Contacts of the helix formed by residues 157 - 163 (chain E) 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 SER 157 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72D ILE* 3.3 23.5 - - - +
76D ASN* 3.2 23.6 + - - +
84D TRP* 3.8 10.0 - - - -
86D HIS* 3.5 18.1 + - - -
151D LEU* 4.9 1.4 - - - +
121E HIS* 3.5 28.5 - - - -
123E ASP* 4.7 2.8 + - - -
153E ARG 4.0 6.6 + - - -
154E ALA* 3.0 16.2 + - - -
155E LEU 3.0 0.6 - - - -
156E ARG* 1.3 79.1 - - - +
158E PHE* 1.3 56.6 - - - +
159E GLY 3.3 0.4 - - - -
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Residues in contact with PHE 158 (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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76D ASN* 3.7 14.6 - - - +
81D TYR* 3.7 18.1 - - + +
43E LEU* 3.3 28.3 - - + +
79E PHE* 4.3 6.3 - + - -
113E VAL* 4.2 25.4 - - + -
115E LEU* 3.3 48.0 - - + -
119E SER* 4.1 4.7 - - - -
120E TYR* 4.8 9.4 - - - -
121E HIS* 3.2 34.1 - + + -
154E ALA 4.7 0.4 - - - -
155E LEU* 3.0 33.3 + - + +
157E SER* 1.3 78.3 - - - +
159E GLY* 1.3 54.7 + - - +
162E LEU* 3.7 15.9 - - + -
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Residues in contact with GLY 159 (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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73D ASN* 4.3 9.2 - - - -
76D ASN* 4.1 6.0 - - - +
43E LEU* 4.0 8.7 - - - +
155E LEU 4.2 0.2 + - - -
156E ARG 3.2 7.5 + - - +
157E SER 3.3 1.8 + - - -
158E PHE* 1.3 82.3 - - - +
160E ASN* 1.3 66.3 + - - -
161E ALA 3.3 2.9 - - - -
162E LEU* 3.3 10.0 + - - +
163E GLY 3.6 0.5 + - - -
164E ASN* 3.0 24.4 + - - +
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Residues in contact with ASN 160 (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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195C ASP* 5.6 0.8 + - - -
69D HIS* 5.8 0.7 - - - -
73D ASN* 3.2 36.6 + - - +
43E LEU 3.1 4.2 + - - -
44E ARG* 3.1 23.2 + - - +
45E GLN 3.2 16.6 - - - +
46E ARG* 4.4 16.3 + - - +
47E LEU* 2.9 13.4 - - - +
159E GLY* 1.3 67.6 - - - -
161E ALA* 1.3 55.8 + - - +
162E LEU 2.9 5.2 - - - -
163E GLY* 2.8 22.7 + - - -
164E ASN* 3.5 10.4 + - - +
165E CYS* 3.6 29.9 + - + +
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Residues in contact with ALA 161 (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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192D LYS* 4.8 9.6 - - + -
42E ALA 3.6 9.9 - - - +
43E LEU* 2.8 43.2 + - + +
45E GLN* 3.0 14.7 + - + +
47E LEU* 3.7 13.4 - - - +
74E LEU* 3.3 25.8 - - - +
78E MET* 5.0 7.1 - - + +
160E ASN* 1.3 70.2 - - - +
162E LEU* 1.3 60.2 + - + +
163E GLY 3.5 0.4 - - - -
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Residues in contact with LEU 162 (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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43E LEU* 3.7 17.5 - - + +
47E LEU* 4.9 0.4 - - - -
66E ILE* 5.0 1.6 - - - -
71E VAL* 4.3 26.1 - - + +
74E LEU* 3.7 35.4 - - + +
75E ALA* 3.8 17.5 - - + +
78E MET* 4.8 4.3 - - + -
79E PHE* 3.8 20.6 - - + -
152E LYS 4.7 0.7 - - - +
155E LEU* 3.4 26.0 - - + +
156E ARG* 3.9 13.5 + - - +
158E PHE* 3.7 26.5 - - + -
159E GLY 3.3 6.2 + - - +
160E ASN 2.9 1.2 - - - -
161E ALA* 1.3 78.4 - - - +
163E GLY* 1.3 58.4 + - - +
164E ASN 3.8 1.1 - - - -
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Residues in contact with GLY 163 (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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47E LEU* 4.0 3.4 - - - +
66E ILE* 3.9 22.2 - - - -
156E ARG* 3.5 13.4 - - - +
160E ASN 2.8 8.6 + - - -
161E ALA 3.5 1.0 - - - -
162E LEU* 1.3 81.0 - - - +
164E ASN* 1.3 63.8 + - - +
165E CYS* 3.1 3.8 + - - -
166E ILE* 3.0 26.4 - - - +
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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