Contacts of the helix formed by residues 246 - 267 (chain C) 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 ARG 246 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832A ASP* 4.9 12.6 - - - +
244C PRO* 3.0 3.5 - - + +
245C PRO* 1.3 110.8 - - + +
247C THR* 1.3 72.5 + - - +
248C SER* 2.6 7.7 + - - -
250C GLN* 4.2 9.2 - - - +
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Residues in contact with THR 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C PRO* 5.1 0.9 - - + -
243C THR* 2.6 26.0 + - + +
244C PRO* 2.6 54.0 - - + +
246C ARG* 1.3 77.5 - - - +
248C SER* 1.3 56.6 + - - +
250C GLN* 3.2 5.4 + - - +
251C TRP* 2.4 64.0 + - + +
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Residues in contact with SER 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C THR* 5.1 3.0 + - - -
244C PRO 3.6 5.4 + - - -
245C PRO 2.5 32.2 + - - -
246C ARG* 3.2 10.5 - - - +
247C THR* 1.3 92.3 + - - +
249C ASN* 1.3 93.6 + - - -
250C GLN 4.4 0.2 - - - -
251C TRP* 3.7 1.9 - - - +
252C LEU* 3.0 19.1 + - - +
305C ASN* 4.0 14.5 + - - +
334C CYS* 5.4 2.2 - - - -
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Residues in contact with ASN 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1208A ARG 5.0 3.6 - - - +
1210A TYR* 5.0 17.7 - - + -
248C SER* 1.3 99.1 + - - +
250C GLN* 1.3 51.4 + - - +
252C LEU* 3.3 5.2 + - - +
253C ASP* 2.7 49.0 + - - +
285C LYS* 5.0 11.3 - - - +
305C ASN* 3.6 17.8 + - - +
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Residues in contact with GLN 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ASN* 6.0 0.4 + - - -
443A ARG* 4.1 19.5 - - - +
1209A ARG 5.5 3.8 - - - +
246C ARG 4.2 7.4 - - - +
247C THR* 3.5 7.2 - - - +
248C SER* 3.1 1.2 - - - -
249C ASN* 1.3 77.1 - - - +
251C TRP* 1.3 62.5 + - + +
253C ASP* 4.2 3.8 - - - -
254C PHE* 2.6 28.7 + - - +
257C ARG* 2.3 47.9 + - - +
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Residues in contact with TRP 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PHE* 6.0 7.9 - + - -
123C GLU* 5.2 7.4 - - - -
205C PRO* 4.2 4.9 + - - +
241C TRP* 3.0 42.1 - + + +
243C THR* 3.6 7.4 - - + -
247C THR* 2.4 67.6 + - + +
248C SER 3.7 0.7 - - - +
250C GLN* 1.3 70.6 - - + +
252C LEU* 1.3 69.2 + - - +
254C PHE* 3.0 53.7 - + + +
255C TRP* 3.1 26.8 + - - -
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Residues in contact with LEU 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C SER 3.0 12.9 + - - +
249C ASN* 3.5 9.2 - - - +
251C TRP* 1.3 76.2 - - - +
253C ASP* 1.3 57.1 + - - +
255C TRP* 2.7 38.2 + - + +
256C LEU* 3.3 28.4 + - + -
285C LYS* 3.5 27.6 - - + +
286C GLY* 3.8 11.9 - - - +
303C LEU* 3.9 19.3 - - + +
304C TRP 5.0 2.2 - - - +
305C ASN* 3.3 37.7 - - + +
337C SER* 5.3 3.4 - - - -
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Residues in contact with ASP 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1208A ARG 2.3 28.8 - - - +
1209A ARG* 3.1 35.2 + - - +
249C ASN* 2.7 34.5 + - - +
250C GLN* 3.6 6.0 + - - +
252C LEU* 1.3 74.8 - - - +
254C PHE* 1.3 59.2 + - - +
256C LEU* 3.2 22.8 - - - +
257C ARG* 2.9 27.4 + - - +
285C LYS* 3.4 21.2 + - - -
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Residues in contact with PHE 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C TRP* 3.9 3.6 - + - -
