Contacts of the helix formed by residues 362 - 379 (chain A) in PDB entry 5Q0S
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 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A GLY 3.8 2.4 + - - -
361A ILE* 1.4 80.4 - - - +
363A ASP* 1.4 66.9 + - - +
364A GLU* 3.9 12.0 + - - +
365A TYR* 3.1 29.1 + - - -
366A ILE* 3.4 9.9 + - - +
457A SER* 2.9 35.2 + - - -
459A ARG* 5.9 3.6 - - - +
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Residues in contact with ASP 363 (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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357A ARG 5.7 0.7 - - - +
361A ILE 4.6 2.8 - - - +
362A SER* 1.4 74.6 - - - +
364A GLU* 1.3 57.3 + - - +
365A TYR 3.1 0.2 - - - -
366A ILE* 3.1 32.2 + - + +
367A THR* 3.4 12.0 + - - +
247C MET* 3.7 34.7 + - - +
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Residues in contact with GLU 364 (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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362A SER* 3.9 10.5 + - - +
363A ASP* 1.3 76.8 - - - +
365A TYR* 1.3 99.4 + - + +
367A THR* 4.4 2.8 + - - -
368A PRO* 3.3 21.2 - - - +
457A SER* 5.8 0.9 - - - -
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Residues in contact with TYR 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ILE* 3.9 9.6 - - + +
362A SER* 3.1 34.0 + - - +
364A GLU* 1.3 106.1 + - + +
366A ILE* 1.3 61.1 + - - +
368A PRO* 3.5 8.7 - - + +
369A MET* 3.1 29.7 + - - +
447A PHE* 5.1 1.4 - - - -
450A HIS* 4.1 27.1 + + + -
453A GLU* 3.3 31.7 + - + +
454A MET* 3.5 44.6 - - + +
457A SER* 3.6 18.8 - - - -
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Residues in contact with ILE 366 (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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356A ILE 3.9 2.0 - - - +
357A ARG* 3.5 69.1 - - + +
361A ILE* 3.6 28.9 - - + +
362A SER 3.4 14.6 + - - +
363A ASP* 3.1 17.7 + - - +
365A TYR* 1.3 73.2 - - - +
367A THR* 1.3 63.6 + - + +
369A MET* 3.3 11.1 + - + +
370A PHE* 2.9 48.8 + - + -
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Residues in contact with THR 367 (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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357A ARG* 4.8 16.2 - - - +
363A ASP 3.4 11.5 + - - +
364A GLU* 4.4 2.8 + - - -
366A ILE* 1.3 78.0 - - + +
368A PRO* 1.4 70.8 - - - +
369A MET 3.3 0.2 + - - -
370A PHE* 3.4 3.7 + - - +
371A SER* 3.0 25.1 + - - -
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Residues in contact with PRO 368 (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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364A GLU 3.3 24.2 - - - +
365A TYR* 3.5 12.8 - - + +
367A THR* 1.4 96.4 - - - +
369A MET* 1.4 53.7 + - - +
371A SER* 3.4 8.5 - - - -
372A PHE* 3.2 22.3 + - - +
443A GLU* 4.7 2.3 - - - +
447A PHE* 3.5 18.8 - - + -
454A MET* 6.6 0.2 - - + -
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Residues in contact with MET 369 (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 PHE* 4.4 5.8 - - + -
356A ILE* 3.8 20.2 - - + -
361A ILE* 4.7 8.7 - - + -
365A TYR 3.1 16.7 + - - +
366A ILE* 3.5 9.6 - - + +
368A PRO* 1.4 76.0 - - - +
370A PHE* 1.3 93.2 + - + +
372A PHE* 3.6 2.1 + - - +
373A TYR* 3.2 64.2 + - + +
447A PHE* 3.6 21.2 - - + -
454A MET* 5.5 2.5 - - - +
501A 9LJ 3.6 31.6 - - + -
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Residues in contact with PHE 370 (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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340A PHE* 3.3 43.1 - + - -
353A GLU* 3.4 33.0 - - + -
356A ILE* 3.8 19.3 - - + -
357A ARG* 3.9 26.2 - - + +
366A ILE* 2.9 56.0 + - + +
367A THR* 4.3 2.7 - - - +
369A MET* 1.3 88.2 - - + +
371A SER* 1.4 65.0 + - - +
372A PHE 3.4 0.2 - - - -
373A TYR* 4.2 7.2 - + - -
374A LYS* 3.1 37.0 + - + +
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Residues in contact with SER 371 (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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367A THR 3.0 18.4 + - - -
