Contacts of the helix formed by residues 158 - 163 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.5 26.2 - - + +
79A PHE* 4.3 5.8 - + - -
113A VAL* 4.0 36.1 - - + -
115A LEU* 3.5 41.3 - - + -
119A SER* 4.0 9.4 - - - -
121A HIS* 3.3 35.2 - + - -
154A ALA 4.8 0.7 - - - -
155A LEU* 2.9 25.8 + - + +
156A ARG 2.8 0.6 + - - -
157A SER* 1.3 78.3 - - - +
159A GLY* 1.3 57.6 + - - +
162A LEU* 3.7 20.9 - - + -
76K ASN* 3.6 15.7 + - - +
81K TYR* 3.6 22.8 - + + +
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Residues in contact with GLY 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.9 10.7 - - - +
155A LEU 4.2 0.4 + - - -
156A ARG 3.0 8.0 + - - +
157A SER 3.3 1.2 + - - -
158A PHE* 1.3 81.7 - - - +
160A ASN* 1.3 66.4 + - - -
161A ALA 3.3 2.2 - - - -
162A LEU* 3.4 9.2 + - - +
163A GLY 3.7 0.3 + - - -
164A ASN* 3.0 26.1 + - - +
73K ASN* 4.5 4.0 - - - -
76K ASN* 4.0 9.9 - - - -
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Residues in contact with ASN 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU 3.0 4.4 + - - -
44A ARG* 3.0 24.9 + - - +
45A GLN 3.0 20.2 - - - +
46A ARG* 4.4 15.5 + - - +
47A LEU* 2.9 12.8 - - - +
159A GLY* 1.3 71.7 - - - -
161A ALA* 1.3 53.1 + - - +
162A LEU 3.0 0.2 - - - -
163A GLY* 2.8 23.6 + - - -
164A ASN 3.5 8.4 + - - +
165A CYS* 3.7 29.0 + - + +
73K ASN* 3.3 33.2 + - - +
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Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA 3.5 11.0 - - - +
43A LEU* 2.8 42.1 + - + +
45A GLN* 3.1 13.2 + - + +
47A LEU* 3.5 13.9 - - - +
74A LEU* 3.2 27.0 - - - +
78A MET* 4.7 9.1 - - + +
159A GLY 3.3 0.2 - - - -
160A ASN* 1.3 71.1 - - - +
162A LEU* 1.3 58.4 + - - +
163A GLY 3.4 0.9 - - - -
192K LYS* 4.7 9.6 - - + -
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.9 12.1 - - + -
66A ILE* 5.0 1.3 - - - -
71A VAL* 4.3 15.8 - - + +
74A LEU* 3.8 20.4 - - + +
75A ALA* 3.8 33.7 - - + +
78A MET* 4.7 4.5 - - + -
79A PHE* 3.7 27.6 - - + -
152A LYS 4.7 0.9 - - - +
155A LEU* 3.4 39.8 - - + +
156A ARG* 3.8 15.2 + - - +
158A PHE* 3.7 16.6 - - + -
159A GLY 3.4 6.8 + - - +
160A ASN 3.0 1.0 - - - -
161A ALA* 1.3 78.5 - - - +
163A GLY* 1.3 57.5 + - - +
164A ASN 3.8 1.8 - - - -
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Residues in contact with GLY 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 3.9 4.2 - - - +
66A ILE* 3.9 22.9 - - - -
156A ARG* 3.7 13.4 - - - +
160A ASN 2.8 10.2 + - - -
161A ALA 3.4 1.4 + - - -
162A LEU* 1.3 79.1 - - - +
164A ASN* 1.3 55.9 + - - +
165A CYS 3.0 7.0 + - - -
166A ILE* 3.0 31.6 - - - +
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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