Contacts of the helix formed by residues 363 - 384 (chain D) in PDB entry 6VVT
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 PRO 363 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D ALA* 1.3 95.1 - - + +
364D GLU* 1.3 65.9 + - - +
365D ILE* 3.3 23.3 - - + -
366D ILE* 3.4 17.0 + - + +
367D VAL* 3.1 18.5 + - - +
231F ASN* 3.8 25.8 - - - +
234F LEU* 3.7 38.6 - - + -
235F GLU* 3.8 10.5 - - + +
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Residues in contact with GLU 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362D ALA 3.7 12.1 - - - +
363D PRO* 1.3 72.6 - - - +
365D ILE* 1.3 61.5 + - + +
367D VAL* 4.3 13.3 - - - +
368D ASN* 2.6 60.6 + - - +
371D LYS* 5.6 1.2 - - - -
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Residues in contact with ILE 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D PRO* 3.4 16.4 - - + -
364D GLU* 1.3 78.0 - - + +
366D ILE* 1.3 57.0 + - + +
368D ASN* 4.2 2.9 - - - +
369D ASN* 2.9 31.0 + - - +
372D ARG* 5.3 1.1 + - - +
169F TYR* 4.5 17.9 - - + -
172F GLN* 4.4 30.3 - - + +
173F ILE* 4.7 3.8 - - + +
176F VAL* 6.3 2.0 - - + -
235F GLU* 3.1 40.4 - - + +
238F LEU* 4.6 15.0 - - + -
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Residues in contact with ILE 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357D LEU* 3.4 26.0 - - + -
362D ALA* 4.5 2.0 - - + -
363D PRO* 3.4 31.4 + - + +
364D GLU 3.3 0.2 - - - -
365D ILE* 1.3 75.7 - - - +
367D VAL* 1.3 65.0 + - - +
369D ASN* 3.3 5.8 + - - +
370D GLU* 3.0 17.2 + - - +
169F TYR* 4.9 2.0 - - - +
234F LEU* 5.2 3.4 - - + -
238F LEU* 4.3 21.1 - - + -
260F GLN* 3.3 26.3 + - - +
263F ASN* 3.7 37.0 - - + +
266F LEU* 5.7 0.9 - - + -
267F ILE* 4.5 14.4 - - + -
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Residues in contact with VAL 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354D LEU* 3.8 5.6 - - + -
357D LEU* 4.3 15.7 - - + +
358D ILE* 3.4 31.4 - - + -
362D ALA* 3.7 23.6 - - + +
363D PRO 3.1 19.1 + - - +
364D GLU* 4.0 16.2 - - - +
366D ILE* 1.3 73.1 - - - +
368D ASN* 1.3 61.7 + - - +
370D GLU* 2.8 22.7 + - - +
371D LYS* 2.9 33.4 + - - +
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Residues in contact with ASN 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D PHE* 3.6 39.4 - - + -
134D TYR* 5.3 2.6 + - - -
256D MET* 4.6 12.7 - - - +
364D GLU* 2.6 49.6 + - - +
365D ILE* 4.2 3.3 - - - +
367D VAL* 1.3 70.9 - - - +
369D ASN* 1.3 61.5 + - - +
371D LYS* 3.3 16.9 + - - +
372D ARG* 3.0 27.5 + - - +
172F GLN* 6.4 0.2 - - - +
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Residues in contact with ASN 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365D ILE 2.9 22.3 + - - +
366D ILE 3.5 5.6 - - - +
368D ASN* 1.3 76.7 - - - +
370D GLU* 1.3 57.5 + - - +
372D ARG* 3.1 28.7 + - - +
373D MET* 3.1 41.4 + - - +
169F TYR* 3.2 38.8 - - + +
256F LEU* 4.5 11.3 - - - +
259F ILE* 4.8 1.8 - - - +
260F GLN* 2.4 29.1 + - - +
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Residues in contact with GLU 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350D ARG* 2.9 22.2 - - - +
353D ARG* 2.6 38.5 + - - +
354D LEU* 3.7 35.7 - - + -
357D LEU* 4.0 6.1 - - + -
366D ILE 3.0 10.9 + - - +
367D VAL 2.8 10.8 + - - +
369D ASN* 1.3 76.7 - - - +
371D LYS* 1.3 53.7 + - - +
373D MET* 3.0 5.8 + - - +
374D LEU* 2.6 35.7 + - + +
