Contacts of the helix formed by residues 158 - 167 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76I ASN* 3.6 16.1 + - - +
81I TYR* 3.8 20.9 - + - +
43J LEU* 3.3 25.2 - - + +
79J PHE* 4.2 7.2 - + - -
113J VAL* 3.8 36.8 - - + -
115J LEU* 3.6 42.0 - - + -
119J SER* 4.1 6.1 - - - -
120J TYR* 4.8 2.5 - - - -
121J HIS* 3.3 33.9 - + - -
154J ALA 4.8 0.7 - - - -
155J LEU* 2.9 34.5 + - + +
157J SER* 1.3 78.6 - - - +
159J GLY* 1.3 57.6 + - - +
162J LEU* 3.7 15.9 - - + -
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Residues in contact with GLY 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73I ASN* 4.5 4.0 - - - -
76I ASN* 4.1 10.1 - - - -
43J LEU* 3.7 10.9 - - - +
156J ARG 3.1 6.7 + - - +
157J SER 3.4 0.6 - - - -
158J PHE* 1.3 82.4 - - - +
160J ASN* 1.3 66.0 + - - -
161J ALA 3.2 2.7 - - - -
162J LEU* 3.1 13.4 + - - +
163J GLY 3.6 0.5 + - - -
164J ASN* 3.3 19.6 + - - +
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Residues in contact with ASN 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I HIS* 6.0 0.2 - - - -
73I ASN* 3.1 37.1 + - - +
43J LEU 3.0 3.6 + - - -
44J ARG* 3.2 24.3 + - - +
45J GLN 3.3 15.9 - - - +
46J ARG* 4.5 13.8 + - + +
47J LEU* 2.8 20.6 - - - +
159J GLY* 1.3 70.8 - - - -
161J ALA* 1.3 58.5 + - - +
162J LEU 3.0 0.2 - - - -
163J GLY 2.9 10.4 + - - -
164J ASN* 3.7 13.8 + - - +
165J CYS* 3.5 26.9 + - + +
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Residues in contact with ALA 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192I LYS* 4.7 9.9 - - + -
42J ALA 3.4 27.1 - - - +
43J LEU* 2.8 22.1 + - + +
45J GLN* 3.0 14.7 + - + +
47J LEU* 3.5 12.2 - - - +
74J LEU* 3.1 27.7 - - - +
78J MET* 4.9 7.4 - - + +
159J GLY 3.2 0.2 - - - -
160J ASN* 1.3 74.0 - - - +
162J LEU* 1.3 59.1 + - - +
163J GLY 3.5 0.4 - - - -
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Residues in contact with LEU 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J LEU* 3.9 11.7 - - + -
47J LEU* 4.9 0.2 - - - -
66J ILE* 5.0 1.3 - - - -
71J VAL* 4.5 15.2 - - + +
74J LEU* 3.7 36.3 - - + +
75J ALA* 3.9 18.2 - - + +
78J MET* 4.7 4.0 - - + -
79J PHE* 3.7 26.9 - - + -
152J LYS 4.6 0.9 - - - +
155J LEU* 3.5 29.2 - - + +
156J ARG* 3.8 14.8 + - - +
158J PHE* 3.7 28.9 - - + -
159J GLY 3.1 7.6 + - - +
160J ASN 3.0 1.2 - - - -
161J ALA* 1.3 80.8 - - - +
163J GLY* 1.3 55.8 + - - +
164J ASN 3.8 0.4 - - - -
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Residues in contact with GLY 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47J LEU* 4.0 3.9 - - - +
66J ILE* 3.8 24.2 - - - +
156J ARG* 3.6 13.2 - - - +
160J ASN 2.9 7.8 + - - -
161J ALA 3.5 1.0 - - - -
162J LEU* 1.3 79.6 - - - +
164J ASN* 1.3 58.0 + - - +
165J CYS 3.1 6.6 + - - -
166J ILE* 2.9 31.7 + - - +
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Residues in contact with ASN 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I HIS* 3.1 38.7 + - - +
72I ILE* 3.3 32.6 - - - +
73I ASN* 3.0 35.8 + - - +
156J ARG* 3.4 24.2 - - - +
159J GLY 3.3 19.6 + - - +
160J ASN* 3.6 3.6 + - - +
162J LEU 3.8 0.4 - - - -
163J GLY* 1.3 75.8 - - - +
165J CYS* 1.3 60.7 + - - +
166J ILE 3.4 0.2 - - - -
167J LEU* 3.8 11.3 + - - +
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Residues in contact with CYS 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J ARG* 4.0 25.4 - - - +
47J LEU* 3.5 45.3 - - - -
52J ILE* 5.8 0.9 - - - -
66J ILE* 5.9 0.7 - - - -
160J ASN* 3.5 18.6 + - + +
163J GLY* 3.1 2.6 - - - -
164J ASN* 1.3 75.4 - - - +
166J ILE* 1.3 56.7 + - - +
167J LEU 2.6 18.7 + - - -
168J ASP* 2.7 20.4 + - - +
171J TYR* 3.3 30.4 - - + -
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Residues in contact with ILE 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52J ILE* 3.8 34.8 - - + -
64J CYS* 3.9 20.7 - - + +
65J TYR* 4.0 25.1 - - - +
66J ILE* 4.1 14.4 - - + +
156J ARG* 3.9 25.1 - - - +
163J GLY* 2.9 25.2 + - - +
165J CYS* 1.3 79.3 - - - +
167J LEU* 1.3 68.1 + - + +
168J ASP 4.9 0.2 - - - -
171J TYR* 4.2 10.5 - - + -
172J LEU* 4.1 17.4 - - + +
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Residues in contact with LEU 167 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67I GLU* 5.1 1.6 - - - +
69I HIS* 3.9 36.1 - - + +
72I ILE* 5.6 3.1 - - + -
153J ARG* 5.8 0.4 - - - +
156J ARG* 3.4 39.3 - - - +
164J ASN* 4.0 16.2 - - - +
165J CYS 2.6 6.5 + - - -
166J ILE* 1.3 84.4 - - + +
168J ASP* 1.3 63.4 + - - +
169J LYS* 3.2 10.7 + - - +
172J LEU* 4.8 3.9 - - - +
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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