Contacts of the helix formed by residues 376 - 397 (chain C) in PDB entry 3F98
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 376 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLU* 3.3 21.2 - - - +
215A THR* 4.9 4.5 + - - +
374C ASP 3.8 1.6 + - - -
375C ILE* 1.3 76.6 - - - +
377C SER* 1.3 59.1 + - - +
378C ASN* 2.8 36.2 + - - +
379C VAL* 3.0 24.7 + - + +
380C ALA* 3.0 24.8 + - - +
563C FMT 3.1 25.8 - - - +
569C FMT 4.8 2.0 + - - -
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Residues in contact with SER 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C ASN* 3.6 14.7 + - - +
358C THR* 2.7 31.0 + - - -
359C PHE* 3.6 21.7 - - - -
372C LYS* 3.2 24.6 + - - +
375C ILE 3.5 0.6 + - - -
376C ASP* 1.3 72.5 + - - +
378C ASN* 1.3 59.5 + - - +
380C ALA* 3.4 1.3 + - - +
381C ILE* 3.0 30.8 + - - +
563C FMT 2.9 16.9 + - - -
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Residues in contact with ASN 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLN* 3.8 11.2 + - + +
212A GLU* 3.8 16.4 - - - +
215A THR* 4.0 23.0 + - - +
55C LYS 5.6 1.0 + - - -
57C PRO* 3.5 16.6 - - - +
359C PHE* 3.8 13.9 - - - -
376C ASP* 2.8 18.3 + - - +
377C SER* 1.3 72.3 - - - +
379C VAL* 1.3 64.0 + - - +
381C ILE* 4.3 1.6 - - - -
382C ASP* 3.0 26.2 + - - +
563C FMT 6.1 1.6 - - - -
579C FMT 2.7 37.5 - - - +
584C FMT 5.4 3.8 + - - -
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Residues in contact with VAL 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLU* 3.6 39.9 - - + +
375C ILE* 3.9 15.7 - - + -
376C ASP* 3.0 22.6 + - + +
378C ASN* 1.3 75.4 - - - +
380C ALA* 1.3 64.3 + - - +
382C ASP* 3.7 4.5 - - - +
383C LEU* 3.1 32.3 + - + +
415C ASN* 3.8 22.9 - - - +
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Residues in contact with ALA 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C ILE* 3.8 20.3 - - + +
353C ASN* 4.0 21.8 - - + +
375C ILE* 3.8 27.4 - - + -
376C ASP 3.0 15.6 + - - +
377C SER 3.8 4.3 - - - +
378C ASN 3.2 0.4 - - - -
379C VAL* 1.3 77.6 - - - +
381C ILE* 1.3 63.0 + - - +
383C LEU* 3.2 4.7 + - - +
384C SER* 3.0 22.9 + - - -
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Residues in contact with ILE 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C PRO* 4.5 2.7 - - + -
162C ALA* 4.4 15.3 - - + -
163C ILE* 4.0 13.9 - - + -
353C ASN 3.5 22.9 + - - +
354C PHE* 4.0 27.4 - - + +
359C PHE* 3.9 15.5 - - + -
377C SER 3.0 16.0 + - - +
378C ASN 3.7 1.6 - - - +
380C ALA* 1.3 78.9 - - - +
382C ASP* 1.3 60.0 + - - +
384C SER* 3.4 5.1 + - - -
385C ASN* 2.8 52.5 + - - +
579C FMT 3.5 30.7 - - - +
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Residues in contact with ASP 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LYS* 5.5 0.3 - - - +
211A GLN* 3.9 9.0 + - - +
212A GLU* 3.8 16.1 - - - +
60C ASN* 3.1 16.2 - - - +
378C ASN 3.0 22.9 + - - +
379C VAL* 3.7 5.4 - - - +
381C ILE* 1.3 79.6 - - - +
383C LEU* 1.3 57.7 + - + +
385C ASN* 4.5 5.0 + - - -
386C LYS* 2.9 51.6 + - + +
579C FMT 2.7 32.4 - - - +
580C FMT 4.0 9.2 - - - +
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Residues in contact with LEU 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C ILE* 5.2 1.1 - - - +
346C ILE* 4.5 6.3 - - + -
375C ILE* 4.5 5.2 - - + -
379C VAL* 3.1 28.6 + - + +
