3.0 6.5 + - - +
57E ASP* 2.8 54.5 + - - +
199E ALA 4.1 15.7 - - - +
200E ALA* 5.9 0.7 - - - -
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Residues in contact with THR 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E GLN 5.2 0.6 + - - -
51E CYS 4.5 2.9 + - - +
53E GLN* 1.3 78.1 - - - +
55E GLY* 1.3 60.8 + - - +
58E ASN* 2.8 45.4 + - - +
68E GLY* 3.8 20.9 - - - +
69E MET* 3.9 10.3 - - - +
70E VAL* 4.4 16.6 - - + -
196E LEU* 2.7 30.5 + - - +
199E ALA* 4.0 12.4 + - - +
200E ALA* 4.0 15.1 - - + +
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Residues in contact with GLY 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E HIS* 3.1 23.0 - - - -
23E ASN* 3.1 10.9 + - - -
25E MET* 3.5 11.5 - - - +
52E ILE 2.8 5.9 + - - -
54E THR* 1.3 81.2 - - - +
56E VAL* 1.3 60.7 + - - +
58E ASN 3.5 4.5 - - - +
68E GLY* 3.0 31.4 + - - -
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Residues in contact with VAL 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ARG* 3.7 20.4 - - - +
205A ASP* 3.4 34.4 - - + +
206A TRP 4.8 5.4 - - - +
208A ASP* 6.4 0.2 - - + -
16E PRO* 3.9 26.0 - - + -
17E ASP 5.4 2.9 - - - +
18E LEU* 4.3 4.7 - - + -
21E HIS* 2.8 28.5 + - + +
25E MET* 4.2 8.1 - - + -
52E ILE* 3.1 21.5 + - + +
53E GLN* 3.0 7.3 + - - +
55E GLY* 1.3 76.4 - - - +
57E ASP* 1.3 63.5 + - - +
59E PRO* 4.5 1.6 - - - +
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Residues in contact with ASP 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LYS* 3.6 23.2 + - - +
203A ALA 4.2 5.8 - - - +
204A ARG* 3.5 18.1 - - - +
205A ASP* 2.5 33.8 + - - +
206A TRP* 4.7 8.5 + - + +
53E GLN* 2.8 31.1 + - - +
54E THR 4.0 3.8 - - - +
56E VAL* 1.3 77.7 - - - +
58E ASN* 1.3 59.8 + - - +
59E PRO* 3.4 9.0 - - - +
199E ALA* 3.8 25.5 - - + +
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Residues in contact with ASN 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LYS* 4.7 4.9 + - - -
23E ASN* 3.4 15.8 + - - -
54E THR* 2.8 40.5 + - - +
55E GLY* 3.5 5.3 - - - +
56E VAL 3.3 0.2 - - - -
57E ASP* 1.3 83.1 - - - +
59E PRO* 1.3 68.5 - - - +
60E GLY* 3.2 5.9 + - - +
66E THR* 4.7 4.0 + - - +
195E PRO* 3.3 36.6 + - - +
196E LEU* 3.3 27.8 - - + +
199E ALA* 4.0 5.5 - - - +
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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