Contacts of the helix formed by residues 306 - 329 (chain G) in PDB entry 7CR3
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 ALA 306 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A ALA* 4.1 20.3 - - + +
275G LEU 6.1 0.2 - - - +
277G THR* 6.1 4.0 - - + +
302G VAL 3.5 19.4 + - - +
303G SER 4.0 3.1 + - - -
304G PHE 3.3 0.4 - - - -
305G PHE* 1.3 76.3 - - - +
307G LEU* 1.3 61.6 + - - +
308G PRO* 3.7 1.3 - - - -
309G ALA* 4.2 10.9 + - + +
310G GLY* 3.9 11.6 + - - -
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Residues in contact with LEU 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ALA* 3.3 26.9 - - - +
312A LEU* 3.7 20.0 - - + -
313A GLY* 3.5 20.0 - - - +
316A PHE* 4.4 17.9 - - + -
235G ALA* 3.9 18.8 - - + -
303G SER 3.4 13.7 + - - +
304G PHE* 3.9 32.8 - - + +
306G ALA* 1.3 74.9 - - - +
308G PRO* 1.3 69.6 - - + +
309G ALA 3.2 2.2 - - - -
310G GLY* 3.0 4.9 + - - -
311G ILE* 2.8 34.3 + - + +
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Residues in contact with PRO 308 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D SER* 4.0 14.4 - - - +
232G LEU* 3.7 26.9 - - + -
235G ALA* 4.2 9.2 - - + -
236G TRP* 3.6 40.2 - - + +
304G PHE 4.2 7.2 - - - +
305G PHE 4.1 10.3 - - - +
306G ALA 3.9 0.9 - - - -
307G LEU* 1.3 93.2 - - + +
309G ALA* 1.3 61.7 + - - +
311G ILE* 4.1 2.2 - - + -
312G LEU* 2.9 33.4 + - + +
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Residues in contact with ALA 309 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D VAL 5.0 0.7 - - - +
303D SER* 4.2 23.8 + - - +
306D ALA* 4.1 29.3 - - + +
307D LEU* 3.3 15.5 - - - +
310D GLY* 5.4 1.4 - - - -
306G ALA* 4.3 12.8 - - + +
307G LEU 3.2 0.8 - - - -
308G PRO* 1.3 82.4 - - - +
310G GLY* 1.3 57.4 + - - +
312G LEU* 5.6 0.4 - - - -
313G GLY* 2.9 24.6 + - - -
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Residues in contact with GLY 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ALA 5.4 3.8 - - - -
310A GLY* 5.4 7.6 - - - -
313A GLY* 4.3 12.4 - - - -
314A SER 4.7 0.3 + - - -
310D GLY* 5.4 8.7 - - - -
306G ALA 3.9 5.9 + - - -
307G LEU 3.0 7.2 + - - -
309G ALA* 1.3 76.6 - - - +
311G ILE* 1.3 65.5 + - - +
313G GLY* 3.7 1.5 - - - -
314G SER* 3.0 25.3 + - - -
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Residues in contact with ILE 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A GLY* 3.6 29.6 - - - +
316A PHE* 3.4 34.1 - - + -
317A ALA* 4.4 3.5 - - - +
228G HIS* 3.9 26.9 - - + +
231G GLU* 4.4 13.0 - - + +
232G LEU* 3.8 24.7 - - + -
235G ALA* 4.8 1.1 - - + -
307G LEU* 2.8 31.6 + - + +
308G PRO* 3.8 3.8 - - + +
310G GLY* 1.3 78.4 - - - +
312G LEU* 1.3 59.7 + - - +
314G SER* 3.7 2.3 - - - -
315G GLY* 2.8 25.5 + - - -
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Residues in contact with LEU 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D SER* 5.8 7.0 - - - +
304D PHE* 5.5 4.3 - - + -
307D LEU* 3.7 25.8 - - + -
221G LEU* 5.1 6.5 - - + -
224G VAL* 4.2 23.3 - - + +
225G VAL* 4.0 22.7 - - + -
228G HIS* 5.0 3.8 - - + -
232G LEU* 4.0 32.1 - - + -
236G TRP* 6.2 2.5 - - + -
308G PRO* 2.9 25.0 + - + +
309G ALA* 5.6 0.2 - - - -
311G ILE* 1.3 76.7 - - - +
313G GLY* 1.3 61.1 + - - +
315G GLY* 3.5 2.4 - - - +
316G PHE* 2.9 34.8 + - + -
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Residues in contact with GLY 313 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D LEU* 3.5 5.1 - - - +
310D GLY 4.3 4.0 - - - -
311D ILE* 3.6 39.2 - - - +
