Contacts of the helix formed by residues 158 - 163 (chain C) 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 PHE 158 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B ASN* 3.8 13.8 + - - +
81B TYR* 3.7 23.2 - + + +
43C LEU* 3.2 29.2 - - + +
79C PHE* 4.2 6.1 - + + -
113C VAL* 3.9 29.6 - - + -
115C LEU* 3.3 43.3 - - + -
119C SER* 3.9 5.6 - - - -
120C TYR* 4.8 3.6 - - - -
121C HIS* 3.5 34.1 - + - -
154C ALA 4.4 2.7 - - - -
155C LEU* 2.9 30.7 + - + +
157C SER* 1.3 78.1 - - - +
159C GLY* 1.3 57.3 + - - +
162C LEU* 3.7 15.7 - - + -
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Residues in contact with GLY 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ASN* 4.3 4.3 - - - -
76B ASN* 3.8 11.4 - - - +
43C LEU* 3.7 8.7 - - - -
156C ARG 3.0 8.8 + - - +
157C SER 3.2 2.2 + - - -
158C PHE* 1.3 81.4 - - - +
160C ASN* 1.3 67.2 + - - -
161C ALA 3.3 2.5 - - - -
162C LEU* 3.0 13.1 + - - -
163C GLY 3.6 0.3 + - - -
164C ASN* 3.3 19.3 + - - -
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Residues in contact with ASN 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B HIS* 5.9 0.2 - - - -
73B ASN* 3.0 34.9 + - - +
43C LEU 3.1 3.6 + - - -
44C ARG* 3.0 24.9 + - - +
45C GLN 3.2 16.2 - - - +
46C ARG* 4.4 14.5 + - - +
47C LEU* 3.0 12.7 - - - +
159C GLY* 1.3 71.0 - - - -
161C ALA* 1.3 59.1 + - - +
163C GLY 2.8 18.7 + - - -
164C ASN* 3.6 12.4 + - - +
165C CYS* 3.5 26.9 + - + +
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Residues in contact with ALA 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B LYS* 4.6 10.8 - - + -
42C ALA 3.4 19.3 - - - +
43C LEU* 2.8 34.0 + - + +
45C GLN* 3.0 14.6 + - + +
47C LEU* 3.7 11.5 - - - +
74C LEU* 3.3 27.0 - - - +
78C MET* 5.0 7.0 - - + -
160C ASN* 1.3 70.9 - - - +
162C LEU* 1.3 60.6 + - + +
163C GLY 3.5 0.7 - - - -
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Residues in contact with LEU 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU* 3.8 11.4 - - + -
47C LEU* 4.9 0.2 - - - -
66C ILE* 5.0 2.9 - - - -
71C VAL* 4.4 21.9 - - + +
74C LEU* 3.8 33.4 - - + +
75C ALA* 3.8 19.1 - - + +
78C MET* 4.8 4.5 - - + -
79C PHE* 3.6 29.8 - - + -
152C LYS 4.5 0.7 - - - +
155C LEU* 3.5 22.9 - - + +
156C ARG* 3.7 16.4 + - - +
158C PHE* 3.7 24.9 - - + -
159C GLY 3.0 7.1 + - - +
160C ASN 2.9 1.2 - - - -
161C ALA* 1.3 78.7 - - - +
163C GLY* 1.3 57.9 + - - +
164C ASN 3.8 2.0 - - - -
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Residues in contact with GLY 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C LEU* 3.9 4.8 - - - +
66C ILE* 3.8 23.8 - - - -
156C ARG* 3.7 11.2 - - - -
160C ASN 2.8 8.4 + - - -
161C ALA 3.5 1.2 - - - -
162C LEU* 1.3 79.6 - - - +
164C ASN* 1.3 57.9 + - - +
165C CYS 3.0 6.3 + - - -
166C ILE* 2.9 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