Contacts of the helix formed by residues 301 - 323 (chain G) in PDB entry 1K7L
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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299G ASN 3.6 0.9 + - - -
300G LEU* 1.3 82.2 - - - +
302G LEU* 1.3 65.4 + - - +
303G ASN* 3.2 18.7 + - - +
304G ASP* 2.7 43.6 + - + +
305G GLN* 3.2 19.8 + - - +
392G LEU* 3.7 17.3 - - - +
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Residues in contact with LEU 302 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300G LEU 5.8 0.4 - - - +
301G ASP* 1.3 81.0 + - - +
303G ASN* 1.3 65.3 + - - +
305G GLN* 3.4 14.4 + - - +
306G VAL* 3.2 17.9 + - + +
691H HIS* 2.9 40.2 - - + +
694H LEU* 3.9 21.1 - - + -
695H GLN* 4.5 22.7 - - - +
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Residues in contact with ASN 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301G ASP* 3.2 12.6 + - - +
302G LEU* 1.3 75.4 - - - +
304G ASP* 1.3 65.1 + - - +
305G GLN 3.1 2.2 - - - -
306G VAL* 3.3 8.8 + - + +
307G THR* 2.8 31.0 + - - +
390G GLY 6.0 0.2 - - - -
392G LEU* 4.4 14.0 - - + +
685H GLU* 4.1 20.4 + - - +
691H HIS* 4.2 20.0 + - - -
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Residues in contact with ASP 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300G LEU* 4.4 20.1 - - + +
301G ASP* 2.7 27.5 + - - +
303G ASN* 1.3 73.3 - - - +
305G GLN* 1.3 61.5 + - - +
307G THR* 3.6 5.2 - - - -
308G LEU* 3.2 28.2 + - - +
390G GLY 4.1 1.0 - - - +
391G LEU* 3.4 14.2 - - + +
392G LEU* 2.5 36.2 + - - +
393G ASN* 2.9 32.2 + - - +
397G ILE* 4.3 4.5 - - + +
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Residues in contact with GLN 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292G LYS* 6.1 0.6 - - - +
297G PHE* 2.7 54.1 - - + +
298G ALA* 3.5 17.8 - - - +
300G LEU* 3.8 10.1 - - + +
301G ASP 3.2 17.4 + - - +
302G LEU* 3.4 13.8 + - - +
303G ASN 3.1 0.4 - - - -
304G ASP* 1.3 74.5 - - - +
306G VAL* 1.3 69.0 + - - +
307G THR 2.9 1.1 - - - -
308G LEU* 2.7 16.6 + - - +
309G LEU* 2.9 15.0 + - - +
694H LEU* 3.2 41.5 + - + +
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Residues in contact with VAL 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302G LEU 3.2 12.0 + - - +
303G ASN* 3.5 12.3 - - + +
305G GLN* 1.3 77.5 - - - +
307G THR* 1.3 61.3 + - - +
309G LEU* 3.6 2.4 + - - +
310G LYS* 2.8 32.5 + - + +
685H GLU* 5.1 7.6 - - - +
687H HIS* 3.4 35.0 - - + +
690H LEU* 4.0 18.2 - - + +
691H HIS* 3.9 31.2 - - + +
694H LEU* 4.0 17.0 - - + +
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Residues in contact with THR 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303G ASN* 2.8 22.2 + - - +
304G ASP* 3.6 6.4 - - - -
305G GLN 2.8 0.8 + - - -
306G VAL* 1.3 76.9 - - - +
308G LEU* 1.3 66.7 + - - +
310G LYS* 2.9 17.6 + - - +
311G TYR* 3.0 19.6 + - + -
388G ARG* 3.8 13.0 - - + -
389G PRO 3.2 26.5 + - - +
390G GLY 4.2 10.6 + - - -
391G LEU* 3.8 21.5 - - + +
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Residues in contact with LEU 308 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297G PHE* 3.6 23.6 - - + -
300G LEU* 3.5 31.4 - - + -
304G ASP 3.2 12.3 + - - +
305G GLN 2.7 10.5 + - - +
307G THR* 1.3 76.2 - - - +
309G LEU* 1.3 63.0 + - - +
311G TYR* 4.0 0.9 - - - +
312G GLY* 3.0 22.7 + - - -
383G ILE* 3.3 30.3 - - + +
384G CYS* 4.4 8.1 - - - -
385G CYS 3.8 26.2 - - - +
388G ARG* 4.1 8.8 + - + -
391G LEU* 3.9 15.3 - - + -
397G ILE* 4.2 9.9 - - + -
400G MET* 6.0 0.7 - - - -
