Contacts of the helix formed by residues 301 - 322 (chain B) 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 ASP 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B LEU* 1.3 71.8 - - - +
302B LEU* 1.3 54.4 + - - +
303B ASN* 2.4 42.0 + - - +
304B ASP* 2.5 36.1 + - - +
305B GLN 3.0 8.3 + - - -
392B LEU* 4.5 11.8 - - - +
393B ASN* 4.3 11.2 - - - +
204D LYS* 3.7 29.5 + - - +
208D LYS* 3.3 20.6 + - - +
697G TYR* 4.6 10.3 - - - -
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU 2.9 9.0 + - - -
301B ASP* 1.3 69.9 + - - +
303B ASN* 1.3 73.5 + - - +
305B GLN* 3.5 30.0 - - - +
306B VAL* 3.5 12.1 + - + +
690F ARG* 5.0 15.3 - - + +
693F LEU* 5.1 4.8 - - + +
694F MET* 4.5 24.5 - - + -
696G LYS 3.7 24.0 - - - +
697G TYR* 3.5 30.1 - - + +
698G ASP 5.2 0.9 - - - +
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Residues in contact with ASN 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ASP* 2.4 30.0 + - - +
302B LEU* 1.3 80.5 - - - +
304B ASP* 1.3 58.4 + - - +
305B GLN 3.1 1.3 - - - -
306B VAL* 3.0 22.2 + - - +
307B THR* 3.1 16.6 + - - -
208D LYS* 3.1 33.5 + - + +
690F ARG* 3.5 23.7 + - - +
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Residues in contact with ASP 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU* 4.9 5.5 - - + +
301B ASP* 2.5 32.3 + - + +
303B ASN* 1.3 73.1 - - - +
305B GLN* 1.3 58.4 + - - +
307B THR* 3.4 6.4 - - - -
308B LEU* 2.8 36.6 + - - +
390B GLY 3.5 5.4 - - - +
391B LEU* 3.0 23.4 - - + +
392B LEU* 2.9 35.2 + - - +
393B ASN* 3.4 15.9 + - - +
397B ILE* 4.3 12.4 - - + +
208D LYS* 4.4 2.6 + - - -
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Residues in contact with GLN 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LYS* 5.6 2.1 - - - +
297B PHE* 3.3 46.4 + - + +
298B ALA* 3.2 24.7 + - - +
300B LEU* 3.2 32.4 + - + -
301B ASP 3.0 5.5 + - - +
302B LEU* 3.5 21.0 - - - +
304B ASP* 1.3 77.2 - - - +
306B VAL* 1.3 60.6 + - - +
308B LEU 3.9 0.2 + - - -
309B LEU* 3.5 28.9 + - - +
689F ILE* 4.2 0.2 - - - +
693F LEU* 4.0 25.4 - - + +
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LEU* 3.5 12.1 + - + +
303B ASN* 3.0 11.0 + - - +
305B GLN* 1.3 77.1 - - - +
307B THR* 1.3 63.0 + - - +
310B LYS* 2.9 34.6 + - + +
686F GLU* 4.0 24.7 - - + +
689F ILE* 3.3 15.0 - - + +
690F ARG* 3.9 41.1 - - + +
693F LEU* 3.5 23.3 - - + -
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Residues in contact with THR 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ASN* 3.1 15.3 + - - -
304B ASP* 3.0 10.3 + - - -
306B VAL* 1.3 77.6 - - - +
308B LEU* 1.3 61.2 + - - +
310B LYS* 4.3 5.8 - - + -
311B TYR* 2.9 45.1 + - + +
388B ARG* 4.4 3.1 - - + -
389B PRO 3.4 26.0 - - - +
390B GLY* 4.0 10.1 + - - +
391B LEU* 3.6 22.0 - - + -
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B PHE* 3.7 26.0 - - + -
300B LEU* 3.8 19.5 - - + -
304B ASP 2.8 19.3 + - - +
305B GLN 4.4 0.4 - - - +
307B THR* 1.3 73.5 - - - +
309B LEU* 1.3 61.9 + - - +
311B TYR* 4.2 0.3 - - - +
312B GLY* 3.2 21.8 + - - -
383B ILE* 3.6 31.3 - - + +
384B CYS* 4.2 6.3 - - + -
385B CYS 3.3 26.2 - - - +
388B ARG* 4.2 9.0 + - + -
391B LEU* 3.9 11.4 - - + -