250C GLN* 2.6 16.2 + - - +
251C TRP* 3.0 55.9 - + + +
253C ASP* 1.3 73.7 - - - +
255C TRP* 1.3 123.7 + + - +
257C ARG* 2.7 38.7 - - + +
258C HIS* 3.2 17.2 + + + +
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Residues in contact with TRP 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C VAL* 5.3 13.0 - - + -
207C GLY* 6.0 0.4 - - - -
239C LEU* 3.1 32.8 - - + -
241C TRP* 2.5 45.6 - + - -
251C TRP 3.1 20.6 - - - -
252C LEU* 2.7 17.5 + - + +
254C PHE* 1.3 94.9 - + - +
256C LEU* 1.3 72.2 + - - +
257C ARG 3.0 0.7 + - - -
258C HIS* 3.0 26.8 + + + -
259C ARG* 2.9 38.9 + - + +
303C LEU* 4.6 11.9 - - + -
336C LEU* 3.8 13.6 - - + +
337C SER* 5.5 4.0 - - - -
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Residues in contact with LEU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1208A ARG* 4.5 5.2 - - - +
1209A ARG* 2.8 41.7 - - - +
252C LEU* 3.3 33.8 + - + -
253C ASP* 3.2 12.1 - - - +
255C TRP* 1.3 80.7 - - - +
257C ARG* 1.3 68.9 + - - +
259C ARG* 3.4 2.4 + - - +
260C LEU* 3.2 28.2 + - + +
275C SER* 5.3 1.6 - - - -
285C LYS* 5.0 1.1 - - - +
287C ASN* 2.6 40.4 - - - +
289C LEU* 5.4 3.4 - - + -
303C LEU* 3.3 19.9 - - + +
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Residues in contact with ARG 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ARG* 4.4 8.2 - - - +
447A GLU* 3.7 30.8 + - + +
1209A ARG* 3.9 39.0 + - - +
250C GLN* 2.3 42.1 + - - +
253C ASP* 2.9 22.5 + - - +
254C PHE* 2.7 45.7 + - + +
256C LEU* 1.3 85.4 - - - +
258C HIS* 1.3 61.4 + - - +
260C LEU* 3.0 10.5 + - - +
261C GLN* 2.5 36.4 + - - +
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Residues in contact with HIS 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C SER* 4.0 30.5 + - - -
118C VAL* 5.5 0.9 - - - -
254C PHE* 3.2 18.7 + + + +
255C TRP* 3.0 29.6 + + + +
257C ARG* 1.3 75.3 - - - +
259C ARG* 1.3 89.0 + - - +
261C GLN* 2.6 28.1 + - + +
262C TRP* 3.2 16.9 + - + +
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Residues in contact with ARG 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C TRP* 2.5 52.2 + - - +
117C SER* 5.4 1.2 + - - -
118C VAL* 5.8 1.6 - - - +
255C TRP* 2.9 41.3 + - + +
256C LEU* 3.9 3.4 - - - +
258C HIS* 1.3 88.7 - - - +
260C LEU* 1.3 64.4 + - + +
262C TRP* 3.0 44.8 + - - +
263C TRP* 2.9 27.7 - - + +
289C LEU* 5.2 7.4 - - + -
301C GLU* 3.0 19.5 + - - -
303C LEU* 5.0 4.9 - - + -
339C ASN* 3.3 27.0 - - - +
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Residues in contact with LEU 260 (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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1209A ARG* 6.0 1.6 - - - +
256C LEU* 3.5 22.0 - - + +
257C ARG* 3.0 10.1 + - - +
259C ARG* 1.3 81.8 - - + +
261C GLN* 1.3 65.1 + - - +
262C TRP 3.3 0.3 + - - -
263C TRP* 3.3 11.3 + - + +
264C ARG* 3.2 46.0 + - - +
273C PHE* 4.0 25.1 - - + +
274C SER 5.0 3.1 - - - +
275C SER* 5.0 10.8 - - - +
289C LEU* 4.8 19.7 - - + -
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Residues in contact with GLN 261 (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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454A GLU* 3.9 25.7 + - + +
257C ARG* 2.5 47.6 + - - +
258C HIS* 2.6 34.4 + - + +
260C LEU* 1.3 74.2 - - + +
262C TRP* 1.3 64.1 + - - +
264C ARG* 4.2 9.6 - - - +
265C LYS* 3.1 27.3 + - - +