260F GLN* 2.9 33.5 + - - +
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Residues in contact with LYS 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ALA 5.1 2.0 + - - -
99D ALA* 4.1 30.4 - - + +
100D PRO 6.0 0.7 - - - +
101D VAL* 5.1 0.9 - - - +
131D PHE* 3.3 33.9 - - + -
259D GLU* 5.8 4.1 + - - +
354D LEU* 4.1 11.6 - - + +
358D ILE* 3.9 12.5 - - - +
364D GLU* 5.6 1.3 - - - -
367D VAL* 2.9 40.2 + - - +
368D ASN* 3.8 15.0 - - - +
370D GLU* 1.3 74.1 - - - +
372D ARG* 1.3 54.0 + - - +
374D LEU* 3.2 8.9 + - - +
375D GLN* 2.7 36.6 + - - +
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Residues in contact with ARG 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ILE 5.4 0.4 - - - -
130D TYR* 3.3 25.6 + - + +
131D PHE* 3.8 37.1 + - + -
365D ILE* 5.3 0.6 + - - +
368D ASN* 3.0 15.1 + - - +
369D ASN* 3.1 37.1 + - - +
371D LYS* 1.3 77.0 - - - +
373D MET* 1.3 63.6 + - + +
375D GLN* 3.4 6.1 + - - +
376D GLU* 3.1 27.9 + - - +
165F SER* 3.9 32.3 + - - +
168F ALA* 3.2 30.4 - - - +
169F TYR* 3.8 21.6 - - - +
172F GLN* 4.0 11.1 + - - -
256F LEU* 6.1 1.5 - - + +
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Residues in contact with MET 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350D ARG* 2.8 53.9 + - + +
353D ARG* 4.0 9.2 - - - +
369D ASN* 3.1 23.1 + - - +
370D GLU* 3.0 10.6 + - - +
372D ARG* 1.3 74.9 - - + +
374D LEU* 1.3 65.1 + - - +
376D GLU* 3.3 5.5 + - - -
377D SER 3.0 9.2 + - - -
256F LEU* 3.5 35.0 - - + -
257F ASP* 3.4 35.7 - - - +
260F GLN* 3.3 27.6 - - + -
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Residues in contact with LEU 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LEU* 4.3 15.7 - - + -
99D ALA* 3.7 26.9 - - + +
101D VAL* 4.0 11.7 - - + -
347D VAL* 3.9 22.4 - - + +
350D ARG* 4.1 12.2 - - + +
351D ASN* 3.9 24.0 - - + +
354D LEU* 4.3 21.1 - - + -
370D GLU 2.6 19.2 + - - +
371D LYS* 3.5 6.1 - - + +
373D MET* 1.3 73.4 - - - +
375D GLN* 1.3 63.2 + - - +
377D SER* 2.6 30.8 + - - +
378D VAL* 3.2 8.7 + - + +
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Residues in contact with GLN 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D VAL* 3.3 20.0 - - + +
102D THR* 2.7 52.2 + - - +
107D PHE* 6.0 0.4 - - - -
129D ILE* 4.1 20.7 - - - +
130D TYR* 4.3 13.9 - - + -
131D PHE* 5.5 1.1 - - + -
258D ALA* 4.0 8.0 + - - +
371D LYS 2.7 20.9 + - - +
372D ARG* 3.5 9.0 - - - +
373D MET 3.3 0.2 - - - -
374D LEU* 1.3 74.1 - - - +
376D GLU* 1.3 61.1 + - - +
378D VAL* 3.5 1.9 + - - +
379D ASP* 3.0 61.3 + - - +
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Residues in contact with GLU 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D TYR* 3.6 19.5 - - + -
350D ARG* 4.4 7.9 + - - +
372D ARG* 3.1 18.6 + - - +
373D MET* 3.8 6.1 - - - +
374D LEU 3.2 0.2 - - - -
375D GLN* 1.3 73.5 - - - +
377D SER* 1.3 59.3 + - - +
379D ASP* 3.4 8.4 + - - +
380D ALA* 2.9 28.8 + - - +
387D ARG* 3.4 16.7 + - - +
165F SER* 2.2 38.2 + - - -
256F LEU* 4.8 9.9 - - - +
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Residues in contact with SER 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343D LEU* 4.8 1.7 - - - +
346D ARG* 4.0 16.8 + - - +
347D VAL* 3.2 41.4 - - - +
350D ARG* 4.0 12.0 - - - +
373D MET 3.0 11.6 + - - -
374D LEU* 2.6 27.9 + - - +
376D GLU* 1.3 74.5 - - - +
