Contacts of the helix formed by residues 247 - 267 (chain F) in PDB entry 3IKM
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 THR 247 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205F PRO* 4.7 2.0 - - + -
243F THR* 2.6 25.6 - - + +
244F PRO* 2.7 52.0 - - + -
246F ARG* 1.3 78.1 - - - +
248F SER* 1.3 57.2 + - - +
250F GLN* 3.2 5.0 + - - +
251F TRP* 2.4 62.6 + - + +
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Residues in contact with SER 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243F THR* 5.2 1.5 + - - +
244F PRO 3.6 4.9 + - - -
245F PRO 2.4 31.4 + - - -
246F ARG* 2.9 15.2 - - - +
247F THR* 1.3 86.8 + - - +
249F ASN* 1.3 93.9 + - - +
250F GLN 4.2 0.7 - - - -
251F TRP* 3.9 1.2 - - - +
252F LEU* 3.1 16.8 + - - +
305F ASN* 4.0 16.0 + - - +
334F CYS* 5.1 4.5 - - - -
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Residues in contact with ASN 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1209D ARG* 2.6 56.7 + - + +
248F SER* 1.3 94.5 + - - +
250F GLN* 1.3 54.3 + - - +
252F LEU* 3.0 7.5 - - - +
253F ASP 2.9 9.2 + - - -
305F ASN* 3.9 14.9 + - - +
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Residues in contact with GLN 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440D ASN* 5.7 0.8 + - - -
443D ARG* 4.7 11.7 - - - +
1206D MET* 3.6 21.5 - - - +
1209D ARG* 3.7 12.2 + - - +
1210D TYR 6.0 0.4 - - - +
246F ARG 4.1 7.4 - - - +
247F THR* 3.4 7.6 - - - +
248F SER* 3.1 1.2 - - - -
249F ASN* 1.3 76.3 - - - +
251F TRP* 1.3 65.0 + - + +
253F ASP* 2.9 2.8 + - - +
254F PHE* 2.8 21.1 + - - +
257F ARG* 2.5 28.9 + - - +
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Residues in contact with TRP 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F PHE* 5.3 15.7 - + - -
123F GLU* 5.1 8.2 + - - -
205F PRO* 4.8 7.1 + - - +
241F TRP* 3.0 40.0 - + + +
243F THR* 3.7 5.4 - - + -
247F THR* 2.4 67.2 + - + +
248F SER 3.9 0.9 - - - +
250F GLN* 1.3 69.6 - - + +
252F LEU* 1.3 70.0 + - - +
254F PHE* 3.0 68.2 - + + +
255F TRP* 3.2 13.9 - - - -
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Residues in contact with LEU 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1209D ARG* 2.6 44.1 + - - +
248F SER 3.1 10.0 + - - +
249F ASN 3.0 13.0 + - - +
251F TRP* 1.3 78.5 - - - +
253F ASP* 1.3 62.3 + - - +
255F TRP* 2.8 30.5 + - + +
256F LEU* 3.3 8.8 + - + -
285F LYS* 3.5 25.1 - - - +
286F GLY* 3.9 13.9 - - - -
303F LEU* 4.7 18.8 - - + -
304F TRP 5.1 4.7 - - - +
305F ASN* 3.7 23.8 - - + +
337F SER* 5.4 2.9 - - - -
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Residues in contact with ASP 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1205D GLY 3.9 4.2 - - - +
1206D MET* 2.9 46.2 + - - +
1208D ARG* 5.7 0.9 + - - -
1209D ARG* 2.4 49.9 + - + +
249F ASN 2.9 5.2 + - - +
250F GLN* 2.9 5.8 + - - +
252F LEU* 1.3 72.9 - - - +
254F PHE* 1.3 56.0 + - - +
255F TRP 3.2 0.2 + - - -
256F LEU* 3.1 19.1 + - - +
257F ARG* 2.7 51.3 + - - +
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Residues in contact with PHE 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443D ARG* 6.3 1.1 - - - +
