Contacts of the helix formed by residues 377 - 393 (chain A) in PDB entry 1JEQ
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 377 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A GLU* 2.5 14.7 + - - -
376A ILE* 1.3 77.2 - - - +
378A SER* 1.3 61.6 + - - +
379A SER 3.4 2.2 - - - -
380A THR* 3.0 22.1 + - - -
381A LEU* 3.2 10.4 + - - +
444B TYR* 6.0 0.7 - - - -
537B PHE* 5.4 1.2 - - - +
538B PRO* 3.8 15.8 - - - +
539B LEU* 3.6 10.1 - - - +
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Residues in contact with SER 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ILE* 3.6 14.6 - - - +
270A SER* 3.3 35.6 + - - -
370A PRO* 4.4 4.0 - - - -
371A GLU 4.9 1.8 - - - -
372A GLU* 4.4 2.0 - - - -
375A VAL* 2.6 31.8 + - - +
376A ILE 3.4 0.4 - - - -
377A GLY* 1.3 72.5 - - - +
379A SER* 1.3 65.9 + - - +
380A THR 2.7 6.5 + - - -
381A LEU* 3.0 2.0 + - - +
382A PHE* 2.7 28.1 + - - +
539B LEU* 3.7 7.4 - - - +
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Residues in contact with SER 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A PRO* 3.8 27.5 - - - +
372A GLU* 2.5 43.7 + - - +
378A SER* 1.3 73.1 - - - +
380A THR* 1.3 57.6 + - - +
382A PHE* 4.4 0.2 - - - -
383A SER* 3.0 28.9 + - - -
438B LEU* 4.6 7.5 - - - +
444B TYR* 3.3 34.1 - - - +
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Residues in contact with THR 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLY* 3.0 15.5 + - - -
378A SER 2.7 2.2 + - - -
379A SER* 1.3 77.1 - - - +
381A LEU* 1.3 68.9 + - - +
383A SER* 2.9 13.3 + - - -
384A ALA* 3.0 12.0 + - - +
443B LYS 5.1 0.3 + - - -
444B TYR* 3.3 37.3 + - - +
446B PRO* 4.3 4.5 - - + +
450B GLN* 3.6 36.6 - - - +
537B PHE* 4.1 6.7 - - + -
538B PRO* 6.3 0.9 - - + -
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Residues in contact with LEU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 3.9 21.5 - - + -
267A ILE* 4.1 14.6 - - + -
269A ILE* 3.5 31.4 - - + -
377A GLY 3.2 7.3 + - - +
378A SER* 3.0 5.6 + - - +
380A THR* 1.3 77.1 - - - +
382A PHE* 1.3 63.3 + - - +
384A ALA* 3.1 3.1 + - - +
385A LEU* 3.0 41.2 + - + +
454B VAL* 4.4 9.6 - - + -
533B ILE* 4.5 5.4 - - + -
537B PHE* 3.5 37.0 - - + -
539B LEU* 4.3 10.3 - - + -
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Residues in contact with PHE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 5.4 3.6 - - + -
269A ILE* 4.1 15.3 - - + +
271A VAL* 4.1 11.2 - - + -
368A VAL* 3.2 37.2 - - + -
369A TYR 3.8 2.7 - - - -
370A PRO* 3.6 47.6 - - + -
378A SER 2.7 19.9 + - - +
379A SER 4.1 1.3 - - - +
381A LEU* 1.3 72.0 - - - +
383A SER* 1.3 60.0 + - - +
385A LEU* 3.1 10.6 + - - +
386A LEU* 2.9 29.3 + - + -
431A GLY* 3.8 17.9 - - - -
432A PHE* 3.5 28.8 - + - -
438B LEU* 4.0 13.2 - - + -
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Residues in contact with SER 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A SER 3.0 19.4 + - - -
380A THR* 2.9 6.3 + - - -
382A PHE* 1.3 84.9 - - - +
384A ALA* 1.3 63.6 + - - +
386A LEU* 3.4 5.3 + - - +
387A ILE* 3.0 36.1 + - - +
438B LEU* 3.8 33.7 + - - +
444B TYR* 4.9 3.4 - - - -
446B PRO* 3.8 18.4 - - - +
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Residues in contact with ALA 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A THR 3.0 11.0 + - - +
381A LEU 3.1 8.7 + - - +
383A SER* 1.3 75.2 - - - +
385A LEU* 1.3 59.0 + - - +
387A ILE* 3.1 4.3 + - - +
388A LYS* 2.8 31.9 + - - +
446B PRO* 4.1 13.6 - - + +
450B GLN 4.8 0.9 - - - +
451B LEU* 4.1 17.0 - - + +
454B VAL* 3.8 22.2 - - + -
537B PHE* 3.9 15.0 - - + -
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Residues in contact with LEU 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 5.8 3.6 - - + -
263A LEU* 4.4 20.0 - - + -
269A ILE* 5.1 7.2 - - + -
347A LEU* 5.9 0.2 - - + -
350A PHE* 3.9 33.4 - - + -
381A LEU* 3.0 38.8 + - + +
382A PHE* 3.1 10.7 + - - +
384A ALA* 1.3 76.3 - - - +
386A LEU* 1.3 57.8 + - - +
388A LYS* 3.0 1.6 + - - +
389A CYS* 2.7 34.6 + - - -
432A PHE* 4.0 13.5 - - + -
454B VAL* 3.9 21.3 - - + +
457B LEU* 5.3 6.5 - - + -
458B ILE* 4.4 1.6 - - + -
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Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A PHE* 2.9 22.5 + - + +
383A SER* 3.8 5.8 - - - +
385A LEU* 1.3 76.2 - - - +
387A ILE* 1.3 62.6 + - + +
389A CYS* 4.3 0.2 - - - +
390A LEU* 3.1 42.6 + - + +
415A PRO* 3.7 11.7 - - + -
416A GLN 3.5 19.3 - - - +
417A GