Contacts of the helix formed by residues 299 - 321 (chain G) in PDB entry 6IY6
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 TYR 299 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295G PHE* 3.8 16.2 - - + -
298G HIS* 1.3 79.0 - + - +
300G HIS* 1.3 77.1 + + - +
301G GLU 3.2 2.2 - - - -
302G VAL* 3.3 8.6 + - - +
303G MET* 3.2 21.0 + - + +
392G ASP* 2.6 34.6 + - - -
393G LYS* 3.4 19.0 - - - +
414G ASN* 3.3 50.0 - - + -
416G TYR* 3.8 20.1 - + - -
430G GLN* 3.6 20.4 - - + +
467G ALA* 4.5 3.5 - - + +
37H SER* 2.9 28.4 + - - +
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Residues in contact with HIS 300 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298G HIS* 3.1 21.2 + + + +
299G TYR* 1.3 103.8 + + - +
301G GLU* 1.3 57.9 + - + +
302G VAL 3.1 0.9 - - - -
303G MET* 3.4 18.6 - - + -
304G GLU* 2.8 49.7 + - - +
345G ARG* 2.9 39.0 + - - -
347G GLU* 5.0 1.6 - - - -
392G ASP* 2.9 20.9 + - - -
393G LYS* 4.4 6.6 - - - -
40H LYS* 3.5 20.2 + - - +
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Residues in contact with GLU 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293G MET* 4.5 6.0 - - + +
295G PHE* 3.6 7.4 - - + +
296G ASN* 2.8 41.6 + - - +
297G TYR* 3.2 21.5 + - - +
298G HIS* 3.2 28.0 + - + +
300G HIS* 1.3 78.4 - - - +
302G VAL* 1.3 57.0 + - - +
304G GLU* 4.5 4.2 - - - +
305G GLU* 3.2 28.1 + - - +
40H LYS* 6.1 0.3 - - - -
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Residues in contact with VAL 302 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G ILE* 5.4 0.4 - - + -
293G MET* 3.3 51.4 - - + +
295G PHE* 3.8 24.7 - - + -
299G TYR 3.3 8.4 + - - +
300G HIS 3.1 0.4 - - - -
301G GLU* 1.3 75.2 - - - +
303G MET* 1.3 55.7 - - - +
305G GLU* 3.0 4.9 + - - +
306G ILE* 2.8 45.8 + - + +
416G TYR* 3.8 9.0 - - - +
467G ALA* 3.8 29.6 - - + +
468G GLY* 4.3 0.9 - - - -
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Residues in contact with MET 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299G TYR* 3.2 11.7 + - - +
300G HIS* 3.4 33.0 - - + +
302G VAL* 1.3 77.3 - - - +
304G GLU* 1.3 63.6 + - + +
306G ILE* 3.4 3.3 + - - -
307G ALA* 3.0 29.7 + - - +
345G ARG* 3.3 34.5 - - + +
390G ILE* 3.9 15.3 - - + -
392G ASP* 3.7 8.3 - - - +
416G TYR* 3.6 52.4 + - + -
418G MET* 3.5 15.1 - - + +
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Residues in contact with GLU 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300G HIS* 2.8 35.0 + - + +
301G GLU* 4.7 4.1 - - - +
303G MET* 1.3 78.7 - - + +
305G GLU* 1.3 58.5 + - - +
307G ALA* 3.8 7.4 - - - +
308G ASP* 3.2 26.2 + - - +
345G ARG* 4.1 17.4 + - - +
390G ILE* 5.7 2.7 - - + -
40H LYS* 5.2 3.5 + - - -
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Residues in contact with GLU 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210G LEU* 6.1 1.6 - - + -
213G LYS* 3.1 48.0 + - + +
215G PHE* 4.8 4.8 - - + -
264G LYS* 5.1 3.5 + - - -
293G MET* 4.0 30.7 - - + +
301G GLU 3.2 20.0 + - - +
302G VAL 3.0 10.6 + - - +
304G GLU* 1.3 74.0 - - - +
306G ILE* 1.3 66.9 + - + +
308G ASP* 3.1 7.5 + - - +
309G THR* 2.9 27.1 + - - -
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Residues in contact with ILE 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210G LEU* 6.1 0.2 - - - -
291G ILE* 4.0 31.9 - - + -
302G VAL* 2.8 25.1 + - + +
303G MET 3.7 6.3 - - - +
305G GLU* 1.3 71.1 - - + +
307G ALA* 1.3 64.3 + - - +
