Contacts of the helix formed by residues 407 - 425 (chain A) in PDB entry 2B9S
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 LYS 407 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A LYS* 4.2 15.2 - - - +
314A ARG* 6.5 0.9 - - - +
405A SER* 3.9 5.8 - - - +
406A ALA* 1.3 74.3 - - - +
408A VAL* 1.3 66.6 + - + +
410A ARG* 3.0 31.3 + - + +
411A THR* 3.3 14.7 + - - -
222B TYR* 5.2 1.3 - - + -
9C T 3.3 21.7 + - - -
10C T 2.9 38.0 + - - -
116E T 3.7 24.2 + - - +
117E C 2.8 32.9 + - - +
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Residues in contact with VAL 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LYS 5.3 1.6 - - - +
272A LYS* 4.0 26.2 - - + +
273A ALA* 3.9 29.2 - - + +
276A LEU* 4.0 11.0 - - + -
403A GLY 4.5 8.3 - - - +
404A LEU* 4.0 10.8 - - + -
405A SER* 3.4 31.9 - - - +
406A ALA 3.1 0.6 - - - -
407A LYS* 1.3 80.8 - - + +
409A PHE* 1.3 58.6 + - - +
410A ARG 3.1 2.0 - - - -
411A THR* 3.3 8.1 + - - -
412A TYR* 2.8 27.2 + - - +
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Residues in contact with PHE 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LEU* 3.8 39.7 - - + -
280A VAL* 4.4 7.6 - - + -
283A ILE* 4.2 25.1 - - + -
305A MET* 5.7 4.9 - - + -
308A ILE* 3.9 27.4 - - + +
309A ASP* 3.8 37.9 - - + -
397A LEU* 4.0 27.1 - - + -
404A LEU* 4.4 5.2 - - + -
405A SER 4.1 10.5 - - - -
406A ALA* 3.3 12.7 + - - +
407A LYS 3.3 0.4 - - - -
408A VAL* 1.3 76.6 - - - +
410A ARG* 1.3 54.6 + - - +
412A TYR* 3.7 7.7 - + - +
413A ASN* 2.7 40.3 + - - +
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Residues in contact with ARG 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ALA* 2.6 52.4 + - + +
313A LEU* 4.5 1.8 - - - +
314A ARG* 3.5 42.4 - - - +
406A ALA 4.0 2.2 + - - +
407A LYS* 3.0 21.9 + - - +
409A PHE* 1.3 78.9 - - - +
411A THR* 1.3 57.6 + - - +
413A ASN* 3.5 1.7 + - - +
414A ALA* 3.0 30.1 + - - +
450A LEU 5.0 0.4 + - - -
451A CYS* 2.9 43.5 + - - +
453A HIS* 3.6 3.8 + - - -
222B TYR* 3.2 31.8 + - + -
301B VO4 2.8 24.6 + - - -
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Residues in contact with THR 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LYS* 4.5 15.6 - - + +
270A PHE* 3.6 37.2 - - + -
273A ALA* 3.7 14.4 - - + -
407A LYS* 3.3 14.6 + - - -
408A VAL* 3.3 10.9 + - - -
410A ARG* 1.3 75.6 - - - +
412A TYR* 1.3 64.9 + - - -
414A ALA 3.5 0.2 + - - -
415A SER* 3.1 28.6 + - - -
221B ASN 5.2 0.2 + - - -
222B TYR* 3.4 20.5 - - - +
10C T 4.4 11.1 + - - -
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Residues in contact with TYR 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ALA* 3.6 29.3 - - + +
276A LEU* 3.7 20.4 - - + -
277A LYS* 3.5 36.4 + - + +
280A VAL* 3.8 29.4 - - + +
284A ARG* 4.1 14.7 + - - -
309A ASP* 4.8 2.2 - - - -
408A VAL 2.8 21.1 + - - +
409A PHE* 3.7 9.2 - + - +
411A THR* 1.3 73.1 - - - +
413A ASN* 1.3 75.8 + - - +
415A SER* 3.9 0.3 - - - -
416A ILE* 2.9 60.8 + - + +
262B PHE* 4.5 5.3 - + - -
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Residues in contact with ASN 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ARG* 5.6 0.5 + - - -
308A ILE 3.7 4.0 + - - -
309A ASP* 2.8 29.6 + - - +
310A ARG 5.1 2.5 - - - +
312A ALA* 3.6 20.0 - - + +
409A PHE* 2.7 32.6 + - - +
410A ARG 3.8 3.8 - - - +
411A THR 3.4 0.2 - - - -
412A TYR* 1.3 89.1 - - - +
414A ALA* 1.3 60.6 + - - +
416A ILE* 3.8 6.1 - - - +
417A THR* 2.6 34.5 + - - -
450A LEU* 3.6 19.5 - - + +
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Residues in contact with ALA 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A ARG 3.0 17.9 + - - +
413A ASN* 1.3 77.4 - - - +
415A SER* 1.3 62.3 + - - +
417A THR* 3.6 3.2 + - - -
418A LEU* 3.4 17.2 + - - +
447A VAL* 3.8 32.0 - - + +
450A LEU* 4.2 5.6 - - - +
451A CYS* 4.3 8.1 - - - -
222B TYR* 3.7 32.1 - - + +
223B ILE* 4.3 2.6 - - - +
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Residues in contact with SER 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A PHE* 4.0 1.7 - - - -
411A THR 3.1 13.6 + - - -
414A ALA* 1.3 75.6 - - - +
416A ILE* 1.3 59.2 + - - +
418A LEU* 3.3 2.1 + - - +
419A ASP* 3.1 22.9 + - - +