121F PHE* 6.2 5.6 - + + -
241F TRP* 3.9 2.2 - + - -
250F GLN* 2.8 2.8 + - - +
251F TRP* 3.0 52.5 - + + +
253F ASP* 1.3 74.8 - - - +
255F TRP* 1.3 123.3 + + - +
257F ARG* 2.5 30.7 - - + +
258F HIS* 2.8 34.2 + + + +
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Residues in contact with TRP 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F VAL* 5.6 10.5 - - + -
239F LEU* 3.7 27.1 - - + -
241F TRP* 2.4 47.7 - + - -
251F TRP 3.2 21.1 - - - -
252F LEU* 2.8 12.2 + - + +
254F PHE* 1.3 97.3 - + - +
256F LEU* 1.3 73.9 + - - +
258F HIS* 2.8 31.3 + + + -
259F ARG* 2.6 37.7 + - + +
303F LEU* 4.2 18.2 - - + -
336F LEU* 4.2 8.9 - - + +
337F SER 5.5 3.1 - - - -
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Residues in contact with LEU 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1202D ASN* 6.1 1.3 - - - +
1208D ARG* 5.3 2.5 - - - +
1209D ARG* 2.7 35.0 - - - +
252F LEU* 3.3 4.9 + - + -
253F ASP* 3.1 21.0 + - - +
255F TRP* 1.3 79.7 - - - +
257F ARG* 1.3 71.8 + - + +
259F ARG* 3.2 3.9 + - + +
260F LEU* 3.1 30.5 + - + +
275F SER* 5.3 2.7 - - - +
285F LYS* 4.2 5.8 - - - +
287F ASN* 2.7 40.8 - - - +
289F LEU* 5.5 4.7 - - + -
303F LEU* 4.4 18.1 - - + +
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Residues in contact with ARG 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443D ARG* 4.8 16.2 - - - +
447D GLU* 4.5 12.9 + - - +
1202D ASN* 4.6 17.9 - - - +
1206D MET* 2.4 61.9 - - + +
250F GLN* 2.5 23.9 + - - +
253F ASP* 2.7 23.1 + - - +
254F PHE* 2.5 47.4 - - + +
256F LEU* 1.3 87.1 - - + +
258F HIS* 1.3 60.6 + - - +
260F LEU* 2.9 7.3 + - - +
261F GLN* 2.3 35.5 + - - +
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Residues in contact with HIS 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F SER* 4.2 27.3 + - - -
118F VAL* 5.6 1.1 - - - -
254F PHE* 2.8 18.8 + + + +
255F TRP* 2.8 31.3 + + + +
257F ARG* 1.3 77.1 - - - +
259F ARG* 1.3 96.5 + - - +
261F GLN* 2.8 16.1 + - + +
262F TRP* 3.2 22.8 + - + +
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Residues in contact with ARG 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F TRP* 2.4 52.1 + - - +
117F SER* 5.7 0.2 - - - -
118F VAL* 6.0 0.6 - - - +
255F TRP* 2.6 40.7 + - + +
256F LEU* 3.8 3.8 - - + +
258F HIS* 1.3 94.1 - - - +
260F LEU* 1.3 64.3 + - + +
262F TRP* 3.0 39.7 + - - +
263F TRP* 3.0 24.6 - - + +
289F LEU* 5.1 12.3 - - + -
301F GLU* 2.7 12.7 + - - -
303F LEU* 4.9 5.4 - - + -
339F ASN* 2.6 37.3 - - - +
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Residues in contact with LEU 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1202D ASN* 4.6 22.7 - - - +
256F LEU* 3.6 22.0 - - + +
257F ARG 2.9 13.2 + - - +
259F ARG* 1.3 75.0 - - + +
261F GLN* 1.3 65.1 + - - +
263F TRP* 3.5 9.3 + - + +
264F ARG* 3.0 46.3 + - - +
273F PHE* 4.1 23.7 - - + +
274F SER 4.8 3.6 - - - +
275F SER* 5.0 9.4 - - - +
289F LEU* 4.7 20.6 - - + -
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Residues in contact with GLN 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454D GLU* 3.7 31.5 + - - +