380C ALA 3.2 5.6 + - - +
382C ASP* 1.3 77.7 - - + +
384C SER* 1.3 56.9 + - - +
386C LYS* 5.4 1.1 - - + -
387C ALA* 2.9 33.1 + - - +
408C LEU* 4.1 24.8 - - + +
413C ASP* 3.6 27.1 - - - +
415C ASN* 3.6 37.7 - - + +
416C LEU* 4.1 19.9 - - + +
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Residues in contact with SER 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C ILE* 5.6 1.0 - - - +
295C LEU* 3.6 17.3 - - - +
317C ILE* 3.8 14.7 - - - +
346C ILE* 4.0 5.1 - - - +
354C PHE* 3.4 34.8 - - - -
380C ALA 3.0 16.3 + - - -
381C ILE* 3.8 10.0 - - - +
383C LEU* 1.3 76.1 - - - +
385C ASN* 1.3 60.5 + - - +
387C ALA* 4.7 0.4 - - - -
388C SER* 2.8 35.1 + - - -
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Residues in contact with ASN 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ASN* 5.9 0.7 - - - +
162C ALA 3.9 6.9 + - - -
163C ILE* 3.7 28.6 - - - +
166C ASP* 3.4 40.4 - - - +
167C LEU* 5.6 3.5 - - + +
381C ILE* 2.8 43.5 + - - +
382C ASP* 4.0 6.6 + - - +
384C SER* 1.3 75.4 + - - +
386C LYS* 1.3 59.3 + - + +
388C SER* 3.4 6.6 + - - -
389C LEU* 2.9 34.1 + - - +
579C FMT 5.3 2.0 + - - -
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Residues in contact with LYS 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LYS* 6.4 0.2 - - - +
60C ASN* 4.4 14.1 - - - +
166C ASP* 5.9 0.7 - - - +
170C HIS* 6.3 1.1 - - + -
382C ASP* 2.9 33.5 + - + +
383C LEU* 6.2 1.1 - - + -
385C ASN* 1.3 74.8 - - + +
387C ALA* 1.3 65.4 + - - +
389C LEU* 3.2 6.8 + - + +
390C ALA 3.0 19.2 + - - -
405C TRP* 3.6 54.5 - - + +
408C LEU* 3.7 13.9 - - + -
559C FMT 3.1 29.9 + - - -
580C FMT 3.0 30.7 + - - -
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Residues in contact with ALA 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C PHE* 3.7 26.2 - - + -
317C ILE* 4.3 1.3 - - + -
344C ILE* 4.0 11.7 - - + -
383C LEU 2.9 18.6 + - - +
384C SER 3.9 2.9 - - - +
386C LYS* 1.3 75.7 - - - +
388C SER* 1.3 57.6 + - - +
390C ALA* 3.3 6.4 + - - +
391C PHE* 2.9 28.9 + - - +
405C TRP 4.8 0.2 - - - -
408C LEU* 3.9 25.8 - - + +
409C ILE* 3.9 2.9 - - - +
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Residues in contact with SER 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C LEU* 5.3 5.2 - - - -
270C ILE* 5.2 5.3 - - - +
293C ILE* 3.6 26.5 - - - +
295C LEU* 4.6 2.4 - - - +
315C PHE* 4.2 1.5 - - - -
317C ILE* 3.5 14.6 - - - +
384C SER* 2.8 24.9 + - - -
385C ASN* 3.5 7.9 - - - -
387C ALA* 1.3 77.2 - - - +
389C LEU* 1.3 57.3 + - - +
391C PHE* 3.2 3.2 + - - +
392C LEU* 2.8 40.5 + - - +
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Residues in contact with LEU 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C ASP* 4.0 7.0 - - - +
167C LEU* 4.0 15.9 - - + -
170C HIS* 3.5 45.8 - - + +
172C PHE* 3.7 29.8 - - + -
385C ASN 2.9 24.2 + - - +
386C LYS* 3.2 6.5 + - + +
388C SER* 1.3 74.5 - - - +
390C ALA* 1.3 58.0 + - - +
392C LEU* 3.3 4.2 + - - +
393C GLN* 2.8 25.5 + - - +
402C PHE* 3.4 34.2 - - + +
405C TRP* 3.7 16.2 - - + -
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Residues in contact with ALA 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C LYS 3.0 9.8 + - - +
387C ALA 3.7 6.5 - - - +
389C LEU* 1.3 75.8 - - - +
391C PHE* 1.3 63.0 + - - +
393C GLN* 3.3 2.9 + - - +
394C LYS* 3.0 24.3 + - - +
