Contacts of the helix formed by residues 375 - 395 (chain A) in PDB entry 3GEB
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 375 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374A VAL* 1.3 77.5 - - + +
376A TRP* 1.3 64.8 + - - +
377A MET 3.3 0.4 - - - -
378A ARG* 3.5 27.4 + - - +
379A LYS* 3.7 32.8 + - - +
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Residues in contact with TRP 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A CYS* 5.8 4.3 - - + -
354A GLY 6.0 0.4 - - - -
355A PHE* 3.4 28.4 + - - +
372A GLY* 3.8 18.6 + - - -
373A GLY* 3.6 29.2 - - - +
375A ASP* 1.3 78.8 - - - +
377A MET* 1.3 89.1 + - - +
379A LYS* 3.0 29.5 + - + +
380A LEU* 3.1 35.7 + - + +
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Residues in contact with MET 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A VAL* 3.5 32.8 - - + -
339A ASP* 2.8 44.7 - - - +
373A GLY* 3.7 23.1 - - - +
374A VAL* 3.4 13.4 + - - +
376A TRP* 1.3 103.8 - - + +
378A ARG* 1.3 58.3 + - - +
380A LEU* 3.4 10.5 + - + +
381A ALA* 3.2 18.7 + - - +
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Residues in contact with ARG 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A SER 4.0 6.3 + - - -
339A ASP* 3.3 57.4 + - - +
374A VAL* 3.2 23.7 + - - +
375A ASP* 3.5 25.1 - - - +
377A MET* 1.3 76.2 - - - +
379A LYS* 1.3 58.6 + - + +
381A ALA* 3.8 1.9 + - - +
382A PHE* 3.2 41.9 + - + -
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Residues in contact with LYS 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A TYR* 4.1 8.3 - - - +
353A ASP* 2.9 40.8 + - - +
354A GLY* 4.2 14.7 - - - +
375A ASP* 3.7 32.4 + - - +
376A TRP* 3.0 19.3 + - + +
378A ARG* 1.3 78.2 - - + +
380A LEU* 1.3 64.1 + - - +
382A PHE* 3.5 10.7 + - + +
383A ARG* 3.2 41.5 + - - +
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Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A LEU* 3.4 31.6 - - + -
328A CYS* 4.2 22.2 - - + -
330A GLN* 4.5 1.6 - - - +
336A VAL* 4.3 17.0 - - + -
376A TRP* 3.1 45.4 + - + +
377A MET* 3.4 20.0 - - - +
379A LYS* 1.3 74.0 - - - +
381A ALA* 1.3 58.4 + - - +
383A ARG* 2.7 30.6 + - - +
384A TYR* 3.0 27.1 + - + -
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Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A VAL* 3.2 39.2 - - - +
337A SER* 4.7 1.3 - - - -
339A ASP 3.9 11.7 - - - +
340A ASP* 4.0 13.8 - - + +
377A MET 3.2 10.6 + - - +
378A ARG 3.9 5.4 - - - +
380A LEU* 1.3 79.2 - - - +
382A PHE* 1.3 58.1 + - - +
384A TYR* 4.0 2.4 - - - +
385A ARG* 2.9 33.3 + - - +
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Residues in contact with PHE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A ASP 5.0 0.7 - - - -
340A ASP* 3.1 28.3 - - - -
341A ASN* 3.2 31.4 - - - -
343A GLN* 3.2 28.3 - - + -
345A LEU* 3.2 15.1 - - + +
348A TYR* 3.8 30.1 - + + -
350A PHE* 3.8 13.4 - - + -
378A ARG* 3.2 25.2 + - + -
379A LYS* 3.5 15.5 - - + +
380A LEU 3.0 0.6 - - - -
381A ALA* 1.3 79.1 - - - +
383A ARG* 1.3 57.5 + - - +
385A ARG* 3.8 13.0 - - - -
386A ARG* 3.0 29.6 + - - +
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Residues in contact with ARG 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A PHE* 3.8 24.1 - - + -
324A ASP* 3.2 31.6 + - - -
325A LEU* 4.1 20.4 - - + -
350A PHE* 3.4 49.8 + - + +
353A ASP* 2.7 38.4 + - - -
354A GLY 3.4 10.6 + - - -
355A PHE* 5.3 2.8 - - - +
379A LYS* 3.2 26.3 + - - +
380A LEU* 2.7 16.5 + - - +
382A PHE* 1.3 73.2 - - - +
384A TYR* 1.3 59.9 + - - +
386A ARG* 3.3 5.2 + - - +
387A VAL* 2.9 32.4 + - - +
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Residues in contact with TYR 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A LEU* 3.4 29.9 + - + +
328A CYS* 3.4 28.2 + - - +
330A GLN* 3.2 39.8 + - - +
333A VAL* 3.6 29.6 - - + +
336A VAL* 4.2 5.8 - - + -
380A LEU* 3.0 29.3 + - + -
381A ALA* 4.0 7.2 - - - +
383A ARG* 1.3 74.4 - - - +
385A ARG* 1.3 67.1 + - - +
387A VAL* 3.2 6.3 + - + +
388A LYS* 3.1 20.6 + - - +
451A LEU* 3.9 28.2 - - + +
452A ILE* 4.0 23.5 - - + +
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Residues in contact with ARG 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A ASP* 5.9 1.3 - - - +
340A ASP* 2.6 39.9 + - - +
342A GLY* 4.2 8.2 + - - -
343A GLN 2.7 37.8 + - - +
344A ASP* 4.8 0.2 - - - +
345A LEU* 3.4 30.9 - - - +
381A ALA 2.9 17.2 + - - +
382A PHE* 3.8 8.6 - - - +