368A PRO* 3.4 10.5 - - - -
369A MET 3.3 0.2 - - - -
370A PHE* 1.4 76.7 - - - +
372A PHE* 1.3 56.6 + - - +
374A LYS* 3.5 4.0 + - - +
375A SER* 3.0 35.0 + - - -
443A GLU* 4.0 10.1 + - - -
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Residues in contact with PHE 372 (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 PHE* 3.8 23.1 - - + -
334A LEU* 4.6 3.6 - - + -
337A ALA* 3.9 9.2 - - + -
368A PRO 3.2 3.6 + - - +
369A MET 3.8 1.1 - - - +
371A SER* 1.3 76.6 + - - +
373A TYR* 1.3 73.1 + + - +
375A SER* 3.2 4.7 + - - -
376A ILE* 2.9 56.1 + - + +
440A ARG* 3.8 23.1 - - + -
443A GLU* 3.8 31.4 + - + +
444A LEU* 3.6 32.1 - - + -
447A PHE* 3.6 34.5 - + + -
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Residues in contact with TYR 373 (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 PHE* 3.5 36.5 - + - -
336A SER* 3.3 10.9 - - - -
337A ALA* 3.6 22.2 - - + -
340A PHE* 3.7 35.4 - + + -
341A ASN* 2.8 27.0 + - - -
356A ILE* 5.5 0.2 - - + -
369A MET* 3.2 41.8 + - + +
370A PHE* 3.9 16.6 - + - +
371A SER 3.5 0.4 - - - -
372A PHE* 1.3 87.2 - + - +
374A LYS* 1.3 56.8 + - - +
376A ILE* 3.5 1.2 + - - +
377A GLY 3.1 9.9 + - - -
501A 9LJ 2.8 40.7 + + - -
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Residues in contact with LYS 374 (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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340A PHE* 4.1 19.7 - - + -
341A ASN* 4.7 4.3 - - - +
353A GLU* 2.9 42.1 + - - -
357A ARG* 5.3 1.0 - - - +
370A PHE* 3.1 25.8 + - + +
371A SER* 4.0 4.3 - - - +
373A TYR* 1.3 74.3 - - - +
375A SER* 1.4 62.5 + - - +
377A GLY* 3.5 1.9 + - - +
378A GLU* 3.2 33.7 + - - +
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Residues in contact with SER 375 (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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371A SER* 3.0 26.0 + - - -
372A PHE* 3.4 9.4 - - - -
374A LYS* 1.4 72.6 - - - +
376A ILE* 1.3 64.7 + - - +
378A GLU* 3.5 26.5 + - - +
379A LEU* 3.8 12.0 + - - +
440A ARG* 3.3 35.9 + - - +
443A GLU* 4.2 4.5 + - - -
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Residues in contact with ILE 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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334A LEU* 4.1 15.7 - - + -
337A ALA* 3.8 14.8 - - + -
341A ASN* 3.6 11.0 - - - +
372A PHE* 2.9 48.6 + - + +
373A TYR 3.5 3.1 - - - +
375A SER* 1.3 76.5 - - - +
377A GLY* 1.3 61.7 + - - +
379A LEU* 3.2 23.9 + - + +
380A LYS 3.9 2.4 + - - -
381A MET* 4.1 19.1 - - - +
386A TYR* 3.4 28.8 + - + +
389A LEU* 5.1 2.9 - - + -
440A ARG* 3.7 25.1 - - + -
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Residues in contact with GLY 377 (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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341A ASN* 3.3 30.3 - - - -
373A TYR 3.1 10.1 + - - -
374A LYS* 3.5 4.7 + - - -
375A SER 3.3 0.6 - - - -
376A ILE* 1.3 76.0 - - - +
378A GLU* 1.3 59.3 + - - +
380A LYS* 3.2 32.4 + - - +
386A TYR* 5.4 0.9 - - - -
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Residues in contact with GLU 378 (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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374A LYS* 3.2 22.3 + - - +
375A SER* 3.7 15.4 + - - +
376A ILE 3.3 0.6 - - - -
377A GLY* 1.3 74.6 - - - +
379A LEU* 1.4 60.1 + - + +
380A LYS* 3.5 11.6 + - - +
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Residues in contact with LEU 379 (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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375A SER 3.8 9.2 + - - +
376A ILE* 3.2 14.8 + - + +
378A GLU* 1.4 75.6 - - + +
380A LYS* 1.4 57.5 + - - +
381A MET* 3.9 11.7 - - + -
427A GLN* 2.8 29.7 + - - -
430A ASN* 5.4 1.3 - - - +
433A HIS* 3.0 34.4 + - + +
436A CYS* 3.4 31.2 - - + -
437A LEU* 3.8 22.0 - - + +
440A ARG* 3.8 35.4 - - + -
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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