Contacts of the helix formed by residues 189 - 199 (chain C) 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 ALA 189 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A ASN* 4.8 4.3 - - - +
157C ALA* 5.0 4.0 - - + +
187C THR* 3.0 17.6 + - - +
188C ARG* 1.3 76.2 - - + +
190C GLY* 1.3 62.4 + - - +
191C ASN 3.4 2.0 - - - -
192C ASP* 3.6 27.5 - - + +
193C ALA* 3.2 16.8 + - - +
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Residues in contact with GLY 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ASN* 4.0 7.2 + - - +
187C THR* 3.9 12.9 - - - +
188C ARG 3.6 4.9 + - - -
189C ALA* 1.3 71.7 - - - +
191C ASN* 1.3 54.1 + - - +
193C ALA* 3.2 2.3 + - - +
194C GLN* 2.7 45.1 + - - +
212C VAL* 4.1 6.2 - - - +
214C ASN* 3.8 21.2 + - - -
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Residues in contact with ASN 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ARG 5.0 3.2 + - - -
189A ALA* 4.6 3.8 - - - +
190A GLY* 3.8 10.1 + - - +
191A ASN* 3.5 45.4 + - - +
214A ASN* 3.9 17.0 - - - +
216A TRP* 4.0 13.7 - - - -
189C ALA 3.4 0.4 - - - -
190C GLY* 1.3 74.4 - - - +
192C ASP* 1.3 56.2 + - - +
194C GLN* 3.4 7.1 - - - +
195C LYS* 2.6 39.4 + - - +
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Residues in contact with ASP 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ALA* 6.3 0.2 - - + -
161C GLU* 3.7 14.7 - - - +
189C ALA* 3.5 26.5 + - + +
190C GLY 3.3 0.6 - - - -
191C ASN* 1.3 81.3 - - - +
193C ALA* 1.3 55.7 + - - +
195C LYS* 3.8 10.4 - - - +
196C PHE* 3.0 28.2 + - - +
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Residues in contact with ALA 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ALA* 4.6 2.2 - - + -
160C LEU* 4.2 16.2 - - + +
161C GLU* 3.7 12.3 + - - +
185C CYS* 4.6 5.2 - - - -
187C THR* 4.2 15.7 - - + -
189C ALA 3.2 11.5 + - - +
190C GLY 3.2 6.5 + - - +
192C ASP* 1.3 79.3 - - - +
194C GLN* 1.3 64.6 + - - +
196C PHE* 3.4 3.6 + - - +
197C ILE* 3.1 30.5 + - - +
212C VAL* 4.5 11.7 - - + -
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Residues in contact with GLN 194 (chain C).
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* 5.1 6.8 - - - +
214A ASN* 3.4 22.9 + - - +
216A TRP* 3.7 14.6 - - + -
190C GLY 2.7 29.4 + - - +
191C ASN* 3.4 10.8 - - - +
193C ALA* 1.3 77.3 - - - +
195C LYS* 1.3 58.7 + - - +
197C ILE* 3.4 12.9 + - - +
198C TYR* 3.0 26.5 + - - +
212C VAL* 4.0 26.5 - - + +
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Residues in contact with LYS 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A TRP* 3.3 32.3 - - + -
191C ASN 2.6 21.3 + - - +
192C ASP* 3.8 11.4 - - - +
194C GLN* 1.3 70.2 - - - +
196C PHE* 1.3 60.6 + - - +
198C TYR* 3.0 3.5 + - + +
199C GLU* 2.8 64.9 + - + +
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Residues in contact with PHE 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C LEU* 3.4 32.5 - - + -
161C GLU* 3.4 47.6 - - + +
163C PHE* 4.3 3.1 - - + -
164C ALA* 3.9 23.8 - - + -
192C ASP 3.0 17.7 + - - +
193C ALA* 3.6 5.8 - - - +
194C GLN 3.3 0.2 - - - -
195C LYS* 1.3 77.9 - - - +
197C ILE* 1.3 61.8 + - - +
199C GLU* 3.4 17.2 + - + +
200C SER* 3.6 13.1 + - - -
203C LEU* 3.6 25.1 - - + -
754C XE 4.0 11.4 - - - -
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Residues in contact with ILE 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C LEU* 4.3 9.4 - - + -
193C ALA 3.1 16.4 + - - +
194C GLN* 3.5 14.6 - - - +
195C LYS 3.1 0.2 - - - -
196C PHE* 1.3 75.9 - - - +
198C TYR* 1.3 64.4 + - - +
200C SER 3.2 21.8 + - - +
203C LEU* 3.8 39.3 - - + +
204C TRP* 3.4 13.8 + - + +
207C ARG* 4.3 13.5 - - + -
210C ILE* 3.5 35.0 - - + +
212C VAL* 3.9 18.4 - - + -
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Residues in contact with TYR 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A TRP* 3.2 63.8 - + + +
217A ILE* 5.3 1.9 - - - +
225B LYS* 3.1 38.0 + - - +
228B ARG* 3.2 33.0 + - + +
232B ARG* 2.6 47.4 + - - -
234B GLN* 5.6 5.6 - - - -
194C GLN 3.0 13.1 + - - +
195C LYS* 3.0 6.7 + - + +
197C ILE* 1.3 77.5 - - - +
199C GLU* 1.3 71.6 + - + +
200C SER 3.2 0.4 - - - -
204C TRP* 3.9 20.0 - + + -
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Residues in contact with GLU 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B ARG* 4.4 23.5 + - - +
232B ARG* 4.2 2.6 + - - -
195C LYS* 2.8 53.2 + - - +
196C PHE* 4.0 10.2 - - + +
197C ILE 3.2 0.6 - - - -
198C TYR* 1.3 93.2 - - + +
200C SER* 1.3 57.2 + - - +
201C ASP* 4.1 1.3 + - - +
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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