384A TYR* 1.3 77.8 - - - +
386A ARG* 1.3 59.2 + - - +
388A LYS* 3.2 18.1 + - + +
389A GLU* 2.9 60.6 + - + +
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Residues in contact with ARG 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PHE* 3.3 25.4 - - + -
345A LEU* 4.0 25.2 + - + +
346A SER* 4.6 11.1 + - - +
350A PHE* 3.7 27.6 - - + -
382A PHE 3.0 19.1 + - - +
383A ARG 3.4 4.7 - - - +
384A TYR 3.2 0.2 - - - -
385A ARG* 1.3 75.9 - - - +
387A VAL* 1.3 60.8 + - - +
389A GLU* 2.6 40.6 + - - +
390A MET* 2.9 52.3 + - + +
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Residues in contact with VAL 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A LEU* 3.9 40.2 - - + +
321A PHE* 4.2 7.9 - - + -
325A LEU* 4.3 2.2 - - + -
333A VAL* 5.0 2.7 - - + -
383A ARG 2.9 21.0 + - - +
384A TYR* 3.4 11.2 - - + +
385A ARG 3.2 0.2 - - - -
386A ARG* 1.3 77.2 - - - +
388A LYS* 1.3 65.6 + - - +
390A MET* 3.1 10.9 + - - +
391A TYR* 3.0 22.4 + - + +
452A ILE* 4.0 15.3 - - + -
455A LEU* 3.6 30.5 - - + -
469A ILE* 4.7 2.9 - - + -
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Residues in contact with LYS 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A VAL* 4.5 8.5 - - + -
334A ASP* 2.5 45.8 + - - -
384A TYR 3.1 12.6 + - - +
385A ARG* 3.3 20.0 - - + +
387A VAL* 1.3 77.3 - - - +
389A GLU* 1.3 57.6 + - + +
391A TYR* 3.4 2.4 - - - +
392A ASN* 3.0 45.5 + - - +
469A ILE* 3.8 34.1 - - + +
470A GLU* 4.7 7.1 + - - +
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Residues in contact with GLU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A LEU* 4.1 8.0 + - - +
385A ARG* 2.9 47.2 + - + +
386A ARG* 2.6 50.6 + - - +
387A VAL 3.2 0.2 - - - -
388A LYS* 1.3 78.0 - - + +
390A MET* 1.3 59.7 + - - +
392A ASN* 4.6 4.0 - - - +
393A THR* 2.9 41.8 + - + +
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Residues in contact with MET 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A HIS* 4.0 32.5 - - + +
320A LEU* 4.3 11.4 - - + -
386A ARG* 2.9 48.9 + - + +
387A VAL* 3.1 9.4 + - - +
389A GLU* 1.3 74.0 - - - +
391A TYR* 1.3 61.5 + - - +
393A THR* 3.9 4.3 - - - -
394A TYR* 2.9 48.2 + - + +
401A LEU* 3.5 32.6 - - + +
459A LEU* 5.3 0.2 - - - -
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Residues in contact with TYR 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 5.9 0.2 - - - +
387A VAL* 3.0 9.8 + - + +
388A LYS 3.4 8.7 - - - +
390A MET* 1.3 79.2 - - - +
392A ASN* 1.3 68.2 + - - +
395A LYS* 2.6 41.0 + - + +
455A LEU* 4.0 22.2 - - + -
458A VAL* 3.5 19.1 - - + +
459A LEU* 3.8 32.5 - - + +
464A GLY* 3.4 29.4 + - - -
467A PHE* 2.8 22.4 + - - +
469A ILE* 3.5 37.5 - - + -
472A ILE* 3.4 18.3 - - + +
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Residues in contact with ASN 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A LYS* 3.0 35.7 + - - +
389A GLU* 4.2 5.0 - - - +
391A TYR* 1.3 92.8 - - - +
393A THR* 1.3 62.4 + - + +
395A LYS* 3.4 40.7 + - - +
469A ILE* 4.5 7.6 + - - +
470A GLU* 5.1 5.1 + - - +
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Residues in contact with THR 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A GLU* 2.9 28.7 + - + +
390A MET* 3.9 0.9 - - - -
392A ASN* 1.3 80.2 - - + +
394A TYR* 1.3 92.8 + - - +
395A LYS 3.8 0.2 - - - -
396A ASN 5.1 0.7 + - - -
397A ASN* 4.5 8.0 + - - +
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Residues in contact with TYR 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A MET* 2.9 38.5 + - + +
391A TYR* 3.5 0.7 - - - -
393A THR* 1.3 99.6 - - - +
395A LYS* 1.3 65.0 + - - +
396A ASN 3.0 3.8 - - - -
397A ASN* 2.9 43.8 + - - +
398A VAL* 3.0 15.1 + - - +
400A GLY* 3.9 8.1 + - - -
401A LEU* 3.6 56.8 - - + -
459A LEU* 4.4 2.2 - - + -
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Residues in contact with LYS 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A TYR* 2.6 27.3 + - + +
392A ASN* 3.4 38.9 + - - +
394A TYR* 1.3 72.2 - - - +
396A ASN* 1.3 79.1 + - - +
398A VAL* 3.8 11.1 - - - +
459A LEU* 3.5 13.5 - - + +
462A GLY* 5.4 5.2 - - - -
464A GLY* 3.4 41.2 + - - +
465A SER* 4.1 14.1 + - - +
468A PRO* 5.6 7.1 - - - +
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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) + - + + + + + -
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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