Contacts of the helix formed by residues 419 - 439 (chain C) in PDB entry 1JIQ
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 GLY 419 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C THR* 6.0 0.2 - - - -
415C PRO* 3.6 17.2 + - - +
416C ILE 2.9 9.4 + - - -
418C LYS* 1.3 78.5 - - - +
420C LEU* 1.3 63.5 + - - +
421C HIS 3.4 2.5 - - - -
422C HIS* 3.4 10.1 + - - +
423C LYS* 3.0 24.1 + - - +
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Residues in contact with LEU 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416C ILE 3.6 1.2 + - - -
417C ARG* 3.0 50.1 + - + +
418C LYS 3.4 1.2 + - - -
419C GLY* 1.3 77.2 - - - +
421C HIS* 1.3 64.3 + - - +
423C LYS* 3.4 17.1 + - + +
424C ILE* 3.2 38.2 + - + +
220D THR* 3.9 19.3 - - + +
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Residues in contact with HIS 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C HIS 5.7 0.9 - - - +
416C ILE* 3.5 28.6 + - + +
417C ARG* 3.7 12.6 - - + -
419C GLY 3.4 0.4 - - - -
420C LEU* 1.3 78.3 - - - +
422C HIS* 1.3 59.6 + - - +
424C ILE* 3.2 5.0 + - - +
425C LEU* 3.0 26.6 + - - +
187D ILE* 2.8 40.3 + - + +
189D GLY* 3.6 16.2 - - - +
192D ILE* 4.1 9.4 - - + -
220D THR* 3.9 20.4 - - + +
221D ASN* 3.1 26.8 + - - -
224D THR* 2.8 26.5 + - - -
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Residues in contact with HIS 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C ILE* 4.5 7.9 - - + -
409C PRO* 2.9 32.9 + - + -
410C VAL 3.0 21.7 + - - -
411C GLN* 4.6 0.2 - - - -
412C THR* 3.5 44.5 + - + -
415C PRO* 5.9 0.2 - - + -
419C GLY* 3.4 11.6 + - - +
420C LEU 3.3 0.6 - - - -
421C HIS* 1.3 75.4 - - - +
423C LYS* 1.3 60.7 + - - +
425C LEU* 3.3 27.3 + - + +
426C LEU* 2.8 52.6 + - + +
188D ASP* 4.9 2.2 + - - -
189D GLY 5.2 1.9 + - - +
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Residues in contact with LYS 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C GLY 3.0 13.9 + - - +
420C LEU* 3.5 21.7 - - + +
422C HIS* 1.3 76.4 - - - +
424C ILE* 1.3 60.2 + - + +
426C LEU* 4.5 7.2 - - - -
427C ALA* 2.9 27.5 + - - +
526D GLU* 2.9 40.7 + - + +
527D PRO* 4.5 1.2 - - - +
529D LEU* 3.5 19.3 - - + +
530D ASP* 2.6 38.6 + - - +
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Residues in contact with ILE 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C LEU* 3.4 33.0 - - + +
421C HIS 3.2 6.6 + - - +
423C LYS* 1.3 74.8 - - + +
425C LEU* 1.3 64.3 + - - +
427C ALA* 3.3 6.0 + - - +
428C ASN* 2.7 45.7 + - - +
187D ILE* 3.7 29.4 - - + -
216D GLN* 3.9 35.0 - - + +
217D GLU* 4.8 3.6 - - + -
220D THR* 4.0 22.4 - - + +
526D GLU* 4.3 10.8 - - - +
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Residues in contact with LEU 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C TYR* 3.4 30.3 - - + +
384C GLY 4.0 8.5 - - - +
385C THR* 4.0 9.6 - - + -
408C ILE* 4.2 5.6 - - + -
421C HIS 3.0 14.3 + - - +
422C HIS* 3.4 33.0 - - + +
424C ILE* 1.3 77.5 - - - +
426C LEU* 1.3 58.4 + - - +
428C ASN* 3.2 4.5 + - - +
429C PHE* 2.9 27.5 + - - +
186D ASN* 3.7 16.2 - - - +
187D ILE* 3.6 25.7 - - + +
188D ASP* 3.7 25.1 - - + +
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Residues in contact with LEU 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C ILE* 3.6 33.4 - - + -
