Contacts of the helix formed by residues 410 - 424 (chain A) in PDB entry 5J3V
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 410 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A HIS* 3.2 20.5 + - + +
409A HIS* 1.3 98.2 + - + +
411A TRP* 1.3 60.1 + - - +
412A VAL* 4.6 2.5 - - + +
413A VAL* 3.3 26.0 + - + +
414A LYS* 2.8 30.2 + - - +
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Residues in contact with TRP 411 (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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310A TYR* 4.9 7.9 - + - -
315A ILE* 3.6 34.8 - - + -
320A GLY 4.5 2.0 - - - -
321A ASP* 3.7 20.8 + - + -
409A HIS 3.5 4.9 + - - +
410A GLU* 1.3 70.5 - - - +
412A VAL* 1.3 91.2 + - + +
414A LYS* 3.7 8.8 - - - +
415A GLU* 2.8 34.1 + - + +
449A ASP* 5.5 2.2 - - - +
451A LYS* 3.7 42.3 - - + +
453A LEU* 3.9 33.0 - - + -
454A VAL* 4.0 20.5 - - + +
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Residues in contact with VAL 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LYS* 4.5 10.5 - - + -
310A TYR* 4.0 34.2 + - + +
315A ILE* 3.8 13.5 - - + -
410A GLU* 3.3 2.4 - - + +
411A TRP* 1.3 118.1 - - + +
413A VAL* 1.3 68.6 + - + +
415A GLU* 3.3 4.4 + - - +
416A SER* 3.2 22.9 + - - -
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Residues in contact with VAL 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LYS* 4.3 22.4 - - + +
405A LEU* 3.4 28.8 - - + +
408A HIS* 3.8 26.0 - - + +
410A GLU* 3.3 36.9 + - + +
412A VAL* 1.3 82.1 - - + +
414A LYS* 1.3 59.6 + - - +
416A SER* 2.9 19.3 + - - -
417A GLY 3.4 5.5 + - - -
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Residues in contact with LYS 414 (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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405A LEU 3.4 10.0 - - - +
406A LEU* 3.4 27.1 - - - +
407A PHE* 5.2 1.3 - - - +
408A HIS* 3.6 20.9 + - - +
409A HIS 5.8 0.7 - - - +
410A GLU 2.8 18.0 + - - +
411A TRP* 3.8 8.7 - - - +
413A VAL* 1.3 76.1 - - - +
415A GLU* 1.3 64.0 + - - +
417A GLY* 3.2 9.9 + - - -
418A ILE* 3.2 22.7 + - + +
442A HIS* 4.2 8.0 + - - -
446A CYS* 3.9 28.1 - - - -
449A ASP* 4.0 20.5 + - - +
454A VAL* 5.2 6.3 - - + -
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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
----------------------------------------------------------
308A MET 4.9 0.2 - - - +
310A TYR* 3.2 25.8 + - + -
376A ARG* 2.8 34.0 + - - -
411A TRP* 2.8 21.7 + - + +
412A VAL* 3.6 7.2 - - - +
414A LYS* 1.3 77.3 - - - +
416A SER* 1.3 66.4 + - - +
418A ILE* 3.2 12.7 + - - +
419A LEU* 3.2 17.7 + - - +
453A LEU* 3.6 23.0 - - + +
454A VAL* 4.1 14.1 - - + +
457A ILE* 3.3 25.8 - - + +
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Residues in contact with SER 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A VAL* 4.9 4.6 + - - +
308A MET* 3.9 23.8 - - - +
309A LYS* 3.7 25.6 + - - +
405A LEU* 4.3 6.9 - - - +
412A VAL 3.2 10.4 + - - -
413A VAL* 2.9 22.3 + - - -
415A GLU* 1.3 85.5 + - - +
417A GLY* 1.3 58.9 + - - +
419A LEU* 3.4 8.3 + - - +
420A VAL* 3.2 27.5 + - - +
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Residues in contact with GLY 417 (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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402A LEU* 3.4 6.6 - - - +
405A LEU* 3.8 34.1 - - - -
406A LEU* 3.3 16.3 - - - +
413A VAL 3.4 2.8 + - - -
414A LYS 3.2 7.5 + - - -
415A GLU 3.2 0.8 - - - -
416A SER* 1.3 80.3 + - - +
418A ILE* 1.3 61.7 + - - +
420A VAL* 3.3 1.9 + - - -
421A LEU 3.2 16.3 + - - -
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Residues in contact with ILE 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A LEU* 3.8 15.7 - - + +
