Contacts of the helix formed by residues 410 - 424 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408B HIS* 3.2 22.1 + - + +
409B HIS* 1.3 97.6 - - + +
411B TRP* 1.3 78.5 + - - +
412B VAL* 4.4 8.1 - - + +
413B VAL* 3.3 18.0 + - + +
414B LYS* 3.2 16.5 + - - +
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Residues in contact with TRP 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B TYR* 5.3 3.8 - + - -
315B ILE* 3.8 27.1 - - + -
320B GLY* 4.0 14.8 - - - -
409B HIS 3.6 4.7 + - - +
410B GLU* 1.3 77.4 + - - +
412B VAL* 1.3 87.3 + - + +
414B LYS* 3.3 14.7 + - - +
415B GLU* 2.9 36.0 + - + +
449B ASP* 5.4 1.6 - - - +
451B LYS* 3.5 43.9 - - + +
453B LEU* 3.7 40.8 - - + -
454B VAL* 4.0 17.6 - - + +
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Residues in contact with VAL 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LYS* 3.7 24.5 - - + +
310B TYR* 3.8 29.5 + - + +
315B ILE* 3.9 13.9 - - + -
410B GLU* 3.2 8.3 - - + +
411B TRP* 1.3 116.6 - - + +
413B VAL* 1.3 64.4 + - + +
415B GLU* 3.5 5.9 + - - +
416B SER* 3.2 21.7 + - - -
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Residues in contact with VAL 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LYS* 4.2 24.5 - - + +
405B LEU* 3.7 27.5 - - + +
408B HIS* 3.5 48.9 - - + +
410B GLU* 3.3 14.3 + - + +
411B TRP 3.3 0.4 - - - -
412B VAL* 1.3 76.2 - - + +
414B LYS* 1.3 63.0 + - - +
416B SER* 2.4 24.2 + - - +
417B GLY* 3.1 5.7 + - - -
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Residues in contact with LYS 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B LEU 3.2 12.9 + - - +
406B LEU* 3.3 29.5 - - - +
407B PHE* 5.4 0.2 - - - -
408B HIS* 4.4 9.8 - - - +
410B GLU 3.2 10.4 + - - +
411B TRP* 3.8 12.6 - - - +
412B VAL 3.3 0.2 - - - -
413B VAL* 1.3 78.0 - - - +
415B GLU* 1.3 63.0 + - - +
417B GLY* 3.0 10.7 + - - -
418B ILE* 3.0 25.1 + - + +
442B HIS* 5.6 2.0 - - + +
446B CYS* 5.1 13.4 - - - -
449B ASP* 3.0 27.7 + - - +
454B VAL* 4.1 24.1 - - - +
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Residues in contact with GLU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B MET 4.8 0.5 - - - +
310B TYR* 3.2 32.9 + - + -
376B ARG* 2.7 29.8 + - - -
411B TRP* 2.9 21.2 + - + +
412B VAL* 3.7 7.6 - - - +
413B VAL 3.3 0.2 - - - -
414B LYS* 1.3 75.7 - - - +
416B SER* 1.3 67.1 + - - +
418B ILE* 3.4 10.3 + - - +
419B LEU* 3.1 18.5 + - - +
453B LEU* 3.7 18.4 - - + +
454B VAL* 4.3 8.1 - - + +
457B ILE* 3.3 35.1 - - + +
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Residues in contact with SER 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B VAL* 4.8 7.2 - - - +
308B MET* 4.2 6.3 - - - +
309B LYS* 3.9 32.6 - - - +
405B LEU* 4.2 10.7 - - - +
412B VAL 3.2 9.3 + - - -
413B VAL* 2.4 29.1 + - - +
415B GLU* 1.3 84.8 + - - +
417B GLY* 1.3 55.7 + - - +
419B LEU* 3.4 6.6 + - - +
420B VAL* 3.0 34.0 + - - +
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Residues in contact with GLY 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B LEU* 3.7 5.8 - - - +
405B LEU* 3.7 32.5 - - - -
406B LEU* 3.6 9.8 - - - +
413B VAL 3.1 1.8 + - - -
414B LYS 3.0 8.0 + - - -
416B SER* 1.3 81.2 + - - +
418B ILE* 1.3 59.2 + - - +
420B VAL* 3.3 4.4 + - - +
421B LEU* 3.0 26.2 + - - +
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Residues in contact with ILE 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B LEU* 4.2 12.6 - - + -
