Contacts of the helix formed by residues 32 - 43 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F CYS* 4.5 0.2 - - - -
203G ALA 4.4 0.3 + - - -
207G SER* 3.0 35.6 + - - +
30H GLN 4.4 4.9 - - - +
31H TYR* 1.3 75.4 - - - +
33H ALA* 1.3 65.8 + - - +
34H GLU* 3.4 21.8 + - - +
35H GLU* 3.4 21.2 + - - +
36H TYR* 2.8 21.5 + - - +
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Residues in contact with ALA 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205F TYR* 3.4 28.3 - - + +
208F CYS* 3.3 44.0 - - + +
32H THR* 1.3 72.4 - - - +
34H GLU* 1.3 71.0 + - - +
36H TYR* 3.8 1.4 - - - +
37H GLN* 3.0 26.5 + - - +
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Residues in contact with GLU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205F TYR* 4.7 7.4 - - - +
203G ALA* 3.4 25.6 - - + +
206G ASN* 4.7 14.0 - - + +
32H THR* 3.1 18.0 + - - +
33H ALA* 1.3 87.4 + - + +
35H GLU* 1.3 63.2 + - - +
37H GLN* 3.8 6.6 + - - +
38H ALA* 3.1 23.2 + - - +
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Residues in contact with GLU 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200G VAL* 4.9 2.7 - - + -
203G ALA* 3.3 15.6 - - + +
204G ARG* 3.1 41.1 + - + +
207G SER* 3.8 15.1 + - - -
31H TYR* 3.6 24.1 - - + -
32H THR* 3.1 16.6 + - - +
34H GLU* 1.3 76.9 - - - +
36H TYR* 1.3 66.4 + - - +
38H ALA* 3.4 1.8 + - - +
39H ILE* 3.0 39.7 + - + +
79H PHE 4.8 1.4 - - - +
116H LYS* 3.1 24.0 + - - -
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Residues in contact with TYR 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F GLU* 3.5 23.8 + - - -
204F ARG* 2.7 51.0 + - + -
205F TYR* 4.6 8.7 - + - -
208F CYS* 4.4 18.8 - - - -
80G GLY* 3.9 4.2 - - - -
81G TYR* 3.4 33.2 - + - -
82G ASN* 3.7 22.4 - - - -
31H TYR* 4.3 11.3 - - + +
32H THR 2.8 21.7 + - - +
33H ALA* 3.8 7.9 - - - +
35H GLU* 1.3 73.6 - - - +
37H GLN* 1.3 71.6 + - + +
40H GLN* 2.8 48.7 + - + +
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Residues in contact with GLN 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F GLU* 4.9 8.5 - - - +
205F TYR* 3.2 47.6 + - + +
33H ALA 3.0 11.9 + - - +
34H GLU* 3.8 5.5 + - - +
36H TYR* 1.3 88.9 - - - +
38H ALA* 1.3 62.8 + - - +
40H GLN* 3.2 3.1 + - + +
41H LYS* 3.0 56.4 + - + +
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Residues in contact with ALA 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199G SER* 3.9 18.5 - - - +
200G VAL* 3.5 35.7 - - + +
203G ALA* 4.5 2.2 - - + -
34H GLU 3.1 15.1 + - - +
35H GLU 3.8 3.6 - - - +
37H GLN* 1.3 79.4 - - - +
39H ILE* 1.3 63.4 + - - +
41H LYS* 3.2 7.0 + - - +
42H ALA* 2.9 23.9 + - - +
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Residues in contact with ILE 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G TYR* 3.4 33.7 - - + +
200G VAL* 3.3 23.1 - - + -
31H TYR* 3.8 8.7 - - + -
35H GLU* 3.0 41.3 + - + +
38H ALA* 1.3 78.4 - - - +
40H GLN* 1.3 62.5 + - - +
42H ALA 3.3 0.2 + - - -
43H LEU* 2.9 34.3 + - + +
78H MET* 3.1 42.2 - - + +
79H PHE* 4.2 8.7 - - + -
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Residues in contact with GLN 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F GLU* 3.5 24.5 + - - +
204F ARG* 3.9 2.4 - - - +
76G ASN* 3.1 25.4 + - - +
77G GLU* 4.0 3.9 + - - -
80G GLY* 3.6 3.8 - - - -
81G TYR* 3.3 28.6 + - - +
36H TYR* 2.8 51.5 + - + +
37H GLN* 3.5 6.5 - - - +
39H ILE* 1.3 73.5 - - - +
41H LYS* 1.3 64.5 + - + +
43H LEU* 3.9 7.4 + - - +
44H ARG* 3.9 33.5 + - - +
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Residues in contact with LYS 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F GLU* 5.6 6.3 + - - +
37H GLN* 3.0 46.3 + - + +
38H ALA* 3.6 8.3 - - - +
40H GLN* 1.3 75.9 - - + +
42H ALA* 1.3 67.8 + - - +
44H ARG* 2.8 47.7 + - - +
45H GLN* 3.9 3.1 + - - +
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Residues in contact with ALA 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197G GLU* 3.1 28.5 - - - +
200G VAL* 4.0 4.9 - - + -
38H ALA 2.9 17.1 + - - +
39H ILE 3.8 0.4 - - - +
41H LYS* 1.3 76.0 - - - +
43H LEU* 1.3 57.2 + - - +
44H ARG 2.9 5.9 + - - -
45H GLN* 2.9 35.3 + - - +
78H MET* 3.6 20.4 - - - -
161H ALA* 3.5 5.4 - - - +
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Residues in contact with LEU 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G TYR* 3.5 34.8 - - + -
39H ILE* 2.9 28.2 + - + +
40H GLN* 4.1 5.6 - - - +
41H LYS 3.2 0.2 - - - -
42H ALA* 1.3 75.7 - - - +
44H ARG* 1.3 57.4 + - + +
78H MET* 3.2 25.1 - - + -
79H PHE* 4.7 3.6 - - + -
158H PHE* 3.5 24.0 - - + +
159H GLY* 3.6 2.2 - - - +
160H ASN 3.0 12.8 + - - -
161H ALA* 2.9 29.7 + - + -
162H LEU* 3.8 34.8 - - + -
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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