Contacts of the helix formed by residues 384 - 407 (chain C) in PDB entry 2GPV
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 384 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C LEU* 5.0 3.0 - - + +
293C SER* 5.8 2.2 - - - +
296C ASP* 2.9 16.4 + - - +
382C ILE* 3.3 11.1 - - - +
383C GLU* 1.3 73.4 - - + +
385C VAL* 1.3 62.4 + - - +
386C GLU* 3.7 8.8 + - - +
387C ALA* 3.1 34.3 + - + +
388C VAL* 3.3 18.4 + - - +
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Residues in contact with VAL 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C ILE* 4.0 28.0 - - + +
383C GLU 3.7 4.3 + - - +
384C ASP* 1.3 69.1 + - - +
386C GLU* 1.3 59.9 + - - +
387C ALA 3.1 1.6 - - - -
388C VAL* 3.2 4.3 + - - +
389C GLN* 2.8 38.2 + - + +
354F LYS* 3.5 29.4 - - - +
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Residues in contact with GLU 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C ASP* 3.8 8.1 - - - +
385C VAL* 1.3 80.8 - - - +
387C ALA* 1.3 55.9 + - - +
389C GLN* 3.5 6.9 + - - +
390C LYS* 2.9 45.7 + - - +
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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
----------------------------------------------------------
292C LEU* 3.6 22.1 - - + +
384C ASP* 3.1 30.4 + - - +
385C VAL 3.1 1.0 - - - -
386C GLU* 1.3 77.0 - - - +
388C VAL* 1.3 60.6 + - - +
390C LYS* 3.1 11.5 + - - +
391C LEU* 3.0 26.7 + - - +
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Residues in contact with VAL 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C LEU* 4.3 13.7 - - + -
296C ASP* 4.5 2.7 - - - +
300C LEU* 4.2 24.0 - - + -
375C ALA* 3.6 11.7 - - - +
382C ILE* 3.9 28.5 - - + -
384C ASP 3.3 16.9 + - - +
385C VAL* 3.2 5.7 + - + +
387C ALA* 1.3 76.8 - - - +
389C GLN* 1.3 57.9 + - - +
391C LEU* 3.3 9.7 + - + +
392C GLN* 3.0 46.6 + - - +
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Residues in contact with GLN 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C VAL* 2.8 22.4 + - + +
386C GLU* 3.6 7.6 - - - +
388C VAL* 1.3 74.9 - - - +
390C LYS* 1.3 66.1 + - - +
392C GLN* 3.2 25.3 + - - +
393C ASP* 2.8 52.0 + - - +
355F LYS* 5.6 6.1 - - - +
359F MET* 6.1 0.5 - - - +
416F LYS* 4.6 12.7 - - - +
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Residues in contact with LYS 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C GLU* 2.9 33.3 + - - +
387C ALA* 3.3 13.5 - - - +
389C GLN* 1.3 76.9 - - - +
391C LEU* 1.3 56.1 + - - +
393C ASP* 3.1 15.3 + - + +
394C VAL* 3.0 39.2 + - + +
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Residues in contact with LEU 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C ILE* 4.0 7.4 - - + -
287C PRO 3.3 26.7 - - - +
288C GLY* 4.7 4.3 - - - -
289C PHE* 4.5 17.7 - - + +
292C LEU* 4.1 26.0 - - + -
300C LEU* 4.4 10.1 - - + -
374C LEU* 6.3 0.7 - - + -
375C ALA* 3.9 20.4 - - + -
387C ALA 3.0 12.6 + - - +
388C VAL* 3.4 9.6 - - - +
390C LYS* 1.3 73.3 - - - +
392C GLN* 1.3 65.8 + - - +
394C VAL* 3.4 9.3 + - + +
395C LEU* 3.2 39.4 + - + +
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Residues in contact with GLN 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C ILE* 5.5 0.8 - - - +
375C ALA* 2.9 41.9 + - + +
376C ASN* 3.6 27.4 + - + +
378C ASP* 5.4 4.0 + - - +
388C VAL* 3.0 28.8 + - - +
