Contacts of the helix formed by residues 222 - 232 (chain E) in PDB entry 1KQN
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 222 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E THR* 4.6 0.4 - - - -
23E MET* 4.2 10.3 - - - -
220E ASP* 2.7 19.0 + - - -
221E ILE* 1.3 72.1 - - - +
223E SER* 1.3 65.2 + - - +
224E THR* 3.7 8.0 + - - -
225E LYS* 3.2 33.6 + - - +
226E ILE* 3.2 23.1 + - - +
781E NAD 5.7 2.2 - - - -
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Residues in contact with SER 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ASN* 3.3 29.0 + - - -
19E PRO* 2.7 25.4 + - - +
21E THR* 4.5 2.2 - - - +
23E MET* 5.4 0.2 - - - +
24E HIS* 3.6 15.2 + - - -
221E ILE 4.0 0.4 + - - -
222E SER* 1.3 73.9 - - - +
224E THR* 1.3 54.7 + - - +
226E ILE* 2.9 9.5 + - - +
227E ARG* 2.8 42.8 + - - +
781E NAD 4.9 7.4 + - - -
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Residues in contact with THR 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222E SER* 3.9 8.7 - - - +
223E SER* 1.3 79.0 - - - +
225E LYS* 1.3 59.0 + - + +
227E ARG* 3.3 28.9 + - - +
228E ARG* 3.0 52.6 + - - +
231E ARG* 5.2 0.5 + - - -
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Residues in contact with LYS 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D LYS* 6.2 1.4 - - - +
198D TYR* 3.5 30.6 + - - +
199D GLU* 6.1 1.1 - - - -
220E ASP* 3.9 24.9 + - - +
222E SER* 3.2 20.9 + - - +
223E SER 3.2 0.6 - - - -
224E THR* 1.3 78.4 - - + +
226E ILE* 1.3 58.6 + - - +
228E ARG* 3.9 13.0 - - - +
229E ALA* 3.0 28.1 + - - +
216F TRP* 2.7 31.6 + - - +
217F ILE* 3.8 28.9 - - + +
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Residues in contact with ILE 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E PRO* 3.8 22.2 - - + -
21E THR* 4.0 17.0 - - + -
221E ILE* 3.8 7.2 - - + -
222E SER 3.2 15.0 + - - +
223E SER* 2.9 10.2 + - - +
225E LYS* 1.3 75.0 - - - +
227E ARG* 1.3 59.9 + - - +
229E ALA* 3.2 5.3 + - - +
230E LEU* 3.0 37.7 + - + +
236E ILE* 3.9 29.8 - - + -
239E LEU* 3.6 43.3 - - + -
240E VAL* 4.5 5.6 - - + -
217F ILE* 4.6 3.8 - - + -
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Residues in contact with ARG 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ASN* 2.9 43.2 + - - +
19E PRO* 3.9 4.0 - - + -
57E LYS* 6.0 2.0 - - - +
58E LYS 4.8 7.1 + - - -
59E GLY 4.6 2.4 + - - -
223E SER* 2.8 18.9 + - - +
224E THR* 3.6 42.3 + - - +
226E ILE* 1.3 76.6 - - - +
228E ARG* 1.3 57.1 + - - +
230E LEU* 3.4 10.7 + - - +
231E ARG* 3.0 35.2 + - - +
254E TYR* 3.3 37.8 - - + +
259E GLU* 2.7 45.1 + - - +
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Residues in contact with ARG 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D TYR* 3.1 42.3 + - + +
199D GLU* 3.8 28.7 + - - +
224E THR* 3.0 42.0 + - + +
225E LYS* 3.9 13.7 - - - +
227E ARG* 1.3 73.3 - - - +
229E ALA* 1.3 68.9 + - - +
231E ARG* 3.3 29.2 + - - +
232E ARG* 3.1 72.3 + - - +
234E GLN* 5.5 0.2 - - - +
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Residues in contact with ALA 229 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225E LYS 3.0 20.1 + - - +
226E ILE* 3.5 6.1 - - + +
228E ARG* 1.3 76.4 - - - +
230E LEU* 1.3 58.0 - - - +
232E ARG 3.2 2.8 + - - -
233E GLY 3.2 3.5 + - - -
234E GLN* 2.8 58.6 + - + +
235E SER 4.8 1.8 - - - +
236E ILE* 3.9 18.6 - - + -
239E LEU* 6.1 0.4 - - + -
26F ARG* 6.0 2.0 - - - +
217F ILE* 5.9 3.6 - - + -
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Residues in contact with LEU 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E ILE* 3.0 34.8 + - + +
227E ARG 3.7 4.3 - - - +
228E ARG 3.2 0.2 - - - -
229E ALA* 1.3 71.9 - - - +
231E ARG* 1.3 57.6 + - - +
232E ARG 3.0 4.7 - - - -
233E GLY* 2.9 20.2 + - - +
234E GLN 4.6 8.1 - - - +
236E ILE* 3.6 31.4 - - + -
248E ILE* 3.7 20.9 - - + -
249E GLU* 6.0 2.0 - - - +
254E TYR* 3.5 45.5 - - + +
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Residues in contact with ARG 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D ASP* 2.7 42.5 + - - +
224E THR 5.2 0.6 + - - -
227E ARG* 3.0 30.4 + - - +
228E ARG* 3.4 37.9 - - - +
230E LEU* 1.3 75.3 - - - +
232E ARG* 1.3 58.9 + - + +
233E GLY 3.4 0.8 + - - -
254E TYR 4.5 4.7 + - - -
255E SER* 3.5 25.4 - - - +
256E SER* 3.5 29.4 - - - +
259E GLU* 3.2 37.5 + - - +
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Residues in contact with ARG 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D TYR* 2.7 45.2 + - - -
199D GLU 4.0 0.4 - - - -
200D SER 3.5 18.4 - - - +
201D ASP* 2.9 32.3 + - - +
204D TRP* 3.2 47.6 + - + +
228E ARG* 3.1 38.2 - - - +
229E ALA 3.2 4.8 + - - +
230E LEU 3.0 1.2 - - - -
231E ARG* 1.3 79.9 - - + +
233E GLY* 1.3 63.2 + - - +
234E GLN* 3.2 20.4 + - + +
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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