Contacts of the helix formed by residues 380 - 397 (chain A) in PDB entry 1HS6
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 SER 380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A GLU* 4.6 18.5 + - - +
349A LEU* 4.9 0.9 - - - -
352A SER* 3.3 21.7 + - - -
379A SER* 1.3 73.6 - - - +
381A VAL* 1.3 59.2 + - - +
382A PRO* 3.5 0.7 - - - -
383A TYR* 3.2 12.2 + - - +
384A GLU* 2.8 42.5 + - - +
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Residues in contact with VAL 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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349A LEU* 4.1 12.6 - - + -
352A SER* 4.2 17.9 - - - -
353A VAL* 5.3 1.3 - - + -
356A PHE* 4.3 5.6 - - + -
362A PHE 3.6 14.6 - - - +
363A THR* 3.6 37.9 - - + +
364A LYS 3.8 12.8 - - - +
365A LEU* 4.8 0.9 - - - +
379A SER* 3.2 13.7 - - - +
380A SER* 1.3 74.7 - - - +
382A PRO* 1.3 77.0 - - + +
385A LYS* 2.7 37.9 + - + +
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Residues in contact with PRO 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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314A PHE* 3.6 35.4 - - + +
315A TRP* 3.7 31.6 - - + +
318A GLU* 4.6 2.0 - - + -
319A GLY 3.7 10.8 + - - -
362A PHE 5.7 0.2 - - - +
365A LEU* 4.4 8.1 - - + +
379A SER* 3.4 21.3 - - - +
381A VAL* 1.3 95.7 - - + +
383A TYR* 1.4 62.8 + - + +
386A GLY* 3.2 19.1 + - - -
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Residues in contact with TYR 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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295A HIS* 4.0 0.4 - + - -
314A PHE* 4.3 2.7 - + - -
318A GLU* 3.1 38.7 + - + -
319A GLY* 3.9 4.5 - - - -
322A VAL* 3.8 25.9 - - + +
378A TYR* 2.7 37.0 + + - -
379A SER 3.3 25.1 - - - -
380A SER* 3.3 11.2 - - - +
381A VAL 3.1 0.2 - - - -
382A PRO* 1.4 82.4 - - + +
384A GLU* 1.3 69.5 + - + +
387A PHE* 3.0 28.2 + - - +
901A BES 2.6 53.5 + - + -
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Residues in contact with GLU 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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322A VAL* 4.4 4.0 - - - +
326A ARG* 2.8 43.0 + - - -
345A GLY* 3.2 37.3 - - - +
346A TRP* 5.4 0.9 - - - -
348A GLU* 4.6 6.6 - - + +
349A LEU* 3.7 18.2 - - + +
380A SER* 2.8 29.5 + - - +
383A TYR* 1.3 82.3 - - + +
385A LYS* 1.3 59.3 + - - +
386A GLY 3.2 0.9 - - - -
387A PHE* 4.1 6.7 - - - +
388A ALA* 2.9 29.1 + - - +
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Residues in contact with LYS 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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349A LEU* 3.8 20.7 - - + +
363A THR 2.6 28.0 + - - +
364A LYS* 4.2 0.6 - - - +
365A LEU* 3.9 29.6 - - + +
381A VAL* 2.7 22.4 + - + +
384A GLU* 1.3 74.5 - - - +
386A GLY* 1.4 57.5 + - - +
388A ALA* 3.3 2.5 + - - +
389A LEU* 2.9 28.6 + - - +
446A ALA 5.0 1.4 + - - -
447A TRP* 3.8 18.3 + - + +
450A SER 3.1 20.8 + - - -
451A PRO 3.9 0.6 + - - -
452A GLY 2.7 26.0 + - - -
453A LEU 4.6 1.8 - - - -
454A PRO* 4.2 23.6 - - + +
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Residues in contact with GLY 386 (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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315A TRP* 3.8 15.8 - - - -
319A GLY* 4.0 8.1 - - - -
365A LEU* 3.5 15.0 - - - +
382A PRO 3.2 20.4 + - - -
384A GLU 3.2 0.6 - - - -
385A LYS* 1.4 75.6 - - - +
387A PHE* 1.3 64.6 + - - +
389A LEU* 3.2 4.5 + - - +
390A LEU* 3.1 25.6 + - - +
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Residues in contact with PHE 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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319A GLY* 3.9 7.9 - - - -
322A VAL* 3.7 18.8 - - + -
323A TYR* 3.6 41.7 - + + -
326A ARG* 3.3 33.4 - - + -
338A ARG* 5.4 4.3 - - + -
342A ALA* 3.4 39.3 - - + -
383A TYR 3.0 20.6 + - - +
384A GLU* 4.1 9.4 - - - +
385A LYS 3.4 0.2 - - - -
386A GLY* 1.3 73.6 - - - +
388A ALA* 1.3 68.1 + - + +
390A LEU* 3.2 4.1 + - - +
391A PHE* 2.9 49.0 + + + -
460A TYR* 5.1 2.2 - + - -
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Residues in contact with ALA 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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346A TRP* 4.2 26.9 - - + -
384A GLU 2.9 20.0 + - - +
385A LYS* 3.6 6.1 - - - +
387A PHE* 1.3 83.6 - - + +
389A LEU* 1.3 64.4 + - - +
391A PHE* 3.8 4.2 - - - +
392A TYR* 3.0 26.5 + - - +
447A TRP* 3.7 15.4 - - + -
454A PRO* 4.4 1.3 - - + -
458A PRO* 3.8 7.2 - - + +
