Contacts of the strand formed by residues 536 - 550 (chain A) in PDB entry 3BRF
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 TRP 536 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A LEU* 3.9 30.5 - - + -
395A PHE* 3.2 24.0 - - - -
396A ASN* 4.0 12.8 - - + -
406A ARG 4.8 1.1 - - - -
407A TYR 4.9 0.4 - - - -
408A LEU* 4.2 18.4 - - + -
417A ALA* 4.9 1.1 - - + -
495A LYS* 3.2 8.3 - - - +
496A CYS* 2.9 37.4 + - - +
497A ALA* 4.7 1.3 - - - -
498A PHE* 4.1 29.2 - + + -
508A LEU* 3.3 44.1 + - + +
510A LEU* 4.2 18.6 - - + -
515A ILE* 3.9 24.9 - - + -
533A GLY 3.9 18.1 + - - -
534A ALA 3.4 13.9 + - - -
535A ALA* 1.3 74.4 - - - +
537A THR* 1.3 66.0 + - - +
538A ILE 4.2 0.2 - - - -
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Residues in contact with THR 537 (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 ALA 3.7 1.0 - - - +
394A LEU* 3.3 7.0 - - - -
395A PHE* 2.7 69.9 + - + -
396A ASN* 5.4 0.5 - - - -
397A ARG* 4.9 2.1 + - - +
493A LEU* 3.6 37.2 - - + +
494A HIS 3.4 3.1 - - - +
495A LYS* 3.0 29.6 + - - +
535A ALA 5.1 0.5 + - - -
536A TRP* 1.3 76.8 + - - +
538A ILE* 1.3 62.8 + - - +
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Residues in contact with ILE 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ILE* 3.8 21.1 - - + -
392A VAL* 4.1 13.5 - - + -
393A ALA 3.6 5.4 - - - +
394A LEU* 3.5 23.8 - - + -
427A ILE* 4.2 18.2 - - + -
471A ILE* 4.1 21.8 - - + -
490A VAL* 3.8 15.3 - - + -
491A SER 3.8 17.4 - - - +
492A GLN* 3.7 0.6 - - - -
493A LEU* 2.7 32.8 + - - -
494A HIS* 3.2 13.6 + - + +
496A CYS* 4.0 8.5 - - - -
498A PHE* 4.7 1.3 - - + -
537A THR* 1.3 73.5 - - - +
539A ILE* 1.3 58.5 + - - +
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Residues in contact with ILE 539 (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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222A ALA* 3.4 28.5 - - + -
224A VAL* 3.9 22.4 - - + +
237A CYS 3.7 13.9 - - - +
238A PRO* 3.6 26.2 - - + -
386A ILE* 5.1 0.9 - - - -
392A VAL* 3.3 7.3 - - - -
393A ALA* 2.9 40.1 + - + +
395A PHE* 4.3 7.6 - - + -
492A GLN* 3.6 12.6 - - - +
493A LEU* 3.9 27.6 - - + +
538A ILE* 1.3 77.3 - - - +
540A SER* 1.3 63.4 + - - +
541A THR* 4.3 0.4 - - + -
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Residues in contact with SER 540 (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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222A ALA* 3.4 6.9 - - - +
223A LYS* 3.0 43.8 + - - +
385A CYS 4.1 2.8 + - - -
386A ILE* 3.8 13.8 - - - +
390A THR* 5.2 4.1 + - - -
391A LYS 3.4 12.7 + - - -
392A VAL* 4.3 2.2 - - - +
492A GLN* 2.7 40.8 + - - -
539A ILE* 1.3 74.5 - - - +
541A THR* 1.3 59.8 + - - +
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Residues in contact with THR 541 (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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221A HIS 3.3 13.2 - - - +
222A ALA* 3.9 10.5 - - + +
223A LYS* 4.2 11.4 + - - +
238A PRO* 4.5 0.9 - - + -
391A LYS* 3.2 37.6 + - - +
392A VAL 4.0 2.6 + - - -
393A ALA* 3.7 31.4 - - + +
422A TRP* 3.7 16.4 - - + -
424A ALA* 4.0 13.5 - - - +
539A ILE* 3.8 2.0 - - + +
540A SER* 1.3 80.7 - - - +
542A ASP* 1.3 66.2 + - - +
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Residues in contact with ASP 542 (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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220A PHE* 3.5 6.5 - - - +
221A HIS* 2.7 48.9 + - - +
223A LYS* 3.5 29.0 + - + +
361A GLN* 3.6 24.3 + - + +
362A ARG 5.5 0.6 - - - +
541A THR* 1.3 77.9 - - - +
543A LYS* 1.3 84.1 + - - +
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Residues in contact with LYS 543 (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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218A SER* 3.6 13.9 + - - -
219A ILE 3.2 8.1 - - - +
220A PHE* 3.5 41.5 - - + -
221A HIS* 5.0 0.9 - - - -
361A GLN* 3.7 11.4 - - - +
542A ASP* 1.3 94.0 + - - +