309G THR* 3.3 9.2 + - - +
310G MET* 3.1 26.6 + - + +
416G TYR* 3.8 27.1 - - + +
418G MET* 3.7 13.0 - - + -
426G LEU* 3.4 26.9 - - + -
468G GLY* 3.8 20.4 - - - +
469G GLY* 3.8 8.1 - - - +
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Residues in contact with ALA 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303G MET 3.0 18.2 + - - +
304G GLU* 3.8 9.0 - - - +
306G ILE* 1.3 72.8 - - - +
308G ASP* 1.3 54.4 + - - +
310G MET* 3.0 6.8 + - - +
311G VAL* 2.9 34.7 + - - +
343G THR* 3.6 21.5 - - + +
388G PHE* 4.0 3.9 - - - -
390G ILE* 3.7 22.9 - - + -
418G MET* 3.9 10.5 - - + +
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Residues in contact with ASP 308 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213G LYS* 2.8 30.9 + - - +
304G GLU 3.2 14.8 + - - +
305G GLU* 3.1 8.3 + - - +
307G ALA* 1.3 76.8 - - - +
309G THR* 1.3 52.9 + - - +
311G VAL* 3.2 13.7 + - - +
312G GLN* 2.7 57.8 + - - +
341G GLU* 5.2 6.7 - - - +
343G THR* 4.5 0.9 + - - -
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Residues in contact with THR 309 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206G PHE* 4.1 28.5 - - + +
209G THR* 3.4 26.3 - - + +
210G LEU* 3.4 31.4 - - + +
213G LYS* 3.5 6.2 - - - +
291G ILE* 4.5 3.4 - - + -
305G GLU 2.9 15.5 + - - -
306G ILE* 3.4 12.1 - - - +
307G ALA 3.2 0.2 - - - -
308G ASP* 1.3 75.5 - - - +
310G MET* 1.3 58.4 + - - +
312G GLN* 3.4 3.3 + - - +
313G ILE* 3.0 31.2 + - + +
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Residues in contact with MET 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206G PHE* 5.4 1.3 - - - -
306G ILE* 3.1 25.4 + - + +
307G ALA 3.0 8.1 + - - +
309G THR* 1.3 74.4 - - - +
311G VAL* 1.3 65.1 + - - +
313G ILE* 3.4 18.0 + - + +
314G PHE* 3.0 49.9 + - + -
388G PHE* 3.5 26.5 - - + -
418G MET* 4.9 1.6 - - - -
425G ILE* 3.8 25.6 - - + -
426G LEU* 5.6 0.2 - - + -
471G ILE* 3.5 35.0 - - + -
476G VAL* 4.2 15.7 - - + -
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Residues in contact with VAL 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307G ALA 2.9 13.8 + - - +
308G ASP* 3.3 16.2 - - - +
310G MET* 1.3 75.5 - - - +
312G GLN* 1.3 52.8 + - - +
314G PHE* 3.0 12.0 + - - +
315G LYS* 2.8 51.7 + - + +
339G PHE* 3.9 16.6 - - + -
340G LEU 4.1 10.8 - - - +
341G GLU* 3.8 22.0 - - - +
343G THR* 3.1 28.0 - - - +
388G PHE* 4.4 9.0 - - + -
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Residues in contact with GLN 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205G LEU* 4.6 5.2 - - - +
209G THR* 3.7 26.2 - - + +
213G LYS* 5.4 0.4 - - - +
308G ASP* 2.7 44.5 + - - +
309G THR 3.6 5.8 - - - +
311G VAL* 1.3 68.6 - - + +
313G ILE* 1.3 59.8 + - - +
315G LYS* 3.8 31.1 - - - +
316G GLY* 3.0 25.5 + - - -
341G GLU* 5.4 0.7 - - - +
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Residues in contact with ILE 313 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202G ILE* 4.1 37.5 - - + +
205G LEU* 3.3 16.5 - - + +
206G PHE* 4.0 46.7 - - + +
309G THR 3.0 20.2 + - - +
310G MET* 3.4 33.0 - - + +
311G VAL 3.2 0.2 - - - -
312G GLN* 1.3 75.5 - - - +
314G PHE* 1.3 68.0 + - + +
316G GLY 3.2 1.4 + - - -
317G LEU* 3.0 34.0 + - + +
471G ILE* 4.8 1.3 - - + -
476G VAL* 5.3 2.0 - - + -
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Residues in contact with PHE 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310G MET* 3.0 37.9 + - + -
311G VAL* 3.0 9.7 + - - +
