Contacts of the helix formed by residues 157 - 163 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72E ILE* 3.2 23.6 - - - +
76E ASN* 3.1 25.3 + - - +
84E TRP* 3.8 8.6 - - - -
86E HIS* 3.5 17.8 + - - -
151E LEU* 5.1 1.4 - - - +
121F HIS* 3.4 28.1 - - - -
123F ASP* 4.7 2.6 + - - -
153F ARG 3.8 7.4 + - - -
154F ALA* 3.2 17.2 + - - -
156F ARG* 1.3 80.0 - - - +
158F PHE* 1.3 55.6 + - - +
159F GLY 3.3 0.2 - - - -
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Residues in contact with PHE 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E ASN* 3.5 13.8 - - - +
81E TYR* 3.7 18.0 - + - +
43F LEU* 3.2 28.7 - - + +
79F PHE* 4.2 6.7 - + - -
113F VAL* 3.9 31.9 - - + -
115F LEU* 3.4 42.0 - - + -
119F SER* 4.0 5.6 - - - -
120F TYR* 4.7 1.8 - - - -
121F HIS* 3.2 41.5 - + - -
154F ALA 4.7 0.4 - - - -
155F LEU* 2.9 33.7 + - + +
157F SER* 1.3 77.9 - - - +
159F GLY* 1.3 54.9 + - - +
162F LEU* 3.8 16.2 - - + -
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Residues in contact with GLY 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E ASN* 4.3 4.5 - - - -
76E ASN* 4.2 11.2 - - - -
43F LEU* 3.8 8.7 - - - +
155F LEU 4.2 0.2 + - - -
156F ARG 3.1 8.2 + - - +
157F SER 3.3 1.6 + - - -
158F PHE* 1.3 81.2 - - - +
160F ASN* 1.3 65.3 + - - -
161F ALA 3.4 2.7 - - - -
162F LEU* 3.3 10.4 + - - +
163F GLY 3.6 0.5 + - - -
164F ASN* 3.1 24.2 + - - +
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Residues in contact with ASN 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D ASP* 5.7 1.0 + - - -
69E HIS* 5.9 0.3 - - - -
73E ASN* 3.2 34.7 + - - +
43F LEU 3.1 4.2 + - - -
44F ARG* 3.1 22.8 + - - +
45F GLN 3.2 15.7 - - - +
46F ARG* 4.4 17.4 + - - +
47F LEU* 3.0 11.8 - - - +
159F GLY* 1.3 66.9 - - - -
161F ALA* 1.3 56.2 + - - +
162F LEU 2.9 4.7 - - - -
163F GLY 2.7 23.4 + - - -
164F ASN 3.4 9.1 + - - +
165F CYS* 3.5 30.7 + - + +
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Residues in contact with ALA 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E LYS* 4.8 9.4 - - + -
42F ALA 3.6 11.0 - - - +
43F LEU* 2.9 35.2 + - + +
45F GLN* 2.9 19.5 + - + +
47F LEU* 3.7 13.2 - - - +
74F LEU* 3.3 25.8 - - - +
78F MET* 5.0 8.0 - - + +
159F GLY 3.4 0.2 - - - -
160F ASN* 1.3 73.3 - - - +
162F LEU* 1.3 61.0 + - + +
163F GLY 3.4 0.4 - - - -
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Residues in contact with LEU 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F LEU* 3.8 11.0 - - + +
47F LEU* 4.8 0.4 - - - -
66F ILE* 5.1 1.1 - - - -
71F VAL* 4.3 20.9 - - + +
74F LEU* 3.7 36.6 - - + +
75F ALA* 3.8 17.9 - - + +
78F MET* 4.7 4.3 - - + -
79F PHE* 3.6 34.5 - - + -
152F LYS 4.8 0.7 - - - +
155F LEU* 3.5 27.6 - - + +
156F ARG* 4.0 13.7 + - - +
158F PHE* 3.8 20.9 - - + -
159F GLY 3.3 6.1 + - - +
160F ASN 2.8 2.8 + - - -
161F ALA* 1.3 77.5 - - - +
163F GLY* 1.3 58.1 + - - +
164F ASN 3.8 1.1 - - - -
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Residues in contact with GLY 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F LEU* 4.0 3.1 - - - +
66F ILE* 4.0 22.4 - - - -
156F ARG* 3.6 14.0 - - - -
160F ASN 2.7 9.2 + - - -
161F ALA 3.4 1.0 - - - -
162F LEU* 1.3 81.0 - - - +
164F ASN* 1.3 58.2 + - - +
165F CYS* 3.1 4.0 - - - -
166F ILE* 2.9 31.2 - - - +
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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