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Residues in contact with LEU 309 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284G VAL* 5.4 2.2 - - + +
287G LEU* 4.5 8.5 - - + -
288G THR* 3.6 38.1 - - + +
291G ALA* 4.2 13.7 - - + -
297G PHE* 4.1 11.4 - - + -
305G GLN 2.9 13.1 + - - +
306G VAL* 4.0 3.4 - - - +
308G LEU* 1.3 76.0 - - - +
310G LYS* 1.3 64.4 + - - +
312G GLY 4.6 0.4 - - - +
313G VAL* 3.2 37.5 + - + +
383G ILE* 4.9 13.0 - - + -
463G ILE* 5.4 1.1 - - - +
690H LEU* 4.2 19.7 - - + -
694H LEU* 3.4 35.2 - - + -
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Residues in contact with LYS 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306G VAL* 2.8 22.1 + - + +
307G THR* 2.9 11.2 + - - +
309G LEU* 1.3 77.6 - - - +
311G TYR* 1.3 73.3 + - + +
313G VAL* 4.3 1.4 - - - +
462G GLU 2.7 16.2 + - - +
463G ILE* 3.4 29.9 - - - +
465G ARG* 2.4 31.5 + - - +
466G ASP* 4.6 4.5 - - - +
467G MET* 2.9 36.2 - - + +
687H HIS* 3.2 35.2 + - + +
690H LEU* 4.6 8.9 - - + +
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Residues in contact with TYR 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307G THR* 3.0 18.9 + - + +
310G LYS* 1.3 91.3 - - + +
312G GLY* 1.3 61.7 + - - +
313G VAL 3.7 0.2 - - - -
314G TYR* 4.8 2.1 + - - +
315G GLU* 3.9 12.8 + - - +
388G ARG* 3.3 31.0 - - + -
389G PRO* 3.3 54.9 - - + +
437G VAL* 5.3 2.4 - - - +
466G ASP 3.7 5.9 + - - -
467G MET* 2.6 53.5 + - + +
468G TYR* 3.8 43.8 + + - -
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Residues in contact with GLY 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308G LEU 3.0 15.1 + - - -
311G TYR* 1.3 77.0 - - - +
313G VAL* 1.3 60.0 + - - +
314G TYR 3.3 2.9 - - - -
315G GLU 3.1 2.3 + - - -
316G ALA* 2.8 28.7 + - - +
382G ILE* 3.1 29.8 - - - +
383G ILE* 5.0 7.2 - - - -
388G ARG* 3.9 4.6 - - - +
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Residues in contact with VAL 313 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284G VAL* 3.2 35.7 - - + -
287G LEU* 3.2 31.4 - - + -
309G LEU* 3.2 25.5 + - + +
310G LYS 4.3 2.5 - - - +
311G TYR 5.3 0.2 - - - -
312G GLY* 1.3 75.2 - - - +
314G TYR* 1.3 86.4 + - + +
316G ALA* 3.1 4.1 + - - +
317G ILE* 2.7 41.7 + - + +
383G ILE* 5.4 1.5 - - - +
463G ILE* 4.2 17.9 - - + -
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Residues in contact with TYR 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280G SER* 4.2 5.2 - - - -
311G TYR 4.8 2.3 + - - +
312G GLY 3.3 0.8 - - - -
313G VAL* 1.3 91.4 - - + +
315G GLU* 1.3 64.9 + - - +
317G ILE* 4.0 11.9 - - + -
318G PHE* 2.9 51.7 + + + -
437G VAL* 3.7 27.4 - - + -
440G HIS* 4.4 1.3 - + - -
460G LEU* 3.1 21.2 - - + +
463G ILE* 3.6 27.6 - - + -
464G TYR* 3.0 40.5 - + - -
467G MET* 4.3 9.9 - - + -
601G 544 2.7 36.8 + - + -
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Residues in contact with GLU 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311G TYR 4.0 6.9 + - - +
312G GLY 3.1 1.6 + - - +
314G TYR* 1.3 77.8 - - - +
316G ALA* 1.3 59.9 + - - +
319G ALA* 3.1 24.3 + - - +
382G ILE* 2.9 23.3 - - + +
388G ARG* 2.8 30.6 + - - -
430G MET* 4.7 5.0 - - - +
433G LEU* 3.4 29.9 - - + +
434G ARG* 3.0 42.4 + - - -
437G VAL* 3.5 21.3 - - + -
468G TYR* 3.3 7.3 + - - -
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Residues in contact with ALA 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G LEU* 3.6 30.7 - - + -
312G GLY 2.8 14.3 + - - +
313G VAL* 3.3 8.7 - - - +
315G GLU* 1.3 76.0 - - - +
317G ILE* 1.3 59.8 + - - +
319G ALA* 3.1 7.1 + - - +
