Contacts of the helix formed by residues 203 - 218 (chain D) in PDB entry 1KKQ
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 LEU 203 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200D THR* 3.8 26.9 - - - +
201D ALA 3.2 0.4 - - - -
202D ASP* 1.3 81.9 - - - +
204D LYS* 1.3 62.1 + - - +
205D SER 3.4 0.4 - - - -
206D LEU* 3.5 27.8 + - + +
207D ALA* 4.5 0.5 + - - +
403D GLY* 4.3 16.2 - - - +
406D HIS* 3.4 33.9 - - + +
407D VAL* 3.2 32.8 - - + +
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Residues in contact with LYS 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ASP* 3.7 29.6 + - - +
392B LEU* 5.5 5.1 - - - +
393B ASN* 5.5 5.1 - - - +
200D THR* 3.3 20.2 + - - +
201D ALA 4.5 0.2 - - - +
202D ASP 3.4 0.2 - - - -
203D LEU* 1.3 76.4 - - - +
205D SER* 1.3 60.2 + - - +
206D LEU 3.1 4.8 + - - -
207D ALA* 4.2 7.6 + - - +
208D LYS* 4.5 7.1 + - - +
697G TYR* 3.2 40.6 - - + +
698G ASP* 4.8 16.4 - - - +
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Residues in contact with SER 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D ASP* 3.2 31.0 + - - -
204D LYS* 1.3 74.5 - - - +
206D LEU* 1.3 57.9 + - - +
207D ALA 3.6 0.2 - - - -
208D LYS* 3.9 7.5 - - - +
209D ARG* 2.9 37.1 + - - +
697G TYR* 3.7 19.6 + - - -
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Residues in contact with LEU 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D ASP 3.7 11.6 + - - +
203D LEU* 3.5 39.5 - - + +
204D LYS 3.1 0.6 - - - -
205D SER* 1.3 77.4 + - - +
207D ALA* 1.3 62.4 + - - +
209D ARG* 3.3 3.9 + - - +
210D ILE* 2.9 57.0 + - + +
294D ILE* 5.7 0.4 - - + -
295D PRO* 4.1 25.4 - - + +
400D MET 5.6 0.2 - - - +
403D GLY* 3.6 24.0 - - - +
404D ILE* 4.2 10.1 - - + +
407D VAL* 4.1 9.4 - - + -
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Residues in contact with ALA 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 4.4 17.2 - - + +
203D LEU 4.5 0.4 + - - -
204D LYS 4.2 5.3 + - - +
205D SER 3.6 0.2 - - - -
206D LEU* 1.3 75.1 - - - +
208D LYS* 1.3 67.1 + - - +
210D ILE* 3.9 0.7 - - - +
211D TYR* 2.9 28.1 + - - +
377D LEU* 3.9 25.2 - - + +
407D VAL* 3.5 25.2 - - + +
411D HIS* 5.2 4.7 - - + -
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Residues in contact with LYS 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ASP* 3.3 25.8 + - - +
303B ASN* 3.1 35.9 + - - +
304B ASP* 4.4 7.1 + - - -
390B GLY 4.5 8.8 + - - -
392B LEU* 4.1 34.5 - - + +
204D LYS 4.5 4.3 + - - +
205D SER* 3.7 13.3 + - - +
206D LEU 3.3 0.4 - - - -
207D ALA* 1.3 79.4 - - - +
209D ARG* 1.3 57.3 + - - +
211D TYR* 3.8 4.2 - - - +
212D GLU* 2.7 62.5 + - + +
700H TRP* 4.8 7.4 - - + -
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Residues in contact with ARG 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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205D SER* 2.9 24.7 + - - +
206D LEU 3.5 4.5 - - - +
208D LYS* 1.3 79.5 - - + +
210D ILE* 1.3 62.3 + - - +
212D GLU* 3.5 1.7 + - - +
213D ALA* 3.2 19.3 + - - +
293D ALA* 2.6 50.0 + - - +
295D PRO* 3.7 20.5 - - + +
699H GLN* 5.9 1.0 - - - +
700H TRP* 2.8 62.6 + - + +
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Residues in contact with ILE 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D LEU* 2.9 44.3 + - + +
209D ARG* 1.3 71.6 - - - +
211D TYR* 1.3 64.4 + - - +
213D ALA* 3.1 20.3 + - - +
214D TYR* 3.2 5.9 + - - +
290D PHE* 3.6 14.1 - - + -
294D ILE* 4.7 5.8 - - + +
295D PRO* 4.0 13.9 - - + -
376D SER 3.4 27.6 - - - +
377D LEU* 3.6 27.4 - - + -
380D ALA* 4.2 5.4 - - + -
404D ILE* 4.1 30.1 - - + -
407D VAL* 6.0 0.2 - - + -
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Residues in contact with TYR 211 (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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390B GLY* 5.1 8.5 + - - -
