Contacts of the helix formed by residues 358 - 377 (chain A) in PDB entry 3BRW
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 GLY 358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A PHE* 3.3 18.8 - - - -
356A ARG* 3.5 10.6 - - - +
357A LYS* 1.3 78.9 - - - +
359A PRO* 1.4 69.8 - - - +
360A GLU* 2.9 12.2 + - - -
361A PHE* 3.3 10.4 + - - +
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Residues in contact with PRO 359 (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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226A PHE* 5.0 0.4 - - + -
358A GLY* 1.4 80.2 - - - +
360A GLU* 1.3 67.4 + - - +
362A GLN* 3.8 19.3 + - + +
363A GLU* 3.2 23.9 + - - +
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Residues in contact with GLU 360 (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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355A PHE* 5.9 3.1 - - + -
356A ARG* 4.0 38.6 - - + +
358A GLY 2.9 1.2 + - - -
359A PRO* 1.3 84.6 - - + +
361A PHE* 1.3 62.9 + - - +
363A GLU* 3.5 9.8 + - - +
364A PHE* 3.6 9.0 + - - +
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Residues in contact with PHE 361 (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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223A PHE* 4.5 6.7 - + - -
226A PHE* 3.3 34.1 - + - -
320A VAL* 4.5 9.4 - - + -
332A TYR* 3.9 16.8 - + - -
334A VAL* 4.1 17.9 - - + -
355A PHE* 3.3 56.3 - + + -
356A ARG* 4.0 23.8 - - + +
358A GLY 3.3 4.4 + - - +
360A GLU* 1.3 76.8 - - - +
362A GLN* 1.3 65.5 + - - +
364A PHE* 3.0 19.0 + + + +
365A LEU* 3.0 41.9 + - + +
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Residues in contact with GLN 362 (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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226A PHE* 3.5 38.1 - - + +
227A LEU* 3.6 27.7 - - + +
228A GLY* 5.2 1.2 - - - -
257A CYS* 5.5 3.1 - - - +
259A PHE* 5.3 2.8 - - - -
358A GLY 3.7 2.8 + - - -
359A PRO* 3.6 22.3 + - + +
360A GLU 3.4 0.6 - - - -
361A PHE* 1.3 79.1 - - - +
363A GLU* 1.3 78.5 + - - +
365A LEU* 3.4 13.4 + - + +
366A LEU* 3.4 30.8 + - + +
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Residues in contact with GLU 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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78A LYS* 3.3 34.4 + - + +
259A PHE* 3.4 36.1 - - + -
359A PRO 3.2 15.4 + - - +
360A GLU* 3.7 5.3 - - - +
361A PHE 3.2 0.6 - - - -
362A GLN* 1.3 85.8 + - - +
364A PHE* 1.3 56.6 + - - +
367A THR* 2.8 29.6 + - - +
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Residues in contact with PHE 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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334A VAL* 5.5 7.6 - - + -
347A PRO* 3.7 42.1 - - + +
348A PRO 3.8 16.8 - - - -
349A LEU* 4.7 4.0 - - + -
350A PRO* 4.4 4.0 - - + -
355A PHE* 3.6 38.6 - + + -
360A GLU 3.6 7.1 + - - +
361A PHE* 3.0 19.7 + + - +
363A GLU* 1.3 79.5 - - - +
365A LEU* 1.3 70.7 + - + +
367A THR* 2.9 18.9 + - - -
368A LYS* 2.9 35.2 + - + -
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Residues in contact with LEU 365 (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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223A PHE* 4.3 11.2 - - + -
226A PHE* 5.5 2.7 - - + -
227A LEU* 3.8 31.2 - - + -