409C PRO 4.5 3.4 - - - +
410C VAL* 4.3 7.6 - - - +
422C HIS* 2.8 46.1 + - + +
423C LYS* 3.7 7.6 - - - +
425C LEU* 1.3 76.8 - - - +
427C ALA* 1.3 63.6 + - - +
429C PHE* 3.2 2.8 + - + +
430C LEU* 3.0 33.2 + - + +
529D LEU* 4.1 11.0 - - + -
549D ILE* 3.8 42.6 - - + -
553D ARG* 6.2 1.6 - - + +
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Residues in contact with ALA 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C LYS 2.9 18.5 + - - +
424C ILE* 3.5 5.6 - - - +
426C LEU* 1.3 76.9 - - - +
428C ASN* 1.3 58.8 + - - +
430C LEU* 3.4 2.3 + - - +
431C ALA* 2.9 30.5 + - - +
522D ALA* 3.9 13.7 - - + +
525D ILE* 4.0 15.0 - - + +
526D GLU* 3.6 36.8 - - + +
529D LEU* 4.0 1.7 - - + +
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Residues in contact with ASN 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C TYR* 4.0 6.5 - - + -
385C THR* 4.3 9.3 - - + +
388C GLN* 2.9 35.2 + - - +
424C ILE* 2.7 46.5 + - - +
425C LEU* 3.7 3.6 - - - +
427C ALA* 1.3 76.6 - - - +
429C PHE* 1.3 65.3 + - - +
431C ALA* 4.3 0.9 - - - -
432C GLN* 3.0 31.7 + - - +
216D GLN* 4.8 6.3 + - - +
217D GLU* 4.4 6.5 + - - +
518D GLY 5.0 2.6 - - - +
519D LYS* 5.5 2.4 - - - +
522D ALA* 4.0 21.2 - - - +
526D GLU* 4.8 0.6 + - - -
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Residues in contact with PHE 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C TYR* 3.7 27.0 - + + -
406C PHE* 3.5 43.0 - - + -
407C LEU 3.5 14.1 - - - -
408C ILE* 3.6 36.3 - - + -
425C LEU 2.9 14.0 + - - +
426C LEU* 3.2 10.5 + - + +
428C ASN* 1.3 75.9 - - - +
430C LEU* 1.3 85.4 + - + +
432C GLN 3.8 3.8 + - - -
433C THR* 3.8 17.5 + - - +
476C SER* 3.9 20.6 - - - -
477C ILE 4.4 0.9 - - - -
478C VAL* 3.9 25.4 - - + -
545D LEU* 4.8 2.0 - - + -
549D ILE* 5.4 1.3 - - + -
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Residues in contact with LEU 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LYS* 5.2 0.2 + - - -
426C LEU 3.0 21.8 + - - +
427C ALA 3.7 3.1 - - - +
429C PHE* 1.3 91.5 - - + +
431C ALA* 1.3 65.4 + - - +
433C THR* 3.3 8.8 + - - -
434C GLU* 3.2 21.7 + - - +
525D ILE* 3.8 26.0 - - + -
529D LEU* 4.1 8.3 - - + -
542D THR* 4.6 10.0 + - + +
545D LEU* 3.6 37.0 - - + +
546D ILE* 3.7 27.1 - - + -
549D ILE* 4.0 19.5 - - + -
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Residues in contact with ALA 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427C ALA 2.9 18.4 + - - +
428C ASN* 3.4 2.4 + - - +
430C LEU* 1.3 77.3 - - - +
432C GLN* 1.3 58.9 + - + +
434C GLU* 3.6 5.0 - - - +
435C ALA* 2.8 31.4 + - - +
518D GLY* 3.6 10.3 - - - +
521D LEU* 3.6 9.3 - - + +
522D ALA* 3.2 34.8 - - + +
525D ILE* 3.8 7.4 - - + +
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Residues in contact with GLN 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C TYR* 3.7 4.0 - - - +
388C GLN* 3.6 35.8 - - - +
392C TYR* 3.2 16.5 - - + +
396C HIS* 2.8 31.2 + - - -
406C PHE* 3.8 21.8 - - + -
428C ASN* 3.0 22.4 + - - +
429C PHE 4.2 0.4 - - - +
430C LEU 3.3 0.2 - - - -
431C ALA* 1.3 79.0 - - + +
433C THR* 1.3 57.7 + - - +
435C ALA* 3.4 2.8 + - - +
436C LEU* 2.9 34.2 + - + +
515D VAL* 5.3 3.2 + - - +
518D GLY* 3.5 27.2 + - - -
519D LYS* 4.7 1.0 - - - +
