Contacts of the helix formed by residues 414 - 437 (chain A) in PDB entry 5IJ0
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 GLU 414 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A VAL* 5.1 5.4 - - - -
413A MET* 1.3 79.9 - - - +
415A GLU* 1.3 67.0 + - + +
416A GLY* 3.6 17.0 + - - +
417A GLU* 3.3 25.2 + - + +
418A PHE* 3.1 22.9 - - - -
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Residues in contact with GLU 415 (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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399A TYR* 3.0 25.1 + - + +
402A ARG* 2.8 36.7 + - - +
405A VAL* 6.0 3.1 - - + -
409A VAL* 5.2 5.7 - - + +
414A GLU* 1.3 72.2 - - + +
416A GLY* 1.3 61.6 + - - +
417A GLU 3.0 2.0 - - - -
418A PHE* 3.1 13.0 + - - +
419A SER* 2.9 25.4 + - - -
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Residues in contact with GLY 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A GLU* 3.4 14.5 + - - +
415A GLU* 1.3 79.6 - - - +
417A GLU* 1.3 55.8 + - - +
419A SER* 3.5 9.7 - - - -
420A GLU* 2.8 40.9 + - - +
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Residues in contact with GLU 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 5.8 2.8 - - - -
189A LEU* 4.1 9.5 - - + +
192A HIS* 4.2 21.7 + - - -
193A THR* 5.1 4.3 - - - +
413A MET* 3.8 26.0 - - + +
414A GLU* 3.3 32.2 + - + +
415A GLU 3.0 0.2 - - - -
416A GLY* 1.3 73.7 - - - +
418A PHE* 1.3 61.2 + - - +
420A GLU* 3.1 18.1 + - - +
421A ALA* 2.9 29.5 + - - +
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Residues in contact with PHE 418 (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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185A TYR* 3.4 26.9 - + + -
189A LEU* 3.8 28.5 - - + -
395A PHE* 3.7 25.7 - + + -
399A TYR* 3.4 30.7 - + + -
405A VAL* 4.3 15.9 - - + -
408A TYR* 3.8 39.9 - + + -
409A VAL* 5.5 0.7 - - + -
413A MET* 4.5 9.6 - - + -
414A GLU 3.1 26.5 - - - -
415A GLU* 3.1 4.7 + - - +
417A GLU* 1.3 78.7 - - + +
419A SER* 1.3 57.4 + - - +
421A ALA* 3.3 6.5 + - - +
422A ARG* 2.8 30.9 + - - +
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Residues in contact with SER 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A TYR* 4.4 12.2 + - - -
415A GLU* 2.9 14.5 + - - -
416A GLY* 3.5 14.6 - - - -
417A GLU 3.2 0.2 - - - -
418A PHE* 1.3 75.9 - - - +
420A GLU* 1.3 57.3 + - - +
422A ARG* 3.1 8.7 + - - +
423A GLU* 2.8 46.4 + - - +
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Residues in contact with GLU 420 (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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192A HIS* 4.9 11.7 + - + +
416A GLY* 2.8 27.0 + - - +
417A GLU* 3.6 17.2 - - - +
419A SER* 1.3 70.1 - - - +
421A ALA* 1.3 61.5 + - - +
423A GLU* 3.2 20.0 + - - +
424A ASP* 2.8 38.6 + - - +
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Residues in contact with ALA 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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188A ILE* 3.6 24.7 - - + +
189A LEU* 4.3 12.1 - - + -
192A HIS* 4.2 29.1 + - + +
417A GLU 2.9 12.9 + - - +
418A PHE* 3.5 11.7 - - - +
420A GLU* 1.3 76.3 - - - +
422A ARG* 1.3 56.9 + - - +
424A ASP* 3.1 4.5 + - - +
425A MET* 2.9 31.7 + - - +
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Residues in contact with ARG 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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188A ILE* 4.5 1.3 - - - +
