Contacts of the helix formed by residues 249 - 264 (chain D) in PDB entry 1KOO
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 ARG 249 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204D LEU* 6.1 2.6 - - - +
233D ARG* 5.3 3.0 - - - +
244D ASP* 5.5 1.6 + - - +
246D VAL* 2.7 49.0 + - - +
248D ASN* 1.3 92.3 - - - +
250D ARG* 1.3 64.7 + - - +
251D SER* 3.4 26.3 + - - +
252D SER* 3.9 4.1 + - - +
253D MET* 3.0 27.2 + - - +
279D ARG* 5.0 2.7 - - - +
282D ASP* 4.2 1.6 - - - -
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Residues in contact with ARG 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C GLU* 3.4 29.3 + - - -
250C ARG* 3.6 35.6 + - - +
251C SER* 2.8 25.6 + - - +
254C ALA* 4.6 13.9 - - - +
248D ASN 4.0 0.6 + - - -
249D ARG* 1.3 73.0 - - - +
251D SER* 1.3 50.8 + - - +
253D MET* 4.8 0.4 - - - -
254D ALA* 2.7 42.0 + - - +
279D ARG* 4.2 24.0 - - - +
281D ASP* 3.0 29.9 + - - +
282D ASP* 2.6 43.7 + - - +
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Residues in contact with SER 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C ARG* 3.4 16.3 - - - +
204D LEU* 3.8 37.0 + - - +
249D ARG* 3.4 25.2 + - - +
250D ARG* 1.3 79.6 - - - +
252D SER* 1.3 76.4 + - - +
254D ALA* 3.3 13.3 - - - +
255D ALA* 3.3 6.8 + - - +
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Residues in contact with SER 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D LEU* 4.0 16.4 - - - +
212D LEU* 5.2 1.9 - - - +
245D VAL* 5.0 3.0 - - - +
246D VAL* 2.9 50.6 + - - +
247D LEU* 3.6 9.4 - - - +
249D ARG* 3.4 5.7 + - - -
251D SER* 1.3 84.4 + - - +
253D MET* 1.3 65.8 + - - +
254D ALA 3.0 1.1 - - - -
255D ALA* 2.9 16.1 + - - +
256D THR* 3.0 14.8 + - - -
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Residues in contact with MET 253 (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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247D LEU* 3.3 49.6 + - + +
249D ARG 3.0 16.8 + - - +
250D ARG 4.3 0.9 - - - +
252D SER* 1.3 75.5 - - - +
254D ALA* 1.3 55.7 + - - +
256D THR* 2.7 28.2 + - - -
257D LEU* 2.9 35.2 + - + +
272D LEU* 4.5 10.8 - - + -
277D LEU* 4.0 17.5 - - + -
282D ASP* 3.7 38.8 - - + +
283D MET* 4.1 25.8 - - + +
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Residues in contact with ALA 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C ARG* 4.1 15.7 - - - +
281C ASP* 5.8 2.2 - - - +
250D ARG 2.7 25.1 + - - +
251D SER* 3.3 7.9 - - - +
253D MET* 1.3 76.3 - - - +
255D ALA* 1.3 51.6 + - - +
257D LEU* 4.3 2.6 - - - +
258D ARG* 2.6 52.8 + - - +
282D ASP 5.4 2.0 + - - -
289D LYS* 4.9 0.6 + - - +
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Residues in contact with ALA 255 (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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204D LEU* 4.5 14.1 - - + -
209D VAL* 4.7 21.8 - - + -
212D LEU* 4.5 16.4 - - + -
251D SER 3.3 7.8 + - - +
252D SER 2.9 12.4 + - - +
254D ALA* 1.3 76.9 - - - +
256D THR* 1.3 66.7 + - - +
258D ARG* 3.2 16.5 - - - +
259D ILE* 3.3 18.5 + - + +
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Residues in contact with THR 256 (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 LEU* 4.6 6.8 - - - +
216D MET* 3.5 27.3 - - + +
229D LEU* 3.7 22.2 - - + -
232D LEU* 4.6 1.2 - - - +
247D LEU* 3.3 26.3 - - + +
252D SER 3.0 11.8 + - - -
253D MET* 2.7 15.2 + - - -
255D ALA* 1.3 73.0 - - - +
257D LEU* 1.3 75.1 + - + +
258D ARG 2.9 0.7 - - - -
259D ILE* 2.8 18.0 + - - +
260D ILE* 3.1 20.6 + - + +
272D LEU* 5.8 0.7 - - + -
