Contacts of the helix formed by residues 198 - 209 (chain D) in PDB entry 4KNF
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 198 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159D TRP* 3.5 21.3 - - + -
194D VAL 3.5 14.5 + - - +
195D VAL* 3.5 16.2 - - - +
196D GLY 3.1 0.4 + - - -
197D TRP* 1.3 77.9 - - - +
199D ILE* 1.3 63.5 + - + +
200D TYR 2.9 1.7 + - - -
201D PRO* 3.1 16.2 - - - +
202D ALA* 3.1 12.1 + - + +
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Residues in contact with ILE 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D VAL 4.7 4.7 - - - +
196D GLY* 3.4 17.3 - - - +
197D TRP 3.2 0.8 - - - -
198D ALA* 1.3 76.8 - - + +
200D TYR* 1.3 56.4 + - - +
202D ALA* 3.4 8.9 - - + +
203D GLY* 2.8 23.2 + - - -
223D ILE* 3.3 37.4 - - + +
226D LEU* 3.8 28.7 - - + -
227D ALA* 3.8 15.7 - - + +
230D VAL* 4.2 22.4 - - + -
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Residues in contact with TYR 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D TRP* 3.4 38.1 - + - -
197D TRP* 3.1 22.0 + - - -
198D ALA 2.9 3.4 + - - -
199D ILE* 1.3 72.3 - - - +
201D PRO* 1.4 66.8 - - + +
203D GLY* 2.9 17.5 + - - -
204D TYR* 2.9 11.6 + - - +
224D TYR* 3.7 13.9 - + - -
227D ALA* 3.4 23.7 + - + -
228D ASP* 2.8 31.4 + - - -
231D ASN* 3.1 28.2 + - - +
301D RET 3.2 63.1 - - + +
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Residues in contact with PRO 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D PHE* 3.6 27.6 - - + -
156D MET* 3.7 12.3 - - + -
159D TRP* 3.8 25.1 - - + -
197D TRP 3.3 7.9 - - - +
198D ALA* 3.1 18.2 - - + +
200D TYR* 1.4 90.8 - - + +
202D ALA* 1.3 54.7 + - - +
204D TYR* 3.6 6.0 - - + +
205D ALA* 2.9 32.2 + - - +
301D RET 3.8 23.5 - - + -
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Residues in contact with ALA 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D ALA 3.1 15.0 + - - +
199D ILE* 3.4 16.6 - - + +
201D PRO* 1.3 77.1 - - - +
203D GLY* 1.3 55.7 + - - +
205D ALA* 3.6 5.9 + - - +
206D ALA* 3.1 26.5 + - - +
223D ILE* 4.5 4.9 - - + +
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Residues in contact with GLY 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ILE 2.8 11.5 + - - -
200D TYR 2.9 4.5 + - - -
202D ALA* 1.3 74.1 - - - +
204D TYR* 1.3 63.0 + - - +
206D ALA* 3.3 4.9 + - - +
207D GLY 3.1 17.5 + - - -
220D LEU* 3.3 17.8 - - - +
223D ILE* 3.5 30.7 - - - +
224D TYR* 4.4 4.5 - - - -
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Residues in contact with TYR 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D GLY* 3.9 24.7 - - - -
141D GLY* 3.6 16.5 - - - -
142D GLU* 3.8 25.6 - - + -
148D VAL* 2.7 28.5 + - - +
151D ALA* 3.8 3.5 - - + +
152D PHE* 3.4 39.5 - + + -
200D TYR 2.9 11.7 + - - +
201D PRO* 3.6 12.1 - - + +
203D GLY* 1.3 73.0 - - - +
205D ALA* 1.3 66.2 + - - +
207D GLY 3.1 1.7 + - - -
208D TYR* 3.0 35.2 + + + +
209D LEU* 4.0 12.3 - - + -
220D LEU* 3.9 3.4 - - - -
224D TYR* 3.9 11.7 - - - +
301D RET 4.1 16.2 - - + -
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Residues in contact with ALA 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D PHE* 4.8 5.6 - - + -
201D PRO 2.9 18.3 + - - +
202D ALA* 3.7 6.5 - - - +
204D TYR* 1.3 75.4 - - - +
206D ALA* 1.3 59.1 - - - +
209D LEU* 2.8 58.9 + - + +
210D MET* 4.0 4.1 - - - +
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Residues in contact with ALA 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ALA 3.1 12.4 + - - +
203D GLY* 3.3 12.8 + - - +
205D ALA* 1.3 78.9 - - - +
207D GLY* 1.3 59.6 + - - +
210D MET* 3.8 26.3 - - + +
216D TYR* 3.3 17.3 - - - +
219D ASN* 4.4 19.4 - - + +
223D ILE* 4.7 9.4 - - + -
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Residues in contact with GLY 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D GLY 3.1 13.0 + - - -
204D TYR 3.1 2.9 + - - -
205D ALA 3.0 1.2 + - - -
206D ALA* 1.3 78.4 - - - +
208D TYR* 1.3 66.6 + - - +
209D LEU 3.8 0.2 - - - -
214D GLY 4.7 0.3 - - - +
215D VAL* 3.5 10.4 - - - +
216D TYR* 2.8 44.9 + - - +
220D LEU* 4.2 9.4 - - - -
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Residues in contact with TYR 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D THR* 4.8 4.3 - - - +
91D THR* 4.5 4.5 + - - -
142D GLU* 2.6 62.8 + - + +
148D VAL* 3.4 38.6 - - + +
204D TYR* 3.0 35.3 + + + +
207D GLY* 1.3 76.9 - - - +
209D LEU* 1.3 69.7 + - + +
210D MET 3.6 3.3 + - - -
211D GLY* 4.6 4.3 + - - -
215D VAL* 3.8 35.7 - - + +
220D LEU* 3.6 26.4 - - + +
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Residues in contact with LEU 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D VAL* 3.2 24.2 - - + +
149D LEU* 4.1 21.8 - - + -
152D PHE* 3.9 34.1 - - + -
204D TYR* 4.0 7.6 - - + -
205D ALA* 2.8 35.2 + - + +
208D TYR* 1.3 97.5 - - + +
210D MET* 1.3 66.8 + - - +
211D GLY 3.2 5.8 + - - +
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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