391B LEU 3.6 26.7 + - - -
392B LEU* 3.6 27.1 - - + -
207D ALA 2.9 18.7 + - - +
208D LYS* 3.8 5.6 - - - +
210D ILE* 1.3 74.2 - - - +
212D GLU* 1.3 73.1 + - + +
214D TYR* 2.8 14.2 + + + +
215D LEU* 3.2 44.3 + - + +
223D VAL* 5.9 1.7 - - - +
372D ASP* 3.6 37.8 - - + +
373D SER* 3.9 15.0 + - - +
376D SER* 3.5 15.0 + - - +
377D LEU* 5.6 0.4 - - + -
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Residues in contact with GLU 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B GLY* 6.1 0.7 - - - -
208D LYS* 2.7 48.8 + - + +
209D ARG 3.7 4.7 - - - +
211D TYR* 1.3 79.1 - - + +
213D ALA* 1.3 56.5 + - - +
215D LEU* 3.2 20.0 + - - +
216D LYS* 3.0 29.6 + - - +
700H TRP* 3.3 46.8 + - + -
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Residues in contact with ALA 213 (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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209D ARG* 3.2 12.4 + - - +
210D ILE* 3.1 14.8 + - - +
211D TYR 3.0 0.4 - - - -
212D GLU* 1.3 81.0 - - - +
214D TYR* 1.3 57.6 + - - +
216D LYS* 3.9 5.8 - - - -
217D ASN* 3.0 34.3 + - - +
290D PHE* 3.6 13.6 - - + -
293D ALA* 3.5 33.7 - - + -
294D ILE* 6.0 0.2 - - - -
700H TRP* 5.9 0.4 - - - -
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Residues in contact with TYR 214 (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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210D ILE 3.2 3.9 + - - +
211D TYR* 2.8 14.5 + + - +
213D ALA* 1.3 75.1 - - - +
215D LEU* 1.3 70.9 + - + +
218D PHE* 3.1 52.6 + + + +
220D MET 5.5 0.4 - - - -
221D ASN* 3.7 16.8 - - + +
222D LYS 4.1 4.0 + - - -
290D PHE* 3.9 8.0 - + + -
320D MET* 4.2 20.4 - - - +
323D SER* 5.0 2.1 + - - -
372D ASP* 2.5 48.4 + - + -
375D ILE* 3.6 33.3 - - + +
376D SER* 3.4 33.9 - - - -
379D VAL* 5.2 0.4 - - + -
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Residues in contact with LEU 215 (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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390B GLY* 5.5 8.7 - - - -
211D TYR* 3.2 49.7 + - + +
212D GLU* 3.5 20.4 - - - +
214D TYR* 1.3 84.9 - - + +
216D LYS* 1.3 59.7 + - - +
218D PHE 4.0 10.2 - - - +
221D ASN* 3.9 25.1 - - - +
223D VAL* 5.9 1.3 - - + -
372D ASP* 5.5 1.6 - - + -
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Residues in contact with LYS 216 (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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212D GLU 3.0 16.9 + - - +
213D ALA* 4.2 3.8 - - - +
215D LEU* 1.3 79.2 - - - +
217D ASN* 1.3 75.7 + - - +
218D PHE 5.5 0.2 - - - -
698H ASP* 3.4 46.9 + - - +
699H GLN* 3.8 1.6 - - - +
700H TRP* 3.6 31.7 - - + +
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Residues in contact with ASN 217 (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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213D ALA* 3.0 30.2 + - - +
216D LYS* 1.3 99.7 - - - +
218D PHE* 1.3 62.6 + - + +
219D ASN 3.8 0.7 + - - -
286D GLU* 3.3 36.5 - - - +
289D GLU* 3.1 34.9 + - + +
290D PHE* 3.9 16.2 - - + +
293D ALA* 4.8 4.2 - - - +
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Residues in contact with PHE 218 (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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214D TYR* 3.1 53.7 + + + +
215D LEU* 4.0 11.5 - - - +
216D LYS 5.4 0.2 - - - -
217D ASN* 1.3 76.9 - - - +
219D ASN* 1.3 68.1 + - - +
220D MET 3.5 17.7 + - - +
221D ASN* 4.8 4.4 + - + +
283D THR 5.0 0.4 - - - -
286D GLU* 3.1 38.4 - - + +
287D LEU* 3.9 16.8 - - + -
290D PHE* 3.4 50.5 - + + -
320D MET* 3.6 31.4 - - + -
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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
------------------------------------------------------------
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