460A TYR* 5.0 1.3 - - - +
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Residues in contact with LEU 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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315A TRP* 3.8 20.4 - - + -
365A LEU* 3.7 24.5 - - + -
385A LYS 2.9 13.7 + - - +
386A GLY* 3.2 9.8 + - - +
388A ALA* 1.3 78.0 - - - +
390A LEU* 1.3 58.3 + - + +
392A TYR* 3.3 5.4 + - + +
393A LEU* 2.9 54.0 + - + +
424A TRP* 4.2 9.2 - - + -
442A VAL* 5.1 0.4 - - + -
444A TRP* 4.5 8.3 - - + -
447A TRP* 3.3 43.0 - - + -
448A LEU* 4.3 11.9 - - + -
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Residues in contact with LEU 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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315A TRP* 4.5 5.6 - - + -
319A GLY 3.6 12.1 - - - +
320A HIS* 3.5 62.4 - - + +
323A TYR* 3.7 26.0 - - + -
386A GLY 3.1 11.0 + - - +
387A PHE* 3.8 3.6 - - - +
389A LEU* 1.3 81.7 - - + +
391A PHE* 1.3 54.4 - - - +
393A LEU* 3.3 6.5 + - + +
394A GLU* 2.9 29.3 + - - +
403A PHE* 3.9 23.3 - - + -
424A TRP* 3.9 22.9 - - + -
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Residues in contact with PHE 391 (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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323A TYR* 4.2 4.2 - + - -
338A ARG* 3.6 28.0 - - + -
339A HIS* 3.8 24.2 - + - -
342A ALA* 4.1 9.0 - - + -
387A PHE* 2.9 38.8 + + + +
388A ALA 3.8 3.8 - - - +
390A LEU* 1.3 73.2 - - - +
392A TYR* 1.3 60.8 + - - +
394A GLU* 3.4 25.0 - - - +
395A GLN* 3.0 47.4 + - - +
458A PRO* 3.6 20.9 - - + -
459A ASN 3.5 17.5 - - - -
460A TYR* 3.6 26.2 - + - -
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Residues in contact with TYR 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 ALA 3.0 18.2 + - - +
389A LEU* 3.5 9.2 - - + +
391A PHE* 1.3 76.9 - - - +
393A LEU* 1.3 67.5 + - + +
395A GLN* 3.2 6.3 + - + +
396A LEU* 2.9 48.3 + - + +
441A GLN* 4.4 4.2 + - - +
442A VAL* 4.0 33.0 - - + +
443A ASP 5.0 0.5 + - - -
447A TRP* 3.5 36.8 + + + -
456A ILE* 3.3 40.5 - - + +
458A PRO* 4.0 21.5 - - + +
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Residues in contact with LEU 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 LEU* 2.9 32.1 + - + +
390A LEU* 3.6 4.7 - - + +
392A TYR* 1.3 78.3 - - + +
394A GLU* 1.3 58.2 + - - +
396A LEU* 4.2 9.9 - - + -
397A LEU* 2.8 52.9 + - + +
403A PHE* 3.7 19.1 - - + -
424A TRP* 3.7 35.4 - - + -
428A LEU* 4.0 8.1 - - + -
439A LEU* 4.5 3.4 - - + -
442A VAL* 4.1 18.2 - - + -
444A TRP* 4.0 19.3 - - + -
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Residues in contact with GLU 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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323A TYR* 2.6 33.6 + - - +
327A HIS* 3.7 1.2 + - - -
338A ARG* 3.0 40.3 + - - -
390A LEU 2.9 14.7 + - - +
391A PHE* 3.4 20.5 - - - +
393A LEU* 1.3 76.5 - - - +
395A GLN* 1.3 66.8 + - - +
397A LEU* 4.0 1.0 - - - -
398A GLY 3.4 2.9 + - - -
399A GLY* 2.8 45.8 + - - +
400A PRO* 3.6 15.2 - - - +
403A PHE* 3.9 15.5 - - + -
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Residues in contact with GLN 395 (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 HIS* 4.5 5.1 - - - -
391A PHE* 3.0 37.2 + - - +
392A TYR* 3.7 7.9 - - + +
394A GLU* 1.3 87.8 + - - +
396A LEU* 1.3 59.7 + - - +
397A LEU 3.6 0.2 + - - -
398A GLY* 3.9 5.4 + - - -
399A GLY* 4.8 2.5 + - - +
458A PRO* 3.5 8.5 - - - +
459A ASN* 2.7 67.3 + - - +
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Residues in contact with LEU 396 (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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392A TYR* 2.9 39.8 + - + +
393A LEU* 3.2 12.8 + - + +
395A GLN* 1.3 78.1 - - - +
397A LEU* 1.3 64.2 + - + +
398A GLY 3.5 0.7 + - - -
438A VAL* 3.2 41.7 - - + +
439A LEU* 4.9 0.7 - - - +
441A GLN* 3.9 14.4 - - + +
442A VAL* 3.9 28.7 - - + +
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Residues in contact with LEU 397 (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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393A LEU* 2.8 29.0 + - + +
394A GLU 4.6 0.9 - - - +
395A GLN 3.4 0.2 - - - -
396A LEU* 1.3 79.8 - - + +
398A GLY* 1.3 56.4 + - - +
399A GLY 3.8 1.6 - - - -
402A ILE* 3.3 10.2 - - + +
403A PHE* 4.1 16.4 - - + -
428A LEU* 4.4 2.0 - - + -
432A PHE* 3.7 41.3 - - + -
435A LYS* 3.0 42.8 + - + +
438A VAL* 4.0 25.4 - - + -
439A LEU* 4.0 30.5 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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