Contacts of the helix formed by residues 197 - 206 (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 GLU 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A LYS* 2.3 35.6 + - - +
194A GLN* 5.1 0.5 + - - -
195A ASP 3.8 2.9 - - - +
196A LEU* 1.3 84.5 - - - +
198A PRO* 1.3 57.9 - - - +
199A SER* 3.3 5.2 - - - -
200A VAL* 3.0 17.4 + - + +
201A GLU* 2.7 30.7 + - - +
42B ALA* 3.0 25.2 - - - +
45B GLN* 3.1 22.9 + - - +
77B GLU* 4.4 12.1 + - + +
78B MET* 4.2 18.6 - - + -
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Residues in contact with PRO 198 (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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194A GLN* 5.5 2.7 - - - +
196A LEU* 3.8 23.1 - - + +
197A GLU* 1.3 87.8 - - - +
199A SER* 1.3 63.1 + - - +
201A GLU* 3.9 7.4 - - + +
202A GLU* 2.9 27.2 + - - +
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Residues in contact with SER 199 (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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197A GLU* 3.3 4.0 - - - -
198A PRO* 1.3 79.0 - - - +
200A VAL* 1.3 64.1 + - - +
202A GLU* 3.7 9.4 - - - +
203A ALA* 3.3 21.8 + - - +
38B ALA* 3.8 17.9 - - - +
42B ALA* 6.5 0.2 - - - -
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Residues in contact with VAL 200 (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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197A GLU* 3.0 23.2 + - + +
199A SER* 1.3 74.2 - - - +
201A GLU* 1.3 67.1 + - - +
202A GLU 2.9 3.2 + - - -
203A ALA* 3.0 3.7 + - - +
204A ARG* 3.0 53.8 + - - +
35B GLU* 4.8 2.6 - - + +
38B ALA* 3.6 38.4 - - + +
39B ILE* 3.5 16.8 - - + +
42B ALA* 4.1 9.0 - - + -
77B GLU 4.4 1.6 - - - +
78B MET* 3.4 11.0 - - - +
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Residues in contact with GLU 201 (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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196A LEU* 4.5 11.2 - - + -
197A GLU* 2.7 20.5 + - - +
198A PRO* 3.9 9.2 - - + +
200A VAL* 1.3 73.5 - - - +
202A GLU* 1.3 56.1 + - - +
204A ARG* 3.6 11.6 + - - +
205A TYR* 3.1 28.7 + - + +
77B GLU* 4.4 2.8 - - - +
36C TYR* 3.3 36.9 + - - -
37C GLN* 4.9 8.0 - - - +
40C GLN* 3.4 24.1 + - - +
41C LYS* 5.7 6.3 - - - +
44C ARG* 4.3 11.3 + - - +
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Residues in contact with GLU 202 (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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198A PRO 2.9 19.2 + - - +
199A SER* 3.7 9.0 - - - +
200A VAL 2.9 1.0 + - - -
201A GLU* 1.3 73.4 - - - +
203A ALA* 1.3 65.7 + - - +
204A ARG 3.0 2.2 + - - -
205A TYR* 3.1 7.2 + - - +
206A ASN* 2.8 39.4 + - - +
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Residues in contact with ALA 203 (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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199A SER 3.3 10.1 + - - +
200A VAL 3.0 6.3 + - - +
202A GLU* 1.3 79.7 - - - +
204A ARG* 1.3 60.7 + - - +
206A ASN* 3.4 12.0 + - - +
207A SER* 3.2 19.6 + - - -
32B THR* 4.3 4.5 + - - -
34B GLU* 3.4 23.0 - - + +
35B GLU* 3.4 32.5 - - - +
38B ALA* 4.4 2.7 - - + -
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Residues in contact with ARG 204 (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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200A VAL* 3.0 29.7 + - - +
201A GLU* 3.6 22.8 + - - +
203A ALA* 1.3 75.6 - - - +
205A TYR* 1.3 59.4 + - - +
207A SER* 2.6 29.8 + - - -
208A CYS* 3.6 9.0 + - - -
35B GLU* 2.9 34.1 + - - +
77B GLU 3.4 15.0 + - - -
78B MET 2.3 38.6 + - - -
79B PHE* 3.2 19.2 + - - +
80B GLY* 3.6 5.5 - - - +
82B ASN* 5.6 0.4 - - - -
116B LYS* 4.9 6.7 - - - +
36C TYR* 2.9 42.1 + - + +
40C GLN* 4.1 1.0 - - - +
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Residues in contact with TYR 205 (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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201A GLU* 3.1 21.1 + - + +
202A GLU* 3.6 6.5 - - + +
204A ARG* 1.3 80.0 - - - +
206A ASN* 1.3 74.4 + - - +
207A SER 3.1 1.0 + - - -
208A CYS* 3.2 20.7 + - - +
33C ALA* 3.2 48.8 - - + +
34C GLU* 4.7 6.6 + - - +
36C TYR* 4.5 7.2 - + - -
37C GLN* 3.3 41.7 + - + +
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Residues in contact with ASN 206 (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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202A GLU* 2.8 39.5 + - - +
203A ALA* 3.7 10.7 - - - +
204A ARG 3.1 0.8 - - - -
205A TYR* 1.3 86.5 - - - +
207A SER* 1.3 57.8 + - - +
208A CYS 3.1 9.4 + - - +
34B GLU* 4.9 12.0 - - + +
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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