389C GLN* 3.4 31.7 + - - +
391C LEU* 1.3 77.2 - - - +
393C ASP* 1.3 58.6 + - - +
395C LEU* 3.4 2.5 + - - +
396C HIS* 2.8 32.6 + - - +
419F MET* 4.5 15.0 - - + +
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Residues in contact with ASP 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C GLN* 2.8 42.6 + - - +
390C LYS* 3.4 15.2 - - + +
392C GLN* 1.3 74.1 - - - +
394C VAL* 1.3 55.9 + - + +
396C HIS* 3.6 7.9 + - - +
397C GLU* 2.7 37.4 + - - +
412F ARG* 4.4 9.8 + - - +
416F LYS* 3.5 28.0 + - - +
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Residues in contact with VAL 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C ILE* 3.2 32.0 - - + +
287C PRO* 5.1 12.3 - - + +
390C LYS* 3.0 30.1 + - + +
391C LEU* 3.7 11.2 - - + +
392C GLN 3.3 0.2 - - - -
393C ASP* 1.3 77.5 - - + +
395C LEU* 1.3 59.9 + - + +
397C GLU* 3.4 12.9 + - - +
398C ALA* 3.1 24.6 + - - +
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Residues in contact with LEU 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C ILE* 4.2 21.8 - - + -
241C LEU* 4.3 5.2 - - + -
286C ILE* 4.1 14.6 - - + -
287C PRO* 4.9 2.2 - - + +
368C THR* 3.8 9.7 - - + +
371C ALA* 3.6 46.4 - - + +
372C ILE* 4.0 16.6 - - + +
375C ALA* 3.8 10.5 - - + -
391C LEU* 3.2 37.4 + - + +
392C GLN* 3.8 2.7 - - - +
394C VAL* 1.3 76.0 - - + +
396C HIS* 1.3 63.9 + - - +
398C ALA* 3.3 7.4 + - - +
399C LEU* 3.1 18.5 + - - +
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Residues in contact with HIS 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C ILE* 4.4 8.2 - - - +
392C GLN 2.8 22.2 + - - +
393C ASP* 3.6 7.7 - - - +
395C LEU* 1.3 69.5 - - - +
397C GLU* 1.3 66.5 + - - +
399C LEU* 3.1 9.8 + - + +
400C GLN* 2.9 35.2 + - + +
414C ALA* 5.7 0.4 - - + -
418C LEU* 3.7 18.8 - - + +
412F ARG* 3.4 52.0 + - + +
415F GLY* 3.5 25.9 - - - -
416F LYS* 4.4 6.7 + - - +
419F MET* 4.3 18.2 - - + -
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Residues in contact with GLU 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ASN* 5.4 2.0 - - - +
393C ASP 2.7 20.2 + - - +
394C VAL* 3.4 12.3 - - - +
396C HIS* 1.3 71.7 - - - +
398C ALA* 1.3 54.8 + - - +
400C GLN* 3.2 3.4 + - - +
401C ASP* 2.7 44.4 + - + +
412F ARG* 3.8 39.8 + - - +
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Residues in contact with ALA 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ASN* 3.5 25.2 + - - +
237C ILE* 4.2 24.2 - - + -
238C VAL* 4.1 7.6 - - + +
368C THR* 4.4 7.9 - - + -
394C VAL 3.1 11.1 + - - +
395C LEU* 3.3 14.4 - - - +
396C HIS 3.2 0.2 - - - -
397C GLU* 1.3 79.7 - - - +
399C LEU* 1.3 57.7 + - - +
401C ASP* 3.2 1.0 + - - +
402C TYR* 2.8 31.2 + - - +
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Residues in contact with LEU 399 (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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238C VAL* 5.7 0.4 - - - -
365C GLU* 4.9 13.7 - - + +
368C THR* 4.3 17.4 - - + +
369C LEU* 5.1 4.7 - - + -
372C ILE* 4.0 13.2 - - + -
395C LEU 3.1 8.2 + - - +
396C HIS* 3.1 11.7 + - + +
398C ALA* 1.3 77.4 - - - +
400C GLN* 1.3 58.3 + - - +
402C TYR* 3.3 5.7 + - + +
403C GLU* 2.9 58.0 + - + +
414C ALA* 4.1 20.6 - - + +
417C MET* 4.3 13.5 - - + -
418C LEU* 4.0 35.4 - - + -