402C PHE* 3.3 27.5 - - - +
403C ASP* 5.5 0.2 - - - -
405C TRP 3.7 26.2 - - - +
406C ASP* 3.7 12.6 - - - +
409C ILE* 3.8 8.9 - - + +
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Residues in contact with PHE 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C CYS* 4.1 18.8 - - + -
292C GLY 3.7 12.8 - - - -
293C ILE* 3.8 13.0 - - + -
313C PRO* 3.8 3.8 - - + -
314C LEU 3.7 21.5 - - - -
315C PHE* 3.6 46.2 - + + -
340C GLU* 4.9 2.2 - - + -
342C LYS* 4.3 15.3 - - + -
387C ALA 2.9 17.8 + - - +
388C SER 3.6 3.8 - - - +
390C ALA* 1.3 76.8 - - - +
392C LEU* 1.3 57.8 + - - +
394C LYS* 3.2 2.7 + - - -
395C HIS* 3.0 65.5 + + - +
409C ILE* 3.6 20.5 - - + +
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Residues in contact with LEU 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C VAL* 4.7 1.3 - - + -
167C LEU* 3.8 22.7 - - + -
172C PHE* 3.7 33.2 - - + -
268C ALA* 3.6 31.9 - - + -
270C ILE* 4.3 13.0 - - + -
291C CYS* 3.9 12.6 - - - -
293C ILE* 4.0 13.5 - - + -
388C SER 2.8 28.2 + - - +
389C LEU* 3.7 5.2 - - - +
391C PHE* 1.3 68.4 - - - +
393C GLN* 1.3 61.4 + - - +
395C HIS 4.6 0.2 - - - +
396C LEU* 2.9 44.5 + - + +
398C LEU* 4.0 2.5 - - + -
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Residues in contact with GLN 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389C LEU 2.8 17.5 + - - +
390C ALA* 3.7 5.2 - - - +
392C LEU* 1.3 76.2 - - - +
394C LYS* 1.3 65.4 + - - +
397C GLY* 3.0 19.8 + - - -
398C LEU* 3.1 38.0 + - + +
400C LYS* 3.1 37.9 + - - +
402C PHE* 3.0 29.6 + - + +
403C ASP* 3.4 33.5 + - + +
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Residues in contact with LYS 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340C GLU* 4.3 12.2 + - - -
342C LYS* 4.6 1.8 - - - +
390C ALA 3.0 16.0 + - - +
391C PHE* 3.2 5.6 + - - +
393C GLN* 1.3 80.9 - - - +
395C HIS* 1.3 90.9 + - + +
396C LEU 3.8 0.2 + - - -
397C GLY* 3.9 5.7 + - - -
406C ASP* 5.0 14.8 + - - +
409C ILE* 3.8 30.1 - - + +
410C GLU* 4.1 16.4 + - - -
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Residues in contact with HIS 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C ARG* 4.6 9.5 - - - +
291C CYS* 4.0 20.9 - - + -
313C PRO* 3.5 19.5 - - + +
340C GLU* 3.6 27.1 - - + +
391C PHE* 3.0 58.6 + + - +
394C LYS* 1.3 109.3 + - + +
396C LEU* 1.3 68.1 + - - +
397C GLY 3.5 0.7 - - - -
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Residues in contact with LEU 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C PRO* 4.6 1.3 - - + -
146C LEU 5.3 0.7 - - - +
172C PHE* 4.3 16.6 - - + -
265C GLU 4.5 3.1 - - - +
266C LYS* 3.3 41.0 - - + +
267C ILE 3.7 26.5 - - - +
268C ALA* 4.3 6.1 - - + +
290C ARG* 3.7 20.2 - - + -
291C CYS* 4.0 15.5 - - - -
392C LEU* 2.9 36.4 + - + +
395C HIS* 1.3 78.3 - - - +
397C GLY* 1.3 62.4 + - - +
398C LEU* 4.2 7.2 - - + -
577C FMT 3.3 18.5 - - - +
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Residues in contact with GLY 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C LYS* 3.8 3.4 - - - -
393C GLN 3.0 9.9 + - - -
394C LYS 3.9 5.4 + - - -
395C HIS 3.5 2.6 - - - -
396C LEU* 1.3 79.3 - - - +
398C LEU* 1.3 65.2 + - - +
399C HIS* 3.7 13.5 + - - -
577C FMT 3.0 25.8 - - - +
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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