295A VAL* 5.0 4.7 - - + -
318A VAL* 3.7 31.4 - - + -
320A VAL* 4.7 4.9 - - + -
361A PHE* 3.0 39.4 + - + +
362A GLN* 3.4 9.6 + - + +
364A PHE* 1.3 84.8 - - + +
366A LEU* 1.3 60.7 + - + +
368A LYS* 3.1 7.9 + - + +
369A LEU* 2.9 44.5 + - + +
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Residues in contact with LEU 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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195A PHE* 4.9 0.2 - - - -
227A LEU* 4.6 4.5 - - + +
257A CYS* 4.2 19.1 - - - -
259A PHE* 3.7 35.2 - - + -
264A ILE* 3.6 23.3 - - + -
266A PHE* 3.8 26.9 - - + -
362A GLN* 3.4 38.9 + - + +
363A GLU 4.2 0.9 - - - +
364A PHE 3.2 0.4 - - - -
365A LEU* 1.3 76.7 - - + +
367A THR* 1.3 61.0 + - - +
369A LEU* 3.4 9.5 + - + +
370A ILE* 2.9 36.7 + - - +
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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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79A VAL* 5.3 6.1 - - + -
80A LYS 5.2 4.5 - - - +
81A LEU* 4.2 17.9 - - + -
259A PHE* 3.4 16.8 - - - -
260A ARG* 4.4 11.1 + - - +
347A PRO* 4.0 16.2 - - + -
363A GLU* 2.8 17.7 + - - +
364A PHE* 2.9 8.2 + - - -
366A LEU* 1.3 76.8 - - - +
368A LYS* 1.3 54.0 + - - +
370A ILE* 3.8 3.5 - - - +
371A ASN* 2.8 57.7 + - - +
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Residues in contact with LYS 368 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A VAL* 4.5 17.7 - - + -
336A VAL* 3.7 18.4 - - - +
344A PHE* 5.3 1.0 - - - -
345A PHE* 3.3 40.1 + - + -
346A GLY* 3.8 9.4 - - - -
347A PRO* 3.0 35.9 + - + +
348A PRO* 4.9 0.2 - - - +
349A LEU* 4.0 24.4 - - - +
364A PHE* 2.9 31.2 + - + +
365A LEU* 3.3 11.7 - - + +
367A THR* 1.3 77.0 - - - +
369A LEU* 1.3 56.3 + - - +
371A ASN* 3.7 1.1 + - - -
372A ALA* 2.9 28.4 + - - +
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Residues in contact with LEU 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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195A PHE* 3.5 46.2 - - + -
266A PHE* 4.0 12.6 - - + -
293A VAL* 3.6 24.6 - - + +
294A ALA 4.6 3.4 - - - -
295A VAL* 3.9 29.8 - - + -
318A VAL* 3.8 20.6 - - + -
365A LEU* 2.9 30.7 + - + +
366A LEU* 3.8 6.5 - - - +
368A LYS* 1.3 74.8 - - - +
370A ILE* 1.3 64.6 + - - +
372A ALA* 3.2 5.3 + - - +
373A GLU 3.1 19.1 + - - -
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Residues in contact with ILE 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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81A LEU* 3.9 23.3 - - + -
193A PHE* 3.6 33.9 - - + -
195A PHE* 4.0 11.7 - - + -
259A PHE* 3.7 28.9 - - + -
260A ARG* 5.7 0.2 - - + -
262A LYS* 4.8 7.0 - - + -
264A ILE* 3.9 14.4 - - + -
366A LEU 2.9 22.5 + - - +
367A THR 3.8 2.7 - - - +
369A LEU* 1.3 74.4 - - - +
371A ASN* 1.3 64.5 + - - +
372A ALA 3.3 0.2 + - - -
373A GLU* 3.3 4.7 + - - +
374A TYR* 3.2 51.0 + - + -
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Residues in contact with ASN 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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79A VAL* 6.1 1.0 - - - +
80A LYS 4.8 3.0 + - - -
81A LEU* 3.6 9.2 - - - +
82A GLU* 2.6 60.6 + - + +
345A PHE* 3.8 5.9 - - - +
346A GLY* 3.6 18.8 - - - +
347A PRO* 3.5 21.2 - - - +
367A THR* 2.8 28.9 + - - +
368A LYS 4.0 0.4 - - - +
370A ILE* 1.3 73.9 - - - +