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Residues in contact with GLN 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C HIS* 2.9 31.7 + - + +
397C GLU* 3.6 8.1 - - - +
399C LEU* 1.3 77.1 - - - +
401C ASP* 1.3 55.8 + - - +
403C GLU* 4.7 3.5 - - - +
404C ALA* 3.1 29.6 + - - +
411C PRO 4.8 8.8 - - - +
414C ALA* 3.7 26.6 - - - +
415C GLY 5.4 0.4 - - - +
400F GLN* 5.5 7.3 - - - +
411F PRO* 5.1 11.3 + - + +
412F ARG* 4.8 15.6 - - + +
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Residues in contact with ASP 401 (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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235C ASN* 3.6 27.7 + - + +
397C GLU* 2.7 30.2 + - + +
400C GLN* 1.3 71.6 - - - +
402C TYR* 1.3 65.4 + - - +
404C ALA* 3.4 9.4 - - - +
405C GLY* 3.3 15.4 + - - -
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Residues in contact with TYR 402 (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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234C TYR* 3.7 27.4 + + - -
235C ASN* 4.8 5.3 - - + +
238C VAL* 4.1 16.4 - - + -
362C GLU* 2.8 25.3 + - - +
364C GLU* 3.5 42.9 + - + -
365C GLU* 3.7 27.1 - - + -
398C ALA 2.8 17.4 + - - +
399C LEU* 3.6 7.2 - - + +
401C ASP* 1.3 73.2 - - - +
403C GLU* 1.3 81.7 + - + +
404C ALA 3.1 0.7 + - - -
405C GLY* 3.1 2.4 + - - -
406C GLN* 2.9 51.6 + - + +
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Residues in contact with GLU 403 (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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365C GLU* 2.8 36.1 - - - +
399C LEU* 2.9 42.6 + - + +
400C GLN* 4.2 5.8 - - - +
402C TYR* 1.3 79.0 - - + +
404C ALA* 1.3 58.4 + - - +
407C HIS* 2.9 43.5 + - - +
410C ASP 4.8 1.5 - - - +
413C ARG* 3.2 29.6 + - + -
414C ALA* 4.1 22.2 - - + +
417C MET* 3.8 8.5 - - - +
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Residues in contact with ALA 404 (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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400C GLN* 3.1 23.3 + - - +
401C ASP* 3.4 14.1 - - - +
402C TYR 3.0 0.8 - - - -
403C GLU* 1.3 79.3 - - - +
405C GLY* 1.3 60.7 + - - +
406C GLN 3.8 0.2 + - - -
408C MET* 3.6 23.8 + - - +
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Residues in contact with GLY 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C ASP 3.3 6.2 + - - -
402C TYR 3.1 4.7 + - - -
404C ALA* 1.3 78.9 - - - +
406C GLN* 1.3 60.8 + - - +
408C MET* 4.7 11.0 - - - +
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Residues in contact with GLN 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C TYR* 4.9 10.3 + - - -
362C GLU* 4.6 8.7 + - - -
402C TYR* 2.9 50.7 + - + +
405C GLY* 1.3 77.1 - - - +
407C HIS* 1.3 78.6 + - + +
408C MET 3.7 1.7 + - - -
409C GLU* 4.2 2.6 - - - +
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Residues in contact with HIS 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C GLU* 3.0 36.9 + - - -
365C GLU* 3.9 1.6 - - - -
402C TYR* 4.2 1.1 - + - -
403C GLU* 2.9 40.6 + - - +
406C GLN* 1.3 97.8 + - + +
408C MET* 1.3 61.9 + - - +
409C GLU* 2.7 32.9 + - - +
410C ASP 2.9 24.6 + - - +
411C PRO* 4.8 0.3 - - - +
413C ARG* 3.5 33.7 + - + -
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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