309G ALA 2.9 18.6 + - - -
310G GLY 3.7 1.3 - - - -
312G LEU* 1.3 78.2 - - - +
314G SER* 1.3 61.7 + - - +
316G PHE 3.3 0.3 + - - -
317G ALA* 3.1 21.3 + - - +
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Residues in contact with SER 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A SER* 3.3 25.3 + - - -
317A ALA* 3.7 22.0 - - - +
318A LEU* 5.4 0.3 - - - +
310D GLY 4.7 1.0 + - - -
314D SER* 3.3 27.7 + - - -
310G GLY 3.0 16.7 + - - -
313G GLY* 1.3 75.3 - - - +
315G GLY* 1.3 57.5 + - - +
317G ALA* 3.6 0.3 - - - +
318G LEU* 3.0 38.3 + - - +
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Residues in contact with GLY 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ALA* 4.4 0.9 - - - +
224G VAL* 4.3 8.0 - - - +
228G HIS* 4.0 25.0 + - - -
311G ILE 2.8 16.3 + - - -
312G LEU* 3.5 4.0 - - - -
313G GLY 3.1 0.6 - - - -
314G SER* 1.3 74.0 - - - +
316G PHE* 1.3 67.3 + - - +
318G LEU* 3.4 4.3 + - - +
319G LYS* 2.9 25.5 + - - +
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Residues in contact with PHE 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D GLU* 2.7 56.9 - - + +
234D THR* 4.9 10.3 - - + -
235D ALA* 5.3 1.1 - - + -
307D LEU* 4.4 17.3 - - + -
311D ILE* 3.4 29.2 - - + -
220G LEU* 4.6 9.9 - - + -
221G LEU* 4.3 28.0 - - + -
224G VAL* 3.4 38.6 - - + -
312G LEU* 2.9 23.2 + - + -
313G GLY 3.8 6.3 - - - +
315G GLY* 1.3 75.7 - - - +
317G ALA* 1.3 63.4 + - - +
319G LYS* 3.3 3.1 + - - -
320G VAL* 3.0 14.0 + - - +
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Residues in contact with ALA 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D HIS* 3.9 22.7 + - + +
311D ILE* 4.4 4.7 - - - +
314D SER* 3.7 29.6 - - - +
318D LEU* 3.9 13.1 - - + +
313G GLY 3.1 14.7 + - - +
314G SER 3.6 7.4 - - - +
315G GLY 3.2 0.4 - - - -
316G PHE* 1.3 76.3 - - - +
318G LEU* 1.3 64.1 + - - +
320G VAL* 3.3 3.8 - - - +
321G GLN* 3.0 23.4 + - - +
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Residues in contact with LEU 318 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ALA* 3.9 31.4 - - + +
318A LEU* 4.0 26.7 - - + -
321A GLN* 4.4 27.0 + - + +
314D SER* 5.4 0.2 - - - +
318D LEU* 4.0 28.7 - - + -
228G HIS* 5.8 1.3 - - + -
314G SER* 3.0 27.6 + - - +
315G GLY* 4.0 4.0 - - - +
317G ALA* 1.3 74.7 - - - +
319G LYS* 1.3 63.3 + - - +
321G GLN* 3.3 10.0 + - - +
322G GLU* 3.0 26.1 + - - +
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Residues in contact with LYS 319 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D GLU* 4.7 2.9 - - - +
220G LEU* 3.4 28.2 - - + +
223G SER* 3.0 29.2 + - - +
224G VAL* 3.6 19.9 - - + +
315G GLY 2.9 19.4 + - - +
316G PHE* 3.8 4.5 - - - +
318G LEU* 1.3 76.6 - - - +
320G VAL* 1.3 58.8 + - - +
322G GLU* 3.3 15.5 - - - +
323G GLN* 2.9 58.6 + - + +
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Residues in contact with VAL 320 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D ALA 4.4 15.3 - - - +
228D HIS* 3.4 30.1 - - + +
231D GLU* 3.3 24.7 - - - +
316G PHE 3.0 10.8 + - - +
317G ALA 3.3 11.0 - - - +
319G LYS* 1.3 77.7 - - - +
321G GLN* 1.3 60.4 + - + +
323G GLN* 3.8 16.2 - - + +
324G HIS* 3.0 27.3 + - + +
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Residues in contact with GLN 321 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D LEU* 4.4 27.2 + - + +
322D GLU* 3.8 23.2 + - - +
317G ALA 3.0 18.6 + - - +
318G LEU* 3.5 12.0 - - - +
319G LYS 3.2 0.2 - - - -
320G VAL* 1.3 80.5 - - + +
322G GLU* 1.3 59.9 + - - +
324G HIS* 3.3 13.7 + - + +
325G ARG* 3.1 61.2 + - - +
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Residues in contact with GLU 322 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A GLN* 3.8 21.7 + - - +
324A HIS* 5.4 11.1 + - - -
325A ARG* 5.2 4.4 + - - +
318G LEU 3.0 15.1 + - - +
319G LYS* 3.3 18.5 - - - +
321G GLN* 1.3 78.7 + - - +
323G GLN* 1.3 68.9 + - + +
325G ARG* 3.7 8.2 - - - +
326G GLN* 2.9 30.7 + - - +
562G TYR* 5.3 13.4 - - - -
563G ASP* 4.5 16.1 - - - +
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Residues in contact with GLN 323 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D GLU* 5.2 1.0 - - - +
319G LYS* 2.9 53.7 + - + +
320G VAL* 3.8 16.5 - - + +
321G GLN 3.3 0.2 - - - -
322G GLU* 1.3 78.1 - - + +
324G HIS* 1.3 61.5 + - - +
326G GLN* 3.7 8.7 - - - +
327G LYS* 2.8 30.9 + - - +
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Residues in contact with HIS 324 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D GLU* 5.4 12.1 + - - -
562D TYR* 5.3 11.4 - + - -
320G VAL* 3.0 16.0 + - + +
321G GLN* 3.4 17.5 - - + +
323G GLN* 1.3 73.2 - - - +
325G ARG* 1.3 78.3 + - + +
327G LYS* 3.0 20.9 + - - +
328G HIS* 3.2 50.6 + + - -
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Residues in contact with ARG 325 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ARG* 4.2 13.7 - - - +
322D GLU* 5.2 4.9 + - - +
325D ARG* 4.2 13.7 - - - +
563D ASP* 3.8 22.6 + - - -
564D VAL* 4.1 31.2 - - + +
321G GLN* 3.1 42.1 + - - +
322G GLU* 3.4 8.9 + - - +
324G HIS* 1.3 90.2 - - + +
326G GLN* 1.3 62.2 + - - +
328G HIS* 3.1 14.8 + - - +
329G PHE* 3.4 24.2 + - + -
563G ASP* 3.6 32.7 + - + +
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Residues in contact with GLN 326 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322G GLU 2.9 20.5 + - - +
323G GLN* 4.1 8.8 - - - +
325G ARG* 1.3 72.1 - - - +
327G LYS* 1.3 61.5 + - - +
329G PHE* 3.5 20.4 + - - +
330G GLU* 4.0 3.6 + - - +
332G ARG* 4.6 15.2 + - - +
559G LEU 5.5 0.2 + - - -
560G ARG* 4.8 3.2 - - - +
561G PRO 3.3 30.5 + - - +
562G TYR* 3.3 42.5 - - + -
563G ASP* 5.2 5.8 - - + +
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Residues in contact with LYS 327 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323G GLN 2.8 19.3 + - - +
324G HIS* 3.0 12.9 + - - +
326G GLN* 1.3 77.7 - - - +
328G HIS* 1.3 79.9 + - + +
329G PHE 3.6 0.5 + - - -
330G GLU* 4.3 16.5 + - - +
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Residues in contact with HIS 328 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562D TYR* 6.2 2.2 - + - -
565D MET* 3.9 29.9 - - + +
324G HIS* 3.2 43.2 + + - +
325G ARG* 3.1 10.9 + - - +
327G LYS* 1.3 100.9 + - + +
329G PHE* 1.3 66.5 + - + +
330G GLU* 3.6 4.8 + - - +
333G ARG* 5.7 1.0 + - - -
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Residues in contact with PHE 329 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564D VAL* 3.8 34.3 - - + -
565D MET* 3.5 51.8 - - + -
568D ILE* 4.1 20.9 - - + -
569D GLU* 4.4 12.6 - - - -
325G ARG* 3.4 23.1 + - + +
326G GLN* 3.5 10.1 + - - +
327G LYS 3.3 1.0 - - - -
328G HIS* 1.3 88.9 - - + +
330G GLU* 1.3 64.5 + - - +
331G LYS* 3.5 17.6 - - + +
332G ARG* 4.9 0.2 + - - -
333G ARG* 5.9 0.2 - - - +
561G PRO* 4.0 16.4 - - - +
562G TYR 5.0 5.2 - - - +
563G ASP* 4.6 15.7 - - + -
566G ASP* 4.9 9.6 - - - +
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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