414A LYS* 3.2 23.0 + - + +
415A GLU* 3.2 6.9 + - - +
417A GLY* 1.3 72.7 - - - +
419A LEU* 1.3 64.4 + - - +
421A LEU* 3.2 4.8 + - - +
422A GLY 3.1 17.0 + - - -
442A HIS* 6.5 0.2 - - + -
443A LEU* 4.2 15.3 - - + -
446A CYS* 4.3 18.2 - - + -
454A VAL* 4.1 20.4 - - + +
457A ILE* 4.1 14.4 - - + +
458A THR* 3.6 23.3 - - - +
461A THR* 3.1 34.8 + - + +
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Residues in contact with LEU 419 (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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308A MET* 3.6 30.7 - - + +
376A ARG* 3.4 37.9 - - + +
380A ALA* 4.4 14.8 - - + -
415A GLU 3.2 8.9 + - - +
416A SER* 3.6 9.4 - - - +
417A GLY 3.3 0.2 - - - -
418A ILE* 1.3 77.9 - - - +
420A VAL* 1.3 59.5 + - - +
422A GLY* 3.1 1.6 + - - +
423A ALA* 2.9 27.0 + - + +
457A ILE* 3.6 23.5 - - + +
460A TRP* 3.6 25.1 - - + -
461A THR* 4.5 1.6 - - - -
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Residues in contact with VAL 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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305A VAL* 3.7 29.2 - - + -
308A MET* 3.8 23.6 - - + -
383A LEU* 3.7 17.0 - - + -
398A ILE* 4.2 23.3 - - + -
401A LEU* 5.4 1.8 - - + -
402A LEU* 4.0 15.7 - - + -
405A LEU* 4.9 0.9 - - + -
416A SER 3.2 16.8 + - - +
417A GLY* 3.5 9.6 - - - +
418A ILE 3.3 0.2 - - - -
419A LEU* 1.3 75.2 - - - +
421A LEU* 1.3 63.7 + - - +
423A ALA* 3.3 0.9 + - - +
424A ILE* 3.2 26.3 + - + +
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Residues in contact with LEU 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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402A LEU* 4.2 13.2 - - + +
406A LEU* 4.3 13.9 - - + -
417A GLY 3.2 10.0 + - - +
418A ILE 3.2 10.7 + - - +
420A VAL* 1.3 78.7 - - - +
422A GLY* 1.3 60.1 + - - +
424A ILE* 3.8 5.9 - - + +
425A ALA 3.7 4.3 + - - -
432A MET* 3.6 26.0 - - + -
436A LEU* 5.9 0.9 - - + -
439A LEU* 3.8 22.2 - - + -
443A LEU* 3.7 40.6 - - + -
461A THR* 3.9 6.1 - - + -
465A TYR* 2.6 49.5 + - + +
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Residues in contact with GLY 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 ILE 3.1 9.9 + - - -
419A LEU 3.1 3.3 + - - -
421A LEU* 1.3 77.4 - - - +
423A ALA* 1.3 56.9 + - - +
424A ILE 3.3 0.4 - - - -
425A ALA* 3.2 10.3 - - - +
460A TRP* 3.7 15.3 - - - -
461A THR* 3.6 17.0 - - - +
464A ARG* 2.6 37.8 + - - -
465A TYR* 4.8 0.4 - - - -
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Residues in contact with ALA 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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308A MET* 4.6 5.4 - - + -
380A ALA* 3.9 24.2 - - + +
383A LEU* 4.6 9.6 - - + -
384A ASP* 3.2 36.6 - - + +
387A ALA* 4.5 0.3 - - - +
419A LEU* 2.9 16.4 + - + +
420A VAL* 3.3 7.6 + - - +
422A GLY* 1.3 77.2 - - - +
424A ILE* 1.3 58.7 + - - +
425A ALA 3.2 3.1 + - - -
426A GLU 4.5 1.6 + - - -
427A GLY 5.3 0.2 + - - -
460A TRP* 3.9 5.8 - - + -
464A ARG* 3.7 9.2 + - - +
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Residues in contact with ILE 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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383A LEU* 3.8 32.3 - - + -
387A ALA* 3.9 14.4 - - + -
394A LEU* 4.7 3.8 - - + -
395A LEU* 4.9 2.0 - - + -
398A ILE* 3.7 30.3 - - + -
402A LEU* 4.2 12.8 - - + -
420A VAL* 3.2 20.9 - - + +
421A LEU* 3.8 8.3 - - - +
423A ALA* 1.3 76.0 - - - +
425A ALA* 1.3 64.9 + - - +
426A GLU 3.5 1.1 - - - -
427A GLY 4.2 1.1 - - - -
428A CYS* 3.0 41.7 + - + +
432A MET* 4.5 17.3 - - + +
465A TYR* 4.6 2.8 + - - +
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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