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Residues in contact with THR 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C LYS* 3.0 26.1 + - - +
406C PHE* 3.6 41.5 - - + -
429C PHE 3.8 6.8 + - - +
430C LEU* 3.3 11.4 + - - -
432C GLN* 1.3 73.5 - - - +
434C GLU* 1.3 62.9 + - - +
436C LEU* 3.3 9.0 + - - +
437C MET* 2.9 30.8 + - - +
472C ARG 5.0 0.3 - - - +
474C THR* 3.4 21.1 + - - +
476C SER* 3.6 14.4 + - - +
545D LEU* 4.7 1.2 - - - +
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Residues in contact with GLU 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C LYS* 4.3 5.4 - - - +
430C LEU 3.2 13.7 + - - +
431C ALA 3.6 2.9 - - - +
433C THR* 1.3 81.7 + - - +
435C ALA* 1.3 57.8 + - - +
437C MET* 3.2 2.6 + - - +
438C ARG* 2.8 46.3 + - + +
521D LEU* 3.5 27.5 - - + +
525D ILE* 3.7 16.6 - - - +
538D HIS* 2.8 38.3 + - - +
539D ASP* 3.7 9.6 + - - +
542D THR* 3.5 21.8 - - - +
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Residues in contact with ALA 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396C HIS* 3.7 17.4 + - + -
431C ALA 2.8 19.4 + - - +
432C GLN 3.7 4.7 - - - +
434C GLU* 1.3 74.1 - - - +
436C LEU* 1.3 65.1 + - - +
438C ARG* 4.9 0.2 - - - -
439C GLY* 3.0 23.0 + - - +
468C PHE* 5.4 0.5 - - - -
470C GLY* 4.6 0.7 - - - -
517D LEU* 3.6 30.4 - - + +
518D GLY* 4.1 10.5 - - - +
521D LEU* 3.7 10.9 - - + +
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Residues in contact with LEU 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392C TYR* 6.0 1.6 - - + -
395C ILE* 3.4 33.4 - - + +
396C HIS* 3.8 24.4 - - + +
404C CYS* 5.1 1.8 - - - -
406C PHE* 3.9 21.3 - - + -
432C GLN* 2.9 23.0 + - + +
433C THR* 3.3 4.7 + - - +
435C ALA* 1.3 75.2 - - - +
437C MET* 1.3 61.3 + - - +
470C GLY* 3.3 6.8 - - - -
471C ASN 3.2 5.0 + - - -
472C ARG* 3.0 52.8 + - + +
474C THR* 3.5 25.8 - - + -
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Residues in contact with MET 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU* 3.4 40.7 - - + +
27C ARG* 3.9 15.1 + - - +
30C PHE* 3.9 17.3 - - + -
57C LYS* 3.9 18.2 - - + -
433C THR 2.9 17.3 + - - +
434C GLU 3.5 2.2 - - - +
436C LEU* 1.3 78.0 - - - +
438C ARG* 1.3 86.9 + - + +
471C ASN* 3.0 23.7 + - - +
472C ARG 4.2 5.4 - - - +
539D ASP* 3.5 39.9 - - + +
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Residues in contact with ARG 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ARG* 2.8 71.2 + - - +
31C ASP* 4.1 19.2 + - - -
434C GLU* 2.8 37.6 + - + +
435C ALA* 4.9 1.6 - - - -
437C MET* 1.3 102.0 - - + +
439C GLY* 1.3 68.8 + - - +
444C GLU* 4.6 4.6 + - - -
468C PHE 4.9 0.2 - - - +
469C GLU 5.2 1.2 - - - +
470C GLY* 4.4 1.8 - - - -
521D LEU* 5.4 4.0 - - + -
539D ASP* 5.0 6.5 - - - +
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Residues in contact with GLY 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ARG* 3.2 7.8 + - - -
435C ALA 3.0 18.4 + - - -
437C MET 3.6 1.0 - - - -
438C ARG* 1.3 87.6 - - - +
440C LYS* 1.3 62.9 + - - +
468C PHE* 3.4 21.8 - - - -
469C GLU 4.5 0.2 - - - -
470C GLY* 3.7 9.6 - - - -
517D LEU* 3.5 13.8 - - - +
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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
------------------------------------------------------------
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