Contacts of the helix formed by residues 384 - 407 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292F LEU* 5.4 2.2 - - + +
293F SER* 5.4 4.3 - - - +
296F ASP* 2.8 17.2 + - - +
382F ILE* 3.6 2.7 - - - -
383F GLU* 1.3 73.1 - - + +
385F VAL* 1.3 61.3 + - - +
386F GLU* 3.0 24.8 - - - +
387F ALA* 3.3 26.8 + - + +
388F VAL* 3.3 21.5 + - - +
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Residues in contact with VAL 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C LYS* 4.7 24.7 - - - +
382F ILE* 3.8 28.9 - - + +
383F GLU 3.8 3.0 + - - +
384F ASP* 1.3 69.6 + - - +
386F GLU* 1.3 80.4 + - + +
388F VAL* 3.3 4.4 + - - +
389F GLN* 3.1 37.5 + - - +
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Residues in contact with GLU 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383F GLU 5.4 0.2 - - - +
384F ASP* 3.0 24.8 - - - +
385F VAL* 1.3 88.5 + - + +
387F ALA* 1.3 63.6 + - - +
389F GLN* 2.8 20.0 + - - +
390F LYS* 3.0 13.9 + - - +
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Residues in contact with ALA 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F LEU* 3.4 25.5 - - + +
384F ASP* 3.3 30.1 + - - +
386F GLU* 1.3 79.0 - - - +
388F VAL* 1.3 57.5 + - - +
390F LYS* 3.3 9.7 + - - +
391F LEU* 3.0 26.0 + - - +
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Residues in contact with VAL 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F LEU* 4.2 22.7 - - + -
296F ASP* 4.3 5.6 - - + +
300F LEU* 4.2 17.5 - - + -
375F ALA* 3.6 21.7 - - - +
382F ILE* 3.7 28.7 - - + -
384F ASP 3.3 11.9 + - - +
385F VAL* 3.3 7.8 + - - +
386F GLU 3.2 0.8 - - - -
387F ALA* 1.3 76.4 - - - +
389F GLN* 1.3 56.9 + - - +
391F LEU* 3.4 8.9 + - + +
392F GLN* 2.9 33.9 + - - +
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Residues in contact with GLN 389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C LYS* 4.6 19.0 - - - +
358C SER* 5.1 12.7 + - - -
359C MET* 6.0 3.6 - - - +
385F VAL* 3.1 32.9 + - - +
386F GLU* 2.8 12.5 + - - +
388F VAL* 1.3 74.3 - - - +
390F LYS* 1.3 57.1 + - - +
391F LEU 3.2 0.4 - - - -
392F GLN* 3.4 22.6 + - + +
393F ASP* 2.8 32.8 + - - +
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Residues in contact with LYS 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F GLU 3.0 10.3 + - - +
387F ALA* 3.5 11.9 - - - +
389F GLN* 1.3 77.1 - - - +
391F LEU* 1.3 57.7 + - - +
393F ASP* 3.3 17.6 + - - +
394F VAL* 2.8 49.3 + - + +
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Residues in contact with LEU 391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286F ILE* 4.4 14.1 - - + -
287F PRO 3.4 25.8 - - - +
288F GLY* 4.6 4.5 - - - -
289F PHE* 4.4 17.9 - - + +
292F LEU* 4.2 24.5 - - + -
300F LEU* 4.5 11.4 - - + -
374F LEU* 6.2 0.9 - - + -
375F ALA* 4.2 19.1 - - + +
387F ALA 3.0 13.1 + - - +
388F VAL* 3.5 10.5 - - - +
389F GLN 3.2 0.2 - - - -
390F LYS* 1.3 74.3 - - - +
392F GLN* 1.3 67.9 + - - +
394F VAL* 3.3 8.2 + - + +
395F LEU* 3.2 28.9 + - + +
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Residues in contact with GLN 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C LYS* 5.9 3.0 + - - +
419C MET* 4.0 20.0 - - + +
372F ILE* 5.2 0.7 - - - +
375F ALA* 2.7 44.0 + - + +
376F ASN* 3.5 26.3 + - - +