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Residues in contact with TRP 262 (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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110C LEU* 4.2 24.9 - - + -
113C GLU* 4.2 2.3 + - + -
114C TRP* 3.2 42.9 - + + +
117C SER* 3.6 27.3 + - - -
258C HIS* 3.2 17.2 + + + +
259C ARG* 3.0 35.6 + - - +
261C GLN* 1.3 78.0 - - - +
263C TRP* 1.3 114.5 + + - +
265C LYS* 2.8 32.1 - - + +
266C PHE* 2.9 45.7 - + - -
349C TYR* 4.5 3.1 - + - -
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Residues in contact with TRP 263 (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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110C LEU* 5.6 1.8 - - + -
259C ARG* 2.9 37.1 + - + +
260C LEU* 3.3 11.6 + - + +
262C TRP* 1.3 100.2 - + - +
264C ARG* 1.3 54.8 + - + +
265C LYS 3.0 1.3 - - - -
266C PHE 2.8 2.4 + - - -
267C ALA* 2.6 38.5 + - - +
273C PHE* 4.2 40.2 - + + -
289C LEU* 5.6 3.6 - - + +
300C ILE* 4.7 7.9 - - + -
301C GLU* 2.4 34.9 + - - -
342C LEU* 5.5 0.9 - - + -
345C GLY* 3.6 30.7 - - - -
348C ALA* 5.6 0.2 - - + -
349C TYR* 2.9 55.7 + + - -
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Residues in contact with ARG 264 (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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451A THR* 6.0 3.9 - - - +
454A GLU* 2.8 31.2 + - + -
455A LEU* 5.5 8.4 - - - +
458A GLU* 3.4 33.2 + - - +
461A LYS* 4.8 1.2 + - - -
260C LEU* 3.2 34.0 + - - +
261C GLN* 4.2 7.1 - - - +
263C TRP* 1.3 78.0 - - + +
265C LYS* 1.3 57.9 + - - +
267C ALA 2.6 31.5 + - - +
270C PRO* 3.2 38.8 + - + +
271C SER* 4.7 5.9 + - - +
273C PHE* 5.2 8.7 + - + -
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Residues in contact with LYS 265 (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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458A GLU* 5.1 0.7 - - - -
461A LYS* 4.4 12.9 + - - +
261C GLN* 3.1 19.1 + - - +
262C TRP* 2.8 20.7 + - + +
264C ARG* 1.3 81.4 - - - +
266C PHE* 1.3 85.8 + - + +
267C ALA 4.6 0.5 - - - +
375C HIS* 4.7 11.7 + - + +
483C LYS* 4.5 12.1 - - - +
484C ASN 4.1 8.2 + - - -
485C VAL* 3.7 47.9 + - + +
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Residues in contact with PHE 266 (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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110C LEU* 5.6 3.6 - - + -
113C GLU* 3.3 42.2 - - + -
262C TRP* 2.9 54.8 + + - -
263C TRP 2.8 3.0 + - - -
265C LYS* 1.3 105.8 - - + +
267C ALA* 1.3 55.5 + - - +
268C MET 4.1 0.2 + - - -
349C TYR* 2.6 45.7 - + + +
375C HIS* 4.1 20.6 - + - -
377C CYS* 4.4 5.4 - - + -
378C LEU* 3.1 45.6 - - + +
483C LYS* 4.9 4.9 - - + -
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Residues in contact with ALA 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A GLU* 4.5 0.2 - - - +
461A LYS* 4.3 12.3 + - - +
263C TRP 2.6 18.5 + - - +
264C ARG 2.6 13.9 + - - +
265C LYS 4.6 1.6 - - - +
266C PHE* 1.3 76.4 - - - +
268C MET* 1.3 62.3 + - - +
270C PRO* 3.3 32.6 - - + +
273C PHE* 3.4 22.2 - - + -
349C TYR* 3.8 2.7 - - + -
352C ASP* 3.2 4.9 - - - +
375C HIS* 6.4 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
------------------------------------------------------------
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