222B TYR 3.2 10.7 + - - -
223B ILE* 4.5 4.7 - - - +
224B ASP* 2.8 29.1 + - - +
227B ILE* 3.3 20.3 - - - +
262B PHE* 3.5 28.8 - - - -
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Residues in contact with ILE 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LYS* 4.3 22.2 - - + -
412A TYR* 2.9 50.4 + - + +
413A ASN* 3.8 12.6 - - - +
415A SER* 1.3 75.4 - - - +
417A THR* 1.3 63.9 + - - +
419A ASP* 4.0 17.7 - - - +
420A ARG* 3.0 33.8 + - + +
262B PHE* 3.8 22.8 - - + +
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Residues in contact with THR 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ASN* 2.6 24.8 + - - -
414A ALA 3.7 5.4 - - - -
415A SER 3.2 0.6 - - - -
416A ILE* 1.3 81.2 - - - +
418A LEU* 1.3 60.8 + - - +
420A ARG* 4.2 3.3 - - - +
421A TRP* 3.3 22.7 + - - +
443A ALA 5.2 0.4 - - - +
446A GLU* 3.4 31.3 - - - +
447A VAL* 4.0 21.8 - - + +
450A LEU* 3.7 14.0 - - + +
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Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ALA 3.4 8.5 + - - +
415A SER 3.3 8.5 + - - +
417A THR* 1.3 78.5 - - - +
419A ASP* 1.3 65.5 + - - +
421A TRP* 3.4 3.5 + - - +
422A PHE* 3.0 57.0 + - + -
440A PHE* 4.6 6.1 - - + -
443A ALA* 3.7 41.5 - - + +
444A ASN* 4.2 4.5 - - - +
447A VAL* 4.2 8.5 - - + +
223B ILE* 3.6 31.2 - - + -
227B ILE* 3.8 9.6 - - + -
228B ILE* 3.8 15.5 - - + -
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Residues in contact with ASP 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LYS* 5.7 0.3 - - - -
415A SER 3.1 16.7 + - - +
416A ILE* 3.7 18.2 - - + +
418A LEU* 1.3 78.1 - - - +
420A ARG* 1.3 64.0 + - - +
422A PHE* 3.1 5.0 + - - +
423A LYS* 3.0 60.2 + - - +
227B ILE* 4.3 18.4 - - + +
260B PHE 4.5 5.2 - - - +
262B PHE* 3.9 31.9 + - + +
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Residues in contact with ARG 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ILE* 3.0 18.5 + - + +
417A THR* 4.2 4.9 - - - +
419A ASP* 1.3 77.6 + - - +
421A TRP* 1.3 57.9 + - - +
423A LYS* 3.1 6.4 + - - -
424A GLU* 2.8 55.3 + - - +
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Residues in contact with TRP 421 (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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417A THR 3.3 16.5 + - - +
418A LEU* 3.7 4.3 - - - +
419A ASP 3.3 1.0 - - - -
420A ARG* 1.3 76.2 - - - +
422A PHE* 1.3 60.0 + + - +
424A GLU* 4.7 4.5 - - - -
425A LYS* 2.9 39.5 + - + +
439A TYR* 3.4 36.1 - + - -
442A LYS* 3.8 23.3 - - + -
443A ALA* 3.5 37.9 - - + +
446A GLU* 3.1 44.9 - - + +
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Residues in contact with PHE 422 (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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418A LEU* 3.0 51.2 + - + -
419A ASP* 3.5 8.7 - - - +
421A TRP* 1.3 79.7 - + - +
423A LYS* 1.3 63.0 + - + +
426A PRO* 3.8 22.9 - - - +
439A TYR* 3.6 22.4 + + - -
440A PHE* 3.9 21.5 - + - -
443A ALA* 4.3 8.3 - - + -
227B ILE* 3.9 19.1 - - + -
228B ILE* 4.9 0.2 - - - -
231B TRP* 3.5 60.6 - + + -
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Residues in contact with LYS 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ASP* 3.0 51.0 + - - +
420A ARG* 3.7 6.1 - - - +
422A PHE* 1.3 80.8 - - + +
424A GLU* 1.3 59.2 + - - +
426A PRO* 4.2 9.2 - - - +
260B PHE 5.1 2.0 - - - -
261B ASP* 2.6 36.5 + - - +
262B PHE 5.5 0.4 + - - -
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Residues in contact with GLU 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A ARG* 2.8 41.3 + - - +
421A TRP* 4.7 3.1 - - - -
423A LYS* 1.3 74.9 - - - +
425A LYS* 1.3 60.5 + - + +
426A PRO* 3.6 7.7 - - - +
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Residues in contact with LYS 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A TRP* 2.9 29.0 + - + +
424A GLU* 1.3 82.2 - - + +
426A PRO* 1.4 56.6 - - - +
439A TYR* 2.5 37.5 + - + -
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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
------------------------------------------------------------
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