Contacts of the helix formed by residues 32 - 43 (chain D) in PDB entry 1KN0
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 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B CYS* 4.2 2.2 - - - -
203C ALA 4.5 0.9 + - - -
207C SER* 3.4 32.9 + - - +
30D GLN 4.5 4.9 - - - +
31D TYR* 1.3 75.6 - - - +
33D ALA* 1.3 67.4 + - - +
34D GLU* 3.6 20.0 + - - +
35D GLU* 3.3 23.3 + - - +
36D TYR* 2.8 21.1 + - - +
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Residues in contact with ALA 33 (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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205B TYR* 3.2 38.4 - - + +
208B CYS* 3.4 40.7 - - + +
32D THR* 1.3 71.7 - - - +
34D GLU* 1.3 71.4 + - - +
36D TYR* 3.7 0.5 - - - +
37D GLN 2.9 20.8 + - - -
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Residues in contact with GLU 34 (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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205B TYR* 4.7 10.7 + - - +
203C ALA* 3.6 23.8 - - + +
206C ASN* 5.0 11.0 - - + +
32D THR* 3.6 17.5 + - - +
33D ALA* 1.3 88.3 + - - +
35D GLU* 1.3 63.5 + - - +
37D GLN* 3.9 4.8 + - - +
38D ALA* 3.2 23.7 + - - +
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Residues in contact with GLU 35 (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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81C TYR* 4.6 0.2 - - - -
200C VAL* 4.9 2.7 - - + +
203C ALA* 3.6 13.2 - - + +
204C ARG* 3.2 43.5 + - + +
207C SER* 3.8 12.8 + - - -
31D TYR* 3.6 26.2 - - + -
32D THR* 3.0 17.0 + - - +
34D GLU* 1.3 76.0 - - - +
36D TYR* 1.3 66.8 + - - +
38D ALA* 3.8 1.1 - - - +
39D ILE* 3.0 41.1 + - + +
79D PHE 4.5 1.4 - - - +
116D LYS* 3.2 24.7 + - - -
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Residues in contact with TYR 36 (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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201B GLU* 3.1 34.5 + - - -
204B ARG* 2.8 43.4 + - + -
205B TYR* 4.5 11.2 - + + -
208B CYS* 4.2 24.2 - - - -
80C GLY* 4.4 2.0 - - - -
81C TYR* 3.4 36.5 + + - -
82C ASN* 3.8 20.4 - - - +
31D TYR* 4.2 10.4 - - + +
32D THR 2.8 20.7 + - - +
33D ALA 3.7 4.5 - - - +
35D GLU* 1.3 72.8 - - - +
37D GLN* 1.3 62.1 + - - +
40D GLN* 2.8 50.4 + - + +
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Residues in contact with GLN 37 (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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201B GLU* 4.7 8.8 - - - +
205B TYR* 3.3 45.6 + - + +
33D ALA 2.9 16.1 + - - +
34D GLU* 3.9 6.4 + - - +
36D TYR* 1.3 84.6 - - - +
38D ALA* 1.3 62.0 + - - +
40D GLN* 3.2 4.2 + - - +
41D LYS* 3.0 56.7 + - + +
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Residues in contact with ALA 38 (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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199C SER* 3.9 20.9 - - - +
200C VAL* 3.8 30.5 - - + +
203C ALA* 4.6 0.4 - - + -
34D GLU 3.2 16.4 + - - +
35D GLU* 3.8 4.9 - - - +
37D GLN* 1.3 78.7 - - - +
39D ILE* 1.3 58.2 + - - +
41D LYS* 3.2 7.8 + - - +
42D ALA* 2.8 29.3 + - - +
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Residues in contact with ILE 39 (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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81C TYR* 3.4 26.2 - - + +
200C VAL* 3.6 15.0 - - + -
204C ARG* 4.1 0.4 - - - +
31D TYR* 3.7 20.2 - - + -
35D GLU* 3.0 38.2 + - + +
38D ALA* 1.3 72.8 - - - +
40D GLN* 1.3 66.4 + - - +
43D LEU* 2.9 35.1 + - + +
78D MET* 3.1 44.9 - - + +
79D PHE* 4.2 8.7 - - + -
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Residues in contact with GLN 40 (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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201B GLU* 3.5 22.4 + - - +
204B ARG* 4.0 2.2 - - - +
76C ASN* 3.0 26.2 + - - +
77C GLU* 3.9 14.1 + - - -
80C GLY* 3.7 2.8 - - - -
81C TYR* 3.1 29.9 + - - +
36D TYR* 2.8 52.2 + - + +
37D GLN* 3.5 6.3 - - - +
39D ILE* 1.3 73.0 - - - +
41D LYS* 1.3 62.5 + - + +
43D LEU* 3.9 6.9 + - - +
44D ARG* 3.9 24.9 + - - +
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Residues in contact with LYS 41 (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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201B GLU* 5.3 9.5 + - - +
37D GLN* 3.0 50.2 + - + +
38D ALA* 3.6 4.9 - - - +
40D GLN* 1.3 74.4 - - + +
42D ALA* 1.3 67.5 + - - +
44D ARG* 3.1 47.3 + - - +
45D GLN* 3.9 4.0 + - - +
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Residues in contact with ALA 42 (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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197C GLU* 3.5 24.7 - - - +
200C VAL* 4.0 4.7 - - + -
38D ALA 2.8 19.7 + - - +
39D ILE 3.3 2.2 + - - +
41D LYS* 1.3 73.5 - - - +
43D LEU* 1.3 63.9 + - - +
44D ARG 2.9 1.9 + - - -
45D GLN* 3.0 34.2 + - - +
78D MET* 3.5 23.1 - - + -
161D ALA* 3.5 4.7 - - - +
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Residues in contact with LEU 43 (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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81C TYR* 3.4 27.6 - - + -
39D ILE* 2.9 34.5 + - + +
40D GLN* 4.1 5.2 - - - +
42D ALA* 1.3 73.2 - - - +
44D ARG* 1.3 56.0 + - - +
45D GLN 3.3 0.4 - - - -
78D MET* 3.6 22.7 - - + -
79D PHE* 4.6 3.1 - - + -
158D PHE* 3.4 30.7 - - + +
159D GLY* 4.4 2.9 - - - -
160D ASN 2.9 12.6 + - - -
161D ALA* 2.8 32.1 + - + -
162D LEU* 3.8 32.1 - - + -
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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