392A ASP* 2.6 41.6 + - - -
393A HIS* 5.5 0.4 - - - +
395A PHE* 4.1 20.7 - - + -
396A ASP* 2.5 50.5 + - - +
399A TYR* 5.5 6.7 - - + -
418A PHE 2.8 14.2 + - - +
419A SER* 3.3 11.4 - - - +
421A ALA* 1.3 75.5 - - - +
423A GLU* 1.3 58.0 + - + +
425A MET* 3.1 7.9 + - - +
426A ALA* 2.8 31.1 + - + +
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Residues in contact with GLU 423 (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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419A SER* 2.8 33.5 + - - +
420A GLU* 3.4 22.0 + - - +
422A ARG* 1.3 76.4 - - + +
424A ASP* 1.3 59.0 + - - +
426A ALA* 3.1 9.3 + - - +
427A ALA* 2.9 29.2 + - - +
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Residues in contact with ASP 424 (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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192A HIS* 2.7 43.4 + - + +
195A LEU* 5.3 9.8 - - + +
196A GLU* 3.6 16.6 - - - +
264A ARG* 4.1 6.8 + - - +
420A GLU* 2.8 18.6 + - - +
421A ALA 3.4 7.6 - - - +
423A GLU* 1.3 78.9 - - - +
425A MET* 1.3 59.3 + - + +
427A ALA* 3.2 10.2 + - - +
428A LEU* 2.8 27.9 + - - +
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Residues in contact with MET 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE* 3.6 31.9 - - + +
191A THR* 3.3 31.4 - - + -
192A HIS* 5.4 1.3 - - + -
195A LEU* 6.4 1.3 - - - -
388A TRP* 3.6 49.1 - - + +
392A ASP* 3.3 18.8 - - + +
421A ALA 2.9 18.2 + - - +
422A ARG* 3.1 5.4 + - - +
424A ASP* 1.3 74.0 - - - +
426A ALA* 1.3 59.7 + - - +
428A LEU* 3.1 18.0 + - + +
429A GLU* 2.8 35.6 + - + +
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Residues in contact with ALA 426 (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 ASP* 4.7 2.3 + - - -
422A ARG* 2.8 16.2 + - + +
423A GLU* 3.4 12.3 - - - +
425A MET* 1.3 73.8 - - - +
427A ALA* 1.3 57.6 + - - +
429A GLU* 3.1 10.7 + - - +
430A LYS* 2.9 36.7 + - + +
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Residues in contact with ALA 427 (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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264A ARG* 3.8 13.7 - - - +
423A GLU 2.9 14.2 + - - +
424A ASP* 3.3 12.3 - - - +
426A ALA* 1.3 75.9 - - - +
428A LEU* 1.3 51.8 + - - +
430A LYS* 3.3 6.2 + - - +
431A ASP* 2.8 43.2 + - - +
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Residues in contact with LEU 428 (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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191A THR* 4.8 3.8 - - - +
195A LEU* 4.6 13.7 - - + -
264A ARG* 3.8 24.5 - - - +
265A ILE* 4.9 4.5 - - + -
267A PHE* 4.3 13.7 - - + -
388A TRP* 4.1 27.8 - - + +
424A ASP 2.8 16.9 + - - +
425A MET* 3.3 35.9 - - + +
427A ALA* 1.3 73.2 - - - +
429A GLU* 1.3 63.5 + - - +
431A ASP* 3.1 10.6 + - - +
432A TYR* 2.9 49.2 + - + -
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Residues in contact with GLU 429 (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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385A ALA* 2.8 27.9 - - - +
388A TRP* 3.0 16.3 - - + +
389A ALA* 2.7 40.2 + - - +
392A ASP* 4.9 6.4 - - + +
425A MET* 2.8 25.4 + - + +
426A ALA* 3.4 10.8 - - - +
428A LEU* 1.3 74.2 - - + +
430A LYS* 1.3 62.7 - - + +
432A TYR* 3.2 6.5 + - - +
433A GLU* 2.8 28.0 + - - +
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Residues in contact with LYS 430 (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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426A ALA* 2.9 23.2 + - + +