313G ILE* 1.3 80.5 - - + +
315G LYS* 1.3 66.0 + - - +
317G LEU* 3.3 3.6 + - + +
318G GLN* 3.1 28.1 + - - +
337G PHE* 3.5 26.0 - + - -
339G PHE* 3.3 30.1 - + + -
388G PHE* 3.7 25.1 - + - -
420G MET* 3.4 40.6 - - + -
476G VAL* 4.9 2.9 - - + -
480G PHE* 3.6 26.7 - + + -
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Residues in contact with LYS 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311G VAL* 2.8 34.1 + - + +
312G GLN* 3.8 34.1 - - - +
314G PHE* 1.3 71.6 - - - +
316G GLY* 1.3 55.8 + - - +
318G GLN* 3.5 5.4 + - - +
319G GLU* 3.1 50.2 + - - +
339G PHE* 3.9 18.3 - - + -
341G GLU* 2.9 32.4 + - - +
159I LYS* 6.3 1.0 - - - +
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Residues in contact with GLY 316 (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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205G LEU* 3.7 23.3 - - - -
312G GLN 3.0 16.1 + - - -
313G ILE 3.5 4.0 - - - -
314G PHE 3.2 0.2 - - - -
315G LYS* 1.3 72.8 - - - +
317G LEU* 1.3 58.0 + - - +
319G GLU* 3.4 5.6 + - - +
320G ARG* 3.0 40.2 + - - +
321G PHE* 4.2 0.6 - - - -
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Residues in contact with LEU 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198G LEU* 3.9 31.0 - - + +
202G ILE* 3.7 26.2 - - + +
205G LEU* 3.7 15.7 - - + -
313G ILE* 3.0 24.3 + - + +
314G PHE* 3.3 0.9 + - + +
316G GLY* 1.3 74.4 - - - +
318G GLN* 1.3 58.2 + - - +
321G PHE* 3.0 52.7 + - + +
325G ILE* 3.4 5.5 - - + +
480G PHE* 3.7 48.0 - - + -
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Residues in contact with GLN 318 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314G PHE 3.1 19.2 + - - +
315G LYS* 4.0 5.5 - - - +
316G GLY 3.3 0.2 - - - -
317G LEU* 1.3 74.1 - - - +
319G GLU* 1.3 61.8 + - + +
322G GLN* 2.7 32.4 + - - +
325G ILE* 4.2 5.2 - - + -
336G PRO* 4.9 5.3 - - - +
337G PHE* 2.7 44.3 + - - +
339G PHE* 4.0 21.3 - - - -
480G PHE* 4.1 12.9 - - + -
156I SER* 4.3 13.6 - - - +
159I LYS* 4.7 16.0 + - - +
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Residues in contact with GLU 319 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315G LYS* 3.1 38.3 + - - +
316G GLY* 3.7 5.8 - - - +
317G LEU 3.3 0.2 - - - -
318G GLN* 1.3 80.5 - - + +
320G ARG* 1.3 72.3 + - + +
322G GLN* 4.3 7.3 - - - +
159I LYS* 6.1 5.8 - - + +
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Residues in contact with ARG 320 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204G HIS* 3.8 29.5 + - - -
205G LEU* 3.9 23.2 - - - +
208G GLU* 5.7 5.9 - - - +
316G GLY* 3.0 15.5 + - - +
319G GLU* 1.3 84.5 + - + +
321G PHE* 1.3 77.9 - - + +
322G GLN* 3.2 10.6 + - - +
323G THR* 4.6 6.9 + - - +
324G GLU* 4.6 0.7 - - - +
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Residues in contact with PHE 321 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197G ARG* 3.2 23.8 - - + -
198G LEU* 3.8 29.2 - - + -
201G GLY* 3.5 25.8 - - - -
204G HIS* 6.3 2.2 - + - -
205G LEU* 4.7 6.7 - - + -
316G GLY 4.2 1.1 - - - -
317G LEU* 3.0 35.6 + - + +
320G ARG* 1.3 99.4 - - + +
322G GLN* 1.3 56.7 + - - +
323G THR 3.3 2.7 - - - -
324G GLU* 3.4 22.2 + - + +
325G ILE* 3.1 29.6 + - - +
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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) + - + + + + + -
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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