378F ASP* 5.3 4.2 + - - +
388F VAL* 2.9 24.6 + - - +
389F GLN* 3.4 26.9 + - + +
391F LEU* 1.3 76.9 - - - +
393F ASP* 1.3 63.8 + - - +
395F LEU* 3.9 1.8 - - - +
396F HIS* 3.0 26.6 + - - +
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Residues in contact with ASP 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C ARG* 3.1 32.8 + - - -
416C LYS* 3.3 31.8 + - - +
389F GLN 2.8 20.9 + - - +
390F LYS* 3.5 23.2 + - + +
391F LEU 3.1 0.2 - - - -
392F GLN* 1.3 75.0 - - - +
394F VAL* 1.3 63.6 + - - +
396F HIS* 3.5 7.5 + - - +
397F GLU* 3.0 23.6 + - - +
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Residues in contact with VAL 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237F ILE* 3.0 33.8 - - + +
287F PRO* 5.6 5.2 - - + +
390F LYS* 2.8 43.3 + - + +
391F LEU* 3.3 10.5 + - + +
393F ASP* 1.3 74.5 - - - +
395F LEU* 1.3 59.7 + - + +
397F GLU* 3.2 20.3 + - - +
398F ALA* 3.0 24.1 + - - +
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Residues in contact with LEU 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237F ILE* 3.9 27.4 - - + -
241F LEU* 4.8 3.4 - - + -
286F ILE* 4.4 16.2 - - + -
287F PRO* 5.3 3.6 - - + +
368F THR* 3.6 10.5 - - + +
371F ALA* 3.4 51.4 - - + +
372F ILE* 3.6 17.9 - - + +
375F ALA* 4.0 14.1 - - + -
391F LEU* 3.2 23.8 + - + +
392F GLN 4.0 1.6 - - - +
394F VAL* 1.3 76.1 - - + +
396F HIS* 1.3 66.6 + - - +
398F ALA* 3.3 8.0 + - - +
399F LEU 3.1 15.1 + - - -
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Residues in contact with HIS 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C ARG* 3.4 36.7 + - + +
415C GLY* 3.4 35.3 - - - -
416C LYS* 4.3 6.1 + - - +
419C MET* 4.1 19.0 - - + -
372F ILE* 4.2 9.9 - - + +
392F GLN 3.0 19.2 + - - +
393F ASP* 3.6 7.9 + - - +
395F LEU* 1.3 75.4 - - - +
397F GLU* 1.3 53.0 + - - +
399F LEU* 2.9 10.0 + - + +
400F GLN* 2.8 56.6 + - + -
418F LEU* 3.7 18.1 - - + +
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Residues in contact with GLU 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C ARG* 3.4 43.5 + - - +
393F ASP* 3.0 14.1 + - - +
394F VAL* 3.3 21.5 - - - +
396F HIS* 1.3 75.9 - - - +
398F ALA* 1.3 56.5 + - - +
400F GLN* 3.6 3.6 - - + +
401F ASP* 2.8 35.8 + - + +
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Residues in contact with ALA 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235F ASN* 3.8 29.2 + - - +
237F ILE* 3.9 25.4 - - + -
238F VAL* 4.3 8.1 - - + +
368F THR* 4.4 7.6 - - + -
394F VAL 3.0 11.6 + - - +
395F LEU* 3.4 10.5 - - - +
396F HIS 3.1 0.4 - - - -
397F GLU* 1.3 72.9 - - - +
399F LEU* 1.3 61.6 + - - +
401F ASP* 3.5 1.3 + - - +
402F TYR* 2.8 29.6 + - - +
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Residues in contact with LEU 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365F GLU* 4.8 12.8 - - + +
368F THR* 3.9 23.2 - - + +
369F LEU* 4.8 4.9 - - + -
372F ILE* 4.0 17.7 - - + -
395F LEU 3.1 8.0 + - - +
396F HIS* 2.9 10.6 + - + +
398F ALA* 1.3 76.6 - - - +
400F GLN* 1.3 65.7 + - - +
402F TYR* 2.9 9.6 + - + +
403F GLU* 2.8 53.9 + - + +
414F ALA* 4.0 25.1 - - + +
417F MET* 4.1 16.4 - - + -
418F LEU* 4.1 16.8 - - + -
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Residues in contact with GLN 400 (chain F).