378D VAL* 1.3 59.0 + - - +
380D ALA* 3.4 6.8 + - - +
381D LEU* 2.9 22.9 + - - +
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Residues in contact with VAL 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LEU* 4.8 1.6 - - + -
101D VAL* 3.8 34.3 - - + -
102D THR 5.0 1.6 - - - +
314D LEU* 5.3 1.6 - - + -
317D VAL* 4.4 19.5 - - + -
347D VAL* 4.0 21.5 - - + -
374D LEU* 3.2 16.9 + - + +
375D GLN 4.0 1.1 - - - +
377D SER* 1.3 78.0 + - - +
379D ASP* 1.3 67.1 + - - +
381D LEU* 3.1 4.1 + - + +
382D PHE* 2.9 54.5 + - + -
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Residues in contact with ASP 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D THR 3.6 5.9 - - - +
104D ILE* 3.5 40.1 + - + +
107D PHE* 5.9 0.7 - - - -
130D TYR* 2.5 30.8 + - - +
375D GLN* 3.0 38.5 + - - +
376D GLU* 3.6 9.2 - - - +
377D SER 3.3 0.2 - - - -
378D VAL* 1.3 77.4 - - - +
380D ALA* 1.3 57.5 + - - +
382D PHE* 3.3 0.6 + - - -
383D ASP 2.9 36.2 + - - +
387D ARG* 5.9 1.6 - - + -
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Residues in contact with ALA 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D LEU* 3.6 11.2 - - + +
346D ARG* 5.7 1.3 - - - +
376D GLU 2.9 17.6 + - - +
377D SER* 3.7 7.2 - - - +
379D ASP* 1.3 77.0 - - - +
381D LEU* 1.3 63.0 + - - +
384D ASN* 3.1 40.2 + - - +
391D VAL* 3.7 30.5 - - + -
401D SER* 3.2 5.0 - - - -
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Residues in contact with LEU 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D VAL* 4.2 11.7 - - + -
340D LEU* 4.4 1.6 - - - +
343D LEU* 3.6 30.5 - - + +
344D TYR* 3.7 52.5 - - + +
347D VAL* 4.3 15.9 - - + -
377D SER 2.9 17.6 + - - +
378D VAL* 3.1 7.4 + - - +
380D ALA* 1.3 78.1 - - - +
382D PHE* 1.3 77.6 + - + +
401D SER* 3.4 1.9 - - - -
402D LEU* 3.2 35.0 + - + +
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Residues in contact with PHE 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121C SER 3.6 15.9 - - - -
1122C LEU* 3.8 20.4 - - + -
1123C CYS* 3.7 22.0 - - + -
103D HIS* 3.7 41.7 - + + -
104D ILE* 4.0 18.2 - - + -
105D TRP* 5.3 1.1 - - - +
314D LEU* 4.4 6.1 - - + -
317D VAL* 4.1 12.8 - - + -
318D PRO 5.6 0.2 - - - -
378D VAL* 2.9 38.1 + - + +
379D ASP* 5.5 0.2 - - - -
381D LEU* 1.3 100.0 - - + +
383D ASP* 1.3 55.1 + - + +
401D SER* 3.0 4.8 + - - -
402D LEU* 3.3 4.6 + - + +
403D SER* 2.7 37.8 + - - -
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Residues in contact with ASP 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D ILE* 3.9 13.6 - - + +
105D TRP* 3.5 13.6 + - + +
379D ASP 2.9 16.9 + - - +
382D PHE* 1.3 71.7 - - - +
384D ASN* 1.3 72.6 + - - +
385D GLY 3.4 0.5 + - - -
386D ARG* 3.2 60.5 + - + +
401D SER* 3.5 2.1 + - - -
403D SER* 3.2 25.2 + - - +
404D ASP* 5.3 1.6 - - - +
407D LYS* 4.9 5.5 + - - -
1231D THR* 4.2 2.6 + - - -
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Residues in contact with ASN 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343D LEU* 4.9 2.1 - - + +
380D ALA* 3.1 31.6 + - - +
383D ASP* 1.3 80.4 - - - +
385D GLY* 1.3 73.0 + - - +
386D ARG 3.4 2.9 + - - -
390D PRO* 3.0 9.7 - - - +
391D VAL* 2.8 54.5 + - - +
399D LEU* 3.2 26.7 + - - +
401D SER* 3.0 18.2 + - - +
404D ASP* 4.4 9.4 - - - +
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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