320G MET* 2.8 35.7 + - + +
379G VAL* 3.8 17.9 - - + -
382G ILE* 4.1 8.0 - - + +
383G ILE* 5.0 2.0 - - + -
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Residues in contact with ILE 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G THR* 6.1 1.8 - - + -
280G SER* 4.2 17.7 - - - +
283G THR* 3.5 30.5 - - + +
284G VAL* 4.1 14.1 - - + -
287G LEU* 4.1 2.2 - - + -
313G VAL* 2.7 39.9 + - + +
314G TYR* 3.4 18.8 + - + +
316G ALA* 1.3 73.7 - - - +
318G PHE* 1.3 69.0 + - + +
320G MET* 3.8 5.9 - - - +
321G LEU* 2.8 47.6 + - + +
601G 544 4.7 11.4 - - + -
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Residues in contact with PHE 318 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314G TYR* 2.9 46.7 + + + +
317G ILE* 1.3 78.7 - - + +
319G ALA* 1.3 61.4 + - - +
321G LEU* 4.1 10.2 - - + +
322G SER* 2.9 24.8 + - - -
325G MET* 5.7 1.0 - - - +
358G LYS* 3.4 43.1 - - + -
361G PHE* 4.4 3.8 - - - -
433G LEU* 3.7 15.7 - - + -
436G LEU* 4.2 17.3 - - + -
437G VAL* 3.9 19.3 - - + -
440G HIS* 3.6 32.3 - + + -
601G 544 4.4 22.4 - + + -
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Residues in contact with ALA 319 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315G GLU 3.1 19.8 + - - +
316G ALA* 3.1 8.2 + - - +
318G PHE* 1.3 79.1 - - - +
320G MET* 1.3 62.1 + - - +
322G SER* 3.2 20.7 + - - -
323G SER* 4.3 2.3 + - - -
361G PHE* 4.7 4.3 - - - -
365G PHE* 3.8 15.3 - - + -
375G ILE* 5.7 4.1 - - + +
378G PHE* 4.0 20.2 - - + -
379G VAL* 4.9 6.3 - - + -
382G ILE* 5.8 0.7 - - + -
433G LEU* 3.9 18.1 - - + +
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Residues in contact with MET 320 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214G TYR* 4.4 13.2 - - + +
218G PHE* 3.8 35.7 - - + -
283G THR* 4.1 14.8 - - + -
287G LEU* 3.6 32.5 - - + -
316G ALA* 2.8 28.9 + - + +
317G ILE* 4.0 2.5 - - - +
319G ALA* 1.3 75.7 - - - +
321G LEU* 1.3 63.9 + - - +
323G SER* 3.2 25.1 + - - -
324G VAL* 4.3 2.9 + - - +
375G ILE* 4.5 12.1 - - + -
379G VAL* 4.1 17.7 - - + -
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Residues in contact with LEU 321 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G THR* 5.1 8.1 - - + -
317G ILE* 2.8 32.2 + - + +
318G PHE* 4.1 13.7 - - + +
319G ALA 3.3 0.4 - - - -
320G MET* 1.3 74.4 - - - +
322G SER* 1.3 66.9 + - - +
324G VAL* 3.1 26.5 + - + +
325G MET* 3.0 27.9 - - - +
330G MET* 3.8 21.8 - - + -
331G LEU 5.7 0.2 - - - +
355G MET* 5.8 1.3 - - - -
358G LYS* 6.2 0.9 - - + -
601G 544 3.6 48.7 - - + +
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Residues in contact with SER 322 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318G PHE 2.9 17.7 + - - -
319G ALA 3.2 10.3 + - - -
320G MET 3.2 0.8 - - - -
321G LEU* 1.3 78.0 - - - +
323G SER* 1.3 63.7 + - - +
325G MET* 2.9 24.4 + - - +
361G PHE* 3.7 18.5 - - - -
362G ALA* 3.9 16.9 - - - +
365G PHE* 3.9 8.5 - - - -
366G ASN* 3.0 31.8 + - - -
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Residues in contact with SER 323 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214G TYR* 5.5 1.0 + - - -
221G ASN 5.0 0.7 - - - -
222G LYS* 3.2 51.0 + - - +
225G ALA* 3.8 9.4 - - - +
226G ARG* 2.4 32.4 + - - +
319G ALA 4.3 1.5 + - - -
320G MET* 3.2 18.2 + - - -
321G LEU 3.1 0.4 - - - -
322G SER* 1.3 78.7 - - - +
324G VAL* 1.3 59.2 + - - +
365G PHE* 5.8 1.4 - - - -
366G ASN* 4.1 4.0 + - - -
375G ILE* 3.9 9.7 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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