1202D ASN* 4.9 7.9 - - - +
257F ARG* 2.3 53.2 + - - +
258F HIS* 2.8 19.6 - - + +
260F LEU* 1.3 77.5 - - + +
262F TRP* 1.3 55.2 + - - +
264F ARG* 3.2 10.2 + - - +
265F LYS* 2.7 38.0 + - - +
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Residues in contact with TRP 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F LEU* 4.4 25.1 - - + -
113F GLU* 4.0 4.2 + - + -
114F TRP* 2.9 50.9 - + + +
117F SER* 3.4 29.2 + - - -
258F HIS* 3.2 20.9 + + + +
259F ARG* 3.0 23.7 + - - +
261F GLN* 1.3 77.0 - - - +
263F TRP* 1.3 123.9 + + - +
265F LYS* 2.9 15.3 + - + +
266F PHE* 2.9 50.7 - + - -
349F TYR* 4.3 3.4 - - - -
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Residues in contact with TRP 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F LEU* 5.5 1.8 - - + -
259F ARG* 3.0 33.9 + - + +
260F LEU* 3.7 11.0 - - + +
261F GLN 3.3 0.4 - - - -
262F TRP* 1.3 102.3 - + - +
264F ARG* 1.3 69.9 + - + +
266F PHE 2.8 4.3 + - - -
267F ALA* 2.7 26.2 + - - +
270F PRO* 4.7 0.2 - - - -
273F PHE* 4.3 37.5 - + + -
289F LEU* 5.4 3.0 - - + +
300F ILE* 4.8 5.4 - - + -
301F GLU* 2.5 38.8 + - - -
342F LEU* 5.5 1.1 - - + -
345F GLY* 3.6 30.3 - - - -
349F TYR* 2.8 53.7 + + - -
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Residues in contact with ARG 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454D GLU* 3.4 26.9 + - - +
455D LEU* 6.4 0.2 - - - +
458D GLU* 2.8 36.9 + - - +
260F LEU* 3.0 37.8 + - - +
261F GLN* 3.4 9.3 - - - +
263F TRP* 1.3 77.8 - - + +
265F LYS* 1.3 65.0 + - - +
267F ALA 2.8 20.4 + - - +
270F PRO* 3.4 36.6 + - + +
271F SER* 4.5 7.3 + - - +
273F PHE* 4.7 13.0 + - + -
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Residues in contact with LYS 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457D ARG* 5.3 0.7 - - - +
461D LYS* 5.7 4.7 + - - -
261F GLN* 2.7 17.6 + - - +
262F TRP* 3.0 19.1 - - + +
264F ARG* 1.3 75.2 - - - +
266F PHE* 1.3 83.3 + - + +
267F ALA 3.5 1.4 + - - +
375F HIS* 4.9 10.2 + - + +
483F LYS* 4.1 15.0 - - - +
484F ASN 3.7 10.7 + - - +
485F VAL* 3.3 54.7 + - + +
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Residues in contact with PHE 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F LEU* 5.5 4.3 - - + -
113F GLU* 3.3 44.0 - - + -
262F TRP* 2.9 51.8 - + - -
263F TRP 2.8 7.5 + - - -
265F LYS* 1.3 101.2 - - + +
267F ALA* 1.3 57.2 + - - +
268F MET 4.1 0.2 + - - -
349F TYR* 2.9 37.4 - + + +
375F HIS* 4.3 19.3 - + - -
377F CYS* 4.8 3.6 - - + -
378F LEU* 3.1 49.1 - - + +
483F LYS* 4.8 5.6 - - + -
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Residues in contact with ALA 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458D GLU* 6.0 0.2 - - - +
461D LYS* 5.7 6.4 - - - +
263F TRP 2.7 18.8 + - - +
264F ARG 2.8 9.1 + - - +
265F LYS 3.3 1.1 - - - +
266F PHE* 1.3 73.7 - - - +
268F MET* 1.3 58.2 + - - +
269F SER 3.1 1.6 - - - -
270F PRO* 3.0 41.3 - - + +
273F PHE* 3.4 18.2 - - + -
349F TYR* 3.9 3.8 - - + -
352F ASP* 2.9 11.4 - - - +
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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