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* 5.5 6.7 - - - +
411C PRO 5.6 4.3 - - - +
412C ARG* 4.4 17.7 - - + -
415C GLY* 5.4 0.9 + - - -
396F HIS* 2.8 40.9 + - + +
397F GLU* 3.6 11.2 - - + +
399F LEU* 1.3 73.7 - - - +
401F ASP* 1.3 56.5 + - - +
403F GLU* 3.5 2.9 + - - +
404F ALA* 2.9 29.9 + - + +
411F PRO 4.9 9.1 + - - -
414F ALA* 3.4 33.1 - - - +
418F LEU* 5.0 0.5 - - - +
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Residues in contact with ASP 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235F ASN* 4.0 23.4 + - + +
397F GLU* 2.8 25.1 + - + +
398F ALA* 4.1 3.6 - - - +
400F GLN* 1.3 72.0 - - - +
402F TYR* 1.3 67.3 + - - +
404F ALA* 4.1 10.2 - - - +
405F GLY* 3.3 15.9 + - - -
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Residues in contact with TYR 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234F TYR* 4.6 21.5 - + + -
235F ASN* 5.3 4.4 - - + +
238F VAL* 4.4 18.8 - - + -
362F GLU* 2.7 26.4 + - - -
364F GLU* 3.5 45.9 + - + +
365F GLU* 3.5 24.7 - - + -
398F ALA 2.8 15.9 + - - +
399F LEU* 2.9 11.9 + - + +
401F ASP* 1.3 76.6 - - - +
403F GLU* 1.3 77.3 - - - +
405F GLY* 3.9 0.2 - - - -
406F GLN* 2.9 57.1 + - + +
407F HIS* 3.8 8.5 - + - -
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Residues in contact with GLU 403 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365F GLU* 2.7 33.8 - - - +
399F LEU* 2.8 28.4 + - + +
400F GLN* 3.9 4.5 - - - +
402F TYR* 1.3 84.1 - - - +
404F ALA* 1.3 65.4 + - - +
405F GLY 3.1 2.2 - - - -
407F HIS* 3.0 56.0 + - - +
410F ASP 5.5 1.3 - - - +
413F ARG* 3.2 20.6 - - + -
414F ALA* 3.9 32.3 - - + +
417F MET* 4.2 2.4 - - - +
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Residues in contact with ALA 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400F GLN* 2.9 20.0 + - + +
401F ASP* 3.8 14.8 - - - +
402F TYR 3.4 0.2 - - - -
403F GLU* 1.3 77.5 - - - +
405F GLY* 1.3 59.8 + - - +
407F HIS 5.2 0.2 - - - -
408F MET* 3.7 29.0 - - - +
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Residues in contact with GLY 405 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401F ASP* 3.3 10.1 + - - -
402F TYR 3.9 1.1 - - - -
403F GLU 3.1 0.2 - - - -
404F ALA* 1.3 81.3 - - - +
406F GLN* 1.3 61.0 - - - +
407F HIS 3.5 0.9 - - - -
408F MET* 4.8 12.0 + - - +
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Residues in contact with GLN 406 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F PRO 5.4 4.2 - - - +
234F TYR* 5.5 7.6 - - + +
362F GLU* 4.6 3.0 + - - +
402F TYR* 2.9 53.5 + - + +
405F GLY* 1.3 75.2 - - - +
407F HIS* 1.3 77.9 + - + +
408F MET 3.9 1.3 - - - -
409F GLU* 4.2 2.9 - - - +
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Residues in contact with HIS 407 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362F GLU* 2.6 42.3 + - - -
402F TYR* 3.8 3.1 - + - -
403F GLU* 3.0 42.3 + - - +
404F ALA* 5.2 0.2 - - - -
406F GLN* 1.3 99.3 + - + +
408F MET* 1.3 60.4 + - - +
409F GLU* 3.2 30.9 + - - +
410F ASP 3.2 21.7 + - - +
411F PRO* 5.0 0.2 - - - +
413F ARG* 3.5 28.1 + - + -
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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