414B LYS* 3.0 24.6 + - + +
415B GLU* 3.9 5.8 - - - +
416B SER 3.4 0.2 - - - -
417B GLY* 1.3 74.8 - - - +
419B LEU* 1.3 61.5 + - - +
421B LEU* 3.3 7.7 + - - +
422B GLY 3.2 9.9 + - - -
442B HIS* 6.3 0.7 - - + -
443B LEU* 3.8 28.7 - - + -
446B CYS* 4.4 10.5 - - - -
454B VAL* 4.1 18.6 - - + -
457B ILE* 3.9 19.1 - - + +
458B THR* 3.7 21.5 - - - +
461B THR* 2.8 37.7 + - + +
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B MET* 3.9 39.3 - - + +
376B ARG* 3.5 31.4 - - + +
380B ALA* 4.4 15.3 - - + -
415B GLU* 3.1 13.9 + - - +
416B SER 3.5 8.7 - - - +
417B GLY 3.2 0.2 - - - -
418B ILE* 1.3 74.9 - - - +
420B VAL* 1.3 59.6 + - - +
422B GLY* 3.2 2.3 + - - -
423B ALA* 2.9 28.2 + - + +
457B ILE* 3.7 29.4 - - + +
460B TRP* 3.9 15.5 - - + -
461B THR* 4.5 0.9 - - - -
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B VAL* 4.2 23.1 - - + +
308B MET* 3.7 29.2 - - + -
383B LEU* 3.9 17.3 - - + -
398B ILE* 4.1 25.1 - - + -
402B LEU* 4.1 11.4 - - + -
405B LEU* 4.5 4.9 - - + -
416B SER 3.0 20.1 + - - +
417B GLY* 3.6 8.1 - - - +
419B LEU* 1.3 74.8 - - - +
421B LEU* 1.3 64.5 + - - +
423B ALA* 3.7 0.8 - - - +
424B ILE* 3.1 27.4 + - + +
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Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B LEU* 3.7 21.7 - - + +
406B LEU* 4.8 13.2 - - + -
417B GLY 3.0 14.1 + - - +
418B ILE* 3.5 9.9 - - - +
419B LEU 3.2 0.2 - - - -
420B VAL* 1.3 77.4 - - - +
422B GLY* 1.3 58.9 + - - +
424B ILE* 3.7 9.5 - - + +
425B ALA 3.7 0.3 + - - -
432B MET* 3.6 31.9 - - + -
436B LEU* 6.1 0.9 - - + -
439B LEU* 3.8 18.6 - - + -
443B LEU* 3.7 37.0 - - + -
461B THR* 4.0 5.6 - - + -
465B TYR* 2.3 38.8 + - + +
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Residues in contact with GLY 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B ILE 3.2 6.3 + - - -
419B LEU 3.2 3.2 + - - -
420B VAL 3.2 0.4 - - - -
421B LEU* 1.3 75.9 - - - +
423B ALA* 1.3 63.0 + - - +
424B ILE 3.3 0.4 - - - -
425B ALA* 3.4 9.3 - - - +
460B TRP* 3.3 22.2 - - - -
461B THR* 3.6 17.5 - - - +
464B ARG* 2.9 29.6 + - - -
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Residues in contact with ALA 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B MET* 4.9 4.0 - - - -
380B ALA* 4.1 21.3 - - + +
383B LEU* 3.8 19.1 - - + -
384B ASP* 3.1 35.3 - - + +
387B ALA* 4.0 1.7 - - - +
419B LEU* 2.9 16.9 + - + +
420B VAL* 3.2 5.4 + - - +
422B GLY* 1.3 80.1 - - - +
424B ILE* 1.3 59.0 + - - +
425B ALA 3.2 1.4 + - - -
426B GLU 4.6 0.3 - - - +
460B TRP* 3.8 9.2 - - + -
464B ARG* 4.0 2.0 + - - +
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Residues in contact with ILE 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B LEU* 3.6 25.4 - - + -
387B ALA* 3.8 13.7 - - + -
394B LEU* 4.8 0.7 - - + -
395B LEU* 4.2 22.2 - - + -
398B ILE* 3.9 35.7 - - + -
399B LEU* 5.5 0.2 - - + -
402B LEU* 4.8 7.4 - - + -
420B VAL* 3.2 20.2 - - + +
421B LEU* 3.7 14.4 - - - +
423B ALA* 1.3 75.6 - - - +
425B ALA* 1.3 64.8 + - - +
426B GLU 3.5 0.7 - - - -
428B CYS* 3.2 34.5 + - + +
432B MET* 4.4 11.5 - - - +
465B TYR* 4.3 3.1 + - - +
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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
------------------------------------------------------------
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