397B ILE* 3.8 32.1 - - + -
400B MET* 5.8 0.2 - - + -
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B LEU* 3.9 20.2 - - + +
288B THR* 3.1 44.2 - - + +
291B ALA* 4.2 12.1 - - + -
297B PHE* 4.4 5.8 - - + -
305B GLN 3.5 11.9 + - - +
308B LEU* 1.3 75.9 - - - +
310B LYS* 1.3 61.0 + - - +
312B GLY 5.2 0.2 - - - -
313B VAL* 2.9 48.0 + - + +
383B ILE* 4.1 22.2 - - + -
689F ILE* 3.4 25.1 - - + -
693F LEU* 4.5 6.7 - - + -
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Residues in contact with LYS 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B VAL* 2.9 23.0 + - + +
307B THR* 3.8 4.5 - - + +
309B LEU* 1.3 80.2 - - - +
311B TYR* 1.3 95.2 + - + +
312B GLY 3.4 0.3 + - - -
313B VAL* 3.7 11.3 + - - +
314B TYR 5.1 0.2 + - - -
682F ASN 3.9 10.8 + - - +
683F MET 4.0 24.5 - - - +
684F GLY* 5.0 4.5 - - - -
685F LEU* 4.4 16.6 - - + +
686F GLU* 3.7 34.4 + - + +
689F ILE* 3.9 9.8 - - + +
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Residues in contact with TYR 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B THR* 2.9 37.0 + - + +
310B LYS* 1.3 110.2 + - + +
312B GLY* 1.3 57.5 + - - +
313B VAL 3.6 0.2 - - - -
314B TYR* 5.3 1.6 + - - +
315B GLU* 4.5 4.2 - - - +
388B ARG* 3.7 32.8 + - + -
389B PRO* 3.4 44.0 + - + +
682F ASN* 4.0 24.9 + - - +
683F MET 6.2 0.2 - - - -
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Residues in contact with GLY 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LEU 3.2 14.5 + - - -
309B LEU 3.8 1.3 - - - -
311B TYR* 1.3 78.8 - - - +
313B VAL* 1.3 65.1 + - - +
314B TYR 3.2 3.1 + - - -
315B GLU* 3.7 6.6 + - - -
316B ALA* 3.4 20.1 + - - +
382B ILE* 4.0 8.1 - - - +
383B ILE* 4.6 6.7 - - - +
388B ARG* 3.4 23.1 - - - +
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Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B VAL* 4.6 23.8 - - + +
287B LEU* 3.6 28.4 - - + +
309B LEU* 2.9 29.1 + - + +
310B LYS* 4.1 7.9 - - - +
311B TYR 3.6 1.0 - - - -
312B GLY* 1.3 79.2 - - - +
314B TYR* 1.3 79.7 + - + +
316B ALA* 3.4 4.8 + - - +
317B ILE* 3.3 28.1 + - + +
383B ILE* 5.8 0.4 - - - -
685F LEU* 3.9 27.4 - - + -
689F ILE* 6.1 2.0 - - + -
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Residues in contact with TYR 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B TYR 5.3 1.3 + - - +
312B GLY* 3.2 1.0 - - - -
313B VAL* 1.3 89.8 - - + +
315B GLU* 1.3 68.5 + - - +
316B ALA 3.0 1.6 - - - -
317B ILE* 3.0 19.7 + - + +
318B PHE* 3.2 25.4 + + + -
437B VAL* 3.2 22.0 - - + -
440B HIS* 5.5 9.4 - + - -
441B ALA* 6.2 1.6 - - + -
776B 471 3.3 59.1 + - + +
682F ASN* 3.3 38.8 - - + +
683F MET* 4.0 23.6 - - + +
685F LEU* 4.5 15.5 - - + +
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Residues in contact with GLU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B TYR 4.5 4.8 + - - +
312B GLY* 3.7 5.9 + - - +
313B VAL 3.5 0.4 - - - -
314B TYR* 1.3 79.9 - - - +
316B ALA* 1.3 61.8 + - - +
319B ALA* 3.2 21.3 + - - +
382B ILE* 3.9 24.7 - - + +
388B ARG* 3.2 35.1 + - - -
430B MET* 4.3 7.4 - - - +
433B LEU* 3.4 35.5 - - + +
434B ARG* 3.4 37.5 + - - +
437B VAL* 3.9 15.9 - - + +