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Residues in contact with LEU 257 (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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253D MET* 2.9 30.0 + - + +
254D ALA* 4.3 2.0 - - - +
256D THR* 1.3 78.7 - - + +
258D ARG* 1.3 63.6 + - - +
260D ILE* 2.8 23.5 + - + -
261D GLU* 2.8 27.0 + - - +
270D LEU* 4.9 4.9 - - + -
272D LEU* 6.1 0.7 - - + -
282D ASP 3.2 26.7 - - - +
283D MET* 3.2 22.4 - - + -
285D SER* 4.7 5.6 - - - +
286D ILE* 4.2 33.0 - - + +
289D LYS* 3.9 19.6 - - + +
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Residues in contact with ARG 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C ASP* 3.1 42.6 + - - +
311C LYS* 3.6 27.7 - - - +
254D ALA* 2.6 34.6 + - - +
255D ALA* 3.2 13.7 - - - +
256D THR 2.8 0.4 + - - -
257D LEU* 1.3 74.3 - - - +
259D ILE* 1.3 62.7 + - + +
261D GLU* 3.2 14.1 + - - +
262D GLU* 3.4 19.9 + - - +
289D LYS* 3.8 3.3 - - - +
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Residues in contact with ILE 259 (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 VAL* 4.0 15.0 - - + +
212D LEU* 4.6 3.1 - - + -
213D LYS* 3.5 44.6 - - + +
216D MET* 3.3 34.3 - - + -
255D ALA* 3.4 12.3 - - + +
256D THR 2.8 12.5 + - - +
258D ARG* 1.3 75.1 - - + +
260D ILE* 1.3 60.4 + - + +
262D GLU* 2.9 9.6 + - - +
263D ASN* 2.5 63.1 + - + +
264D ILE* 5.5 4.9 - - + -
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Residues in contact with ILE 260 (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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216D MET* 4.2 9.2 - - + -
227D LEU* 4.1 19.1 - - + -
229D LEU* 5.1 0.2 - - + -
256D THR* 3.3 26.7 - - + +
257D LEU* 2.8 32.8 + - + +
259D ILE* 1.3 76.1 - - + +
261D GLU* 1.3 62.9 + - - +
264D ILE* 2.8 48.8 + - + +
267D LEU* 3.5 26.0 - - + -
270D LEU* 4.4 14.4 - - + -
286D ILE* 5.8 3.1 - - + -
289D LYS* 4.3 9.6 - - + +
290D ALA* 5.0 3.6 - - + -
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Residues in contact with GLU 261 (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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281C ASP* 4.2 0.7 - - - +
311C LYS* 3.2 33.1 + - - +
257D LEU 2.8 11.1 + - - +
258D ARG* 3.2 26.7 + - - +
260D ILE* 1.3 72.3 - - - +
262D GLU* 1.3 62.8 + - - +
265D PRO* 3.1 25.3 - - - +
288D GLN 5.5 0.2 - - - +
289D LYS* 3.3 61.9 + - + +
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Residues in contact with GLU 262 (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 LYS* 4.1 14.8 + - - -
258D ARG* 3.4 14.2 + - - +
259D ILE* 2.9 13.5 + - - +
261D GLU* 1.3 86.7 - - - +
263D ASN* 1.3 85.0 + - - +
265D PRO* 3.5 13.3 - - - +
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Residues in contact with ASN 263 (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 LYS* 3.7 17.8 - - - +
259D ILE* 2.5 43.9 + - + +
262D GLU* 1.3 98.9 + - - +
264D ILE* 1.3 64.9 + - + +
265D PRO* 3.0 12.6 - - - +
266D GLU* 3.9 4.5 - - - +
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Residues in contact with ILE 264 (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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216D MET* 6.0 4.0 - - + -
217D SER* 6.5 0.2 - - - -
220D TYR* 3.5 50.3 - - + +
227D LEU* 4.3 19.3 - - + -
259D ILE* 5.5 4.3 - - + -
260D ILE* 2.8 35.9 + - + +
263D ASN* 1.3 83.5 - - + +
265D PRO* 1.3 53.8 - - - +
266D GLU* 2.9 29.9 + - - +
267D LEU* 3.4 31.0 + - + +
289D LYS 4.3 3.6 - - - +
290D ALA* 5.1 0.2 - - - +
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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