Contacts of the helix formed by residues 197 - 206 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B LYS* 2.5 29.9 + - - +
194B GLN* 5.3 0.9 + - - -
195B ASP 3.7 2.9 - - - +
196B LEU* 1.3 83.6 - - - +
198B PRO* 1.3 65.8 - - - +
199B SER* 3.3 5.6 - - - -
200B VAL* 3.0 17.8 + - + +
201B GLU* 2.8 25.5 + - - +
42C ALA* 3.1 24.5 - - - +
45C GLN* 2.9 24.8 + - - +
77C GLU* 4.5 13.2 + - - +
78C MET* 4.2 18.4 - - + -
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Residues in contact with PRO 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B GLN* 5.6 2.9 - - - +
196B LEU* 3.9 21.1 - - + +
197B GLU* 1.3 85.6 - - - +
199B SER* 1.3 63.7 + - - +
201B GLU* 3.7 7.0 - - + +
202B GLU* 2.9 26.9 + - - +
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Residues in contact with SER 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B GLU* 3.3 4.2 - - - -
198B PRO* 1.3 81.5 - - - +
200B VAL* 1.3 65.0 + - - +
202B GLU* 3.5 9.1 - - - +
203B ALA* 3.2 20.3 + - - +
38C ALA* 3.9 17.1 - - - +
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Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B GLU* 3.0 25.0 + - + +
199B SER* 1.3 75.0 - - - +
201B GLU* 1.3 67.3 + - - +
202B GLU 2.9 2.5 + - - -
203B ALA* 3.0 2.9 + - - +
204B ARG* 2.9 53.9 + - - +
35C GLU* 4.7 4.0 - - + -
38C ALA* 3.5 37.5 - - + +
39C ILE* 3.4 24.5 - - + +
42C ALA* 4.3 8.3 - - + -
77C GLU 4.6 0.4 - - - +
78C MET* 3.5 4.9 - - - +
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Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B LEU* 4.6 12.8 - - + -
197B GLU 2.8 19.7 + - - +
198B PRO* 3.7 9.0 - - + +
200B VAL* 1.3 72.1 - - - +
202B GLU* 1.3 64.1 + - - +
204B ARG* 3.3 15.8 + - - +
205B TYR* 3.0 25.2 + - + +
77C GLU* 4.8 2.4 + - - +
36D TYR* 3.1 37.3 + - - -
37D GLN* 4.7 10.0 - - - +
40D GLN* 3.5 19.9 + - - +
41D LYS* 5.3 8.5 + - - +
44D ARG* 4.4 10.2 + - - +
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Residues in contact with GLU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B PRO 2.9 18.4 + - - +
199B SER* 3.5 8.9 - - - +
200B VAL 2.9 0.6 + - - -
201B GLU* 1.3 77.1 - - - +
203B ALA* 1.3 64.0 + - - +
205B TYR* 3.0 16.3 + - - +
206B ASN* 2.9 31.7 + - - +
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Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B SER 3.2 10.1 + - - +
200B VAL 3.0 5.7 + - - +
202B GLU* 1.3 80.4 - - - +
204B ARG* 1.3 61.2 + - - +
206B ASN* 3.6 10.6 + - - +
207B SER* 3.3 19.4 + - - -
32C THR* 4.3 4.9 + - - -
34C GLU* 3.5 23.5 - - + +
35C GLU* 3.4 32.3 - - - +
38C ALA* 4.6 1.8 - - + -
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Residues in contact with ARG 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B VAL* 2.9 31.9 + - - +
201B GLU* 3.3 22.8 + - - +
203B ALA* 1.3 75.7 - - - +
205B TYR* 1.3 59.8 + - - +
207B SER* 2.7 28.2 + - - -
208B CYS* 3.6 9.4 + - - -
35C GLU* 3.1 32.9 + - - +
77C GLU 3.5 12.7 + - - -
78C MET 2.5 36.2 + - - -
79C PHE* 3.3 20.2 + - - +
80C GLY* 3.7 5.5 - - - +
82C ASN* 5.5 0.9 - - - -
116C LYS* 4.8 6.7 - - - +
36D TYR* 2.8 50.2 + - + +
40D GLN* 4.0 0.8 - - - +
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Residues in contact with TYR 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B GLU* 3.0 20.6 + - + +
202B GLU* 3.0 6.3 + - - +
204B ARG* 1.3 79.3 - - - +
206B ASN* 1.3 70.8 + - - +
207B SER 3.1 4.7 + - - -
208B CYS* 3.2 16.2 + - - +
33D ALA* 3.2 50.6 - - + +
34D GLU* 4.6 7.3 + - - +
36D TYR* 4.5 11.0 - + - -
37D GLN* 3.3 43.5 + - + +
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Residues in contact with ASN 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B GLU* 2.9 41.9 + - - +
203B ALA* 3.8 9.1 - - - +
205B TYR* 1.3 88.0 - - - +
207B SER* 1.3 57.5 + - - +
208B CYS 3.3 8.7 + - - +
34C GLU* 5.0 12.1 - - - +
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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