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Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B LEU* 3.7 28.7 - - + -
312B GLY 3.4 10.3 + - - +
313B VAL* 3.4 10.7 + - - +
314B TYR 3.0 0.4 - - - -
315B GLU* 1.3 81.7 - - - +
317B ILE* 1.3 60.7 + - - +
319B ALA* 3.4 5.6 + - - +
320B MET* 3.1 32.2 + - + +
379B VAL* 4.2 13.5 - - + -
382B ILE* 4.1 10.9 - - + +
383B ILE* 4.8 2.9 - - + -
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Residues in contact with ILE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B SER* 4.4 7.4 - - - +
283B THR* 3.7 32.1 - - + -
284B VAL* 5.1 10.5 - - + -
287B LEU* 3.9 8.1 - - + -
313B VAL* 3.3 16.6 - - + +
314B TYR* 3.0 17.1 + - + +
316B ALA* 1.3 77.8 - - - +
318B PHE* 1.3 68.5 + - + +
320B MET* 3.3 6.3 + - - +
321B LEU* 2.8 33.8 + - + +
776B 471 4.0 43.3 - - + -
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Residues in contact with PHE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B TYR* 3.2 22.2 + + + +
317B ILE* 1.3 79.7 - - + +
319B ALA* 1.3 65.6 + - - +
320B MET 3.3 0.3 + - - -
321B LEU* 3.3 19.3 + - + +
322B SER* 3.0 17.2 + - - -
355B MET* 5.6 0.9 - - + -
358B LYS* 3.8 26.0 - - + -
361B PHE* 4.1 6.5 - - + -
433B LEU* 3.6 17.5 - - + -
436B LEU* 3.9 24.0 - - + -
437B VAL* 3.8 34.3 - - + -
440B HIS* 3.8 36.1 - + + -
776B 471 4.3 25.8 - + + -
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B GLU 3.2 18.9 + - - +
316B ALA* 3.6 6.5 - - - +
318B PHE* 1.3 76.2 - - - +
320B MET* 1.3 59.1 + - - +
322B SER* 3.3 16.2 + - - -
323B SER* 4.5 2.9 + - - -
361B PHE* 4.5 4.7 - - - -
365B PHE* 3.8 16.0 - - + -
375B ILE* 5.2 3.8 - - + +
378B PHE* 4.0 20.4 - - + -
379B VAL* 4.6 5.6 - - + -
382B ILE* 4.2 5.2 - - + -
433B LEU* 3.5 22.1 - - + +
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Residues in contact with MET 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B TYR* 4.4 14.1 - - - +
218B PHE* 3.3 49.6 - - + -
283B THR* 5.3 5.8 - - + -
287B LEU* 3.9 20.9 - - + -
316B ALA* 3.1 18.9 + - + +
317B ILE* 3.9 5.6 - - - +
319B ALA* 1.3 76.2 - - - +
321B LEU* 1.3 63.7 + - - +
322B SER 3.2 2.9 - - - -
323B SER* 3.1 24.2 + - - +
324B VAL* 4.2 2.4 + - - +
375B ILE* 4.3 6.7 - - + -
379B VAL* 3.7 23.6 - - + -
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Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ILE* 2.8 26.6 + - + +
318B PHE* 3.3 28.2 + - + +
320B MET* 1.3 74.3 - - - +
322B SER* 1.3 53.6 + - - +
324B VAL* 2.7 42.4 + - + +
325B MET* 3.5 27.2 + - + +
330B MET* 3.6 30.1 - - + -
355B MET* 4.4 9.0 - - + -
358B LYS* 5.0 3.1 - - + -
776B 471 4.0 27.8 - - + +
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Residues in contact with SER 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ARG* 4.1 0.3 + - - -
318B PHE 3.0 17.0 + - - -
319B ALA 3.3 10.3 + - - -
320B MET 3.2 0.2 - - - -
321B LEU* 1.3 74.6 - - - +
323B SER* 1.3 59.6 + - - +
324B VAL 3.1 0.8 + - - -
325B MET* 3.7 9.6 + - - +
361B PHE* 3.8 12.8 - - - -
362B ALA* 3.5 35.1 - - - +
365B PHE* 4.0 8.5 - - - -
366B ASN* 2.5 38.7 + - - +
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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