427A ALA* 3.8 6.1 - - - +
429A GLU* 1.3 76.6 - - + +
431A ASP* 1.3 61.1 + - - +
433A GLU* 3.1 30.3 + - - +
434A GLU* 2.8 42.6 + - + +
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Residues in contact with ASP 431 (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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264A ARG* 3.0 40.0 + - + +
265A ILE* 4.4 16.2 - - + -
427A ALA* 2.8 24.5 + - - +
428A LEU* 3.1 10.0 + - + +
430A LYS* 1.3 77.8 - - - +
432A TYR* 1.3 58.0 + - - +
434A GLU* 3.3 12.0 + - - +
435A VAL* 2.9 38.1 + - + +
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Residues in contact with TYR 432 (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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265A ILE* 3.4 31.7 - - + +
267A PHE* 3.2 31.8 + + - +
313A MET* 4.3 8.7 - - + +
380A ASN* 5.4 1.7 + - - +
381A THR 3.3 21.4 + - - -
382A THR* 3.8 32.6 - - + +
384A ILE* 3.5 17.3 - - + +
385A ALA* 3.4 26.7 - - + -
388A TRP* 4.5 3.6 - + - -
428A LEU* 2.9 47.4 + - + -
429A GLU 3.5 5.4 - - - +
431A ASP* 1.3 75.1 - - - +
433A GLU* 1.3 54.1 + - - +
435A VAL* 3.7 3.9 - - + +
436A GLY* 2.7 33.1 + - - -
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Residues in contact with GLU 433 (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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382A THR* 6.1 0.4 - - - -
429A GLU 2.8 16.6 + - - +
430A LYS* 3.1 42.4 + - - +
431A ASP 3.2 0.2 - - - -
432A TYR* 1.3 76.3 - - - +
434A GLU* 1.3 65.5 + - + +
436A GLY* 3.1 11.5 + - - -
437A VAL* 3.2 18.2 + - + +
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Residues in contact with GLU 434 (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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430A LYS* 2.8 30.2 + - + +
431A ASP* 3.8 10.7 - - - +
433A GLU* 1.3 74.7 - - + +
435A VAL* 1.3 63.9 + - + +
437A VAL* 3.2 25.5 + - - +
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Residues in contact with VAL 435 (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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262A TYR* 4.0 24.0 - - + -
265A ILE* 3.7 21.8 - - + -
313A MET* 3.4 33.2 - - - -
344A VAL* 4.0 5.4 - - - +
346A TRP* 3.5 35.2 + - + +
382A THR* 5.9 0.7 - - + -
431A ASP* 2.9 21.9 + - + +
432A TYR* 3.9 3.6 - - + +
434A GLU* 1.3 77.4 - - + +
436A GLY* 1.3 63.0 + - - +
437A VAL 3.2 1.9 + - - -
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Residues in contact with GLY 436 (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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311A LYS* 5.0 11.3 + - - +
344A VAL* 4.6 13.2 - - - +
382A THR* 4.0 16.6 - - - -
432A TYR 2.7 18.5 + - - -
433A GLU* 3.1 5.1 + - - -
435A VAL* 1.3 75.4 - - - +
437A VAL* 1.3 64.0 + - - +
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Residues in contact with VAL 437 (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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311A LYS* 5.8 1.6 + - - -
344A VAL* 4.8 1.5 - - - +
345A ASP* 3.8 27.4 - - - +
346A TRP* 5.3 2.9 - - - -
433A GLU* 3.4 17.9 - - + +
434A GLU* 3.4 17.0 - - - +
435A VAL 3.1 6.8 - - - -
436A GLY* 1.3 82.9 - - - +
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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
------------------------------------------------------------
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