544A ALA* 1.3 68.8 + - - +
545A GLU* 2.5 34.5 + - + +
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Residues in contact with ALA 544 (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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217A ILE 3.6 2.1 - - - +
218A SER* 3.4 2.3 - - - -
219A ILE* 2.8 37.6 + - + +
221A HIS* 5.3 0.2 - - + -
359A VAL 3.6 24.7 - - - +
360A SER* 4.0 11.2 - - - -
361A GLN* 3.9 17.3 - - - +
543A LYS* 1.3 75.5 - - - +
545A GLU* 1.3 60.4 + - - +
546A TYR* 3.9 12.1 - - + +
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Residues in contact with GLU 545 (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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216A VAL* 3.8 18.4 - - + +
217A ILE 3.4 2.9 - - - +
218A SER* 3.2 17.9 + - - +
543A LYS* 2.5 36.5 + - + +
544A ALA* 1.3 71.3 - - - +
546A TYR* 1.3 75.5 + - - +
547A ARG* 2.7 33.9 + - + -
564A VAL* 4.5 12.1 - - - +
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Residues in contact with TYR 546 (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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215A CYS 3.7 0.5 - - - +
216A VAL* 3.3 4.7 - - - +
217A ILE* 2.8 56.1 + - + +
219A ILE* 4.4 3.8 - - + -
358A PHE* 3.8 31.2 - + + -
359A VAL* 2.5 39.5 + - + +
360A SER 5.0 0.2 + - - -
544A ALA* 3.9 21.3 - - + +
545A GLU* 1.3 79.6 - - - +
547A ARG* 1.3 63.8 + - - +
548A PHE* 4.9 1.7 - - + -
562A CYS* 3.7 36.6 - - + -
563A PRO 5.2 0.2 - - - -
564A VAL* 4.9 10.8 - - + -
584A ARG* 3.0 31.1 + - - -
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Residues in contact with ARG 547 (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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210A LYS* 6.2 0.4 - - - +
214A GLU* 3.0 28.8 + - - -
215A CYS 3.2 5.8 - - - +
216A VAL* 3.6 17.0 - - + +
545A GLU* 2.7 33.2 + - + +
546A TYR* 1.3 80.5 - - - +
548A PHE* 1.3 63.3 + - - +
562A CYS* 5.1 2.1 - - - +
650A TYR* 3.5 26.6 - - - +
651A SER* 3.9 28.2 + - - +
652A SER 4.6 1.6 + - - -
653A GLY* 3.5 30.7 - - - +
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Residues in contact with PHE 548 (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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206A PHE* 5.7 0.4 - - - -
214A GLU* 3.8 3.9 - - - +
215A CYS* 2.8 60.0 + - + +
217A ILE* 4.8 3.6 - - + -
249A TRP* 3.6 27.4 - + - -
252A LYS* 3.7 20.0 - - + -
358A PHE* 4.4 10.5 - + - -
546A TYR 4.9 1.1 - - - -
547A ARG* 1.3 79.8 - - - +
549A PHE* 1.3 66.6 + - - +
550A GLU* 4.8 4.7 - - + -
559A ILE* 3.7 46.4 - - + -
562A CYS* 4.6 8.5 - - - -
648A VAL* 4.5 2.7 - - + -
649A VAL 3.2 9.2 - - - +
650A TYR* 3.7 24.0 - - + -
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Residues in contact with PHE 549 (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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202A ARG* 5.7 2.0 - - + -
205A ASP* 5.4 3.6 - - - -
206A PHE* 3.2 48.2 - + + -
213A TYR* 3.0 52.9 - + + +
214A GLU* 4.1 0.4 - - - -
215A CYS* 5.3 2.9 - - - -
248A GLY 6.1 0.2 - - - -
251A LEU* 3.9 11.2 - - + -
252A LYS* 6.4 1.6 - - + -
255A ARG* 3.8 30.1 - - - -
548A PHE* 1.3 80.5 - - - +
550A GLU* 1.3 55.9 + - - +
551A ALA* 2.7 40.7 + - + -
648A VAL* 4.0 2.5 - - - -
649A VAL* 2.8 36.1 + - + +
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Residues in contact with GLU 550 (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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215A CYS* 6.1 0.2 - - - -
252A LYS* 2.8 34.4 + - + +
255A ARG* 2.8 36.2 + - - +
548A PHE* 4.8 5.6 - - + -
549A PHE* 1.3 72.2 - - - +
551A ALA* 1.3 53.6 + - - +
552A MET 2.8 18.4 - - - +
553A GLY 3.3 12.6 - - - +
554A GLN* 2.9 33.1 - - - +
555A VAL* 3.6 28.1 + - + +
559A ILE* 3.7 18.9 - - + +
647A GLY 3.7 0.9 - - - -
648A VAL* 3.8 11.9 - - + +
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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