372A ALA* 1.3 56.8 + - - +
374A TYR* 3.6 8.0 + - - +
375A ALA* 3.0 27.5 + - - +
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Residues in contact with ALA 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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293A VAL* 3.9 21.5 - - + -
316A ALA* 4.6 4.0 - - + +
318A VAL* 5.5 1.8 - - + -
345A PHE* 3.6 26.0 - - + -
368A LYS 2.9 20.9 + - - +
369A LEU* 3.2 11.9 - - + +
370A ILE 3.1 0.2 - - - -
371A ASN* 1.3 75.8 - - - +
373A GLU* 1.3 64.5 + - - +
375A ALA* 3.1 13.0 + - - +
376A CYS* 3.2 17.5 + - - -
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Residues in contact with GLU 373 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A SER* 4.3 0.3 + - - -
192A ASN 5.2 0.7 - - - +
193A PHE* 3.3 33.3 - - + +
194A LYS* 4.4 8.8 + - - +
195A PHE* 3.7 15.1 - - + -
292A ILE* 3.9 35.0 - - + +
293A VAL* 3.6 11.8 + - + +
369A LEU 3.1 12.2 + - - +
370A ILE 3.3 6.9 + - - +
372A ALA* 1.3 74.3 - - - +
374A TYR* 1.3 57.5 + - - +
376A CYS* 2.8 22.2 + - - +
377A TYR* 2.9 48.4 + - + -
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Residues in contact with TYR 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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81A LEU* 4.5 8.1 - - + -
82A GLU 3.5 18.7 - - - +
83A CYS* 3.7 35.7 - - + -
84A ASN 5.0 1.6 - - - +
188A VAL 3.3 26.0 - - - -
189A ILE* 3.2 13.2 - - - +
190A SER* 2.9 37.2 + - - -
193A PHE* 3.8 8.6 - + - -
262A LYS* 4.5 2.5 - - - -
370A ILE* 3.2 44.2 + - + +
371A ASN* 3.8 4.9 - - - +
372A ALA 3.3 0.2 - - - -
373A GLU* 1.3 77.0 - - - +
375A ALA* 1.3 61.0 + - - +
377A TYR* 3.5 31.7 - + - +
378A LYS* 3.8 13.5 - - - +
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Residues in contact with ALA 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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342A VAL* 4.5 4.0 - - + -
343A PRO* 3.4 31.2 - - + +
344A PHE 5.1 1.1 - - - +
345A PHE* 3.7 28.7 - - + -
371A ASN 3.0 13.5 + - - +
372A ALA 3.2 11.0 - - - +
373A GLU 3.1 0.4 - - - -
374A TYR* 1.3 76.3 - - - +
376A CYS* 1.3 61.4 + - - +
378A LYS* 3.2 24.3 + - - +
379A ALA 3.7 1.2 + - - -
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Residues in contact with CYS 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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292A ILE* 3.5 26.5 - - + -
293A VAL* 4.1 1.3 - - - -
315A HIS* 3.7 23.6 - - + -
316A ALA* 4.0 15.3 - - - -
342A VAL* 3.7 19.5 - - + -
372A ALA 3.2 15.5 - - - -
373A GLU 2.8 7.8 + - - +
375A ALA* 1.3 71.8 - - - +
377A TYR* 1.3 62.0 + - - +
378A LYS 3.0 2.2 - - - -
379A ALA* 2.8 18.1 + - + +
382A PHE* 3.0 28.3 - - + -
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Residues in contact with TYR 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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187A HIS 5.8 0.7 - - - -
188A VAL* 4.2 28.3 - - + -
190A SER* 3.4 23.3 + - - -
193A PHE* 5.4 0.2 - + - -
292A ILE* 6.0 2.0 - - + -
373A GLU* 2.9 68.2 + - + -
374A TYR* 3.5 24.9 - + + +
375A ALA 3.3 0.2 - - - -
376A CYS* 1.3 76.3 - - + +
378A LYS* 1.3 60.7 + - + +
382A PHE* 3.9 12.6 - + + +
383A ALA* 3.8 20.8 + - - +
386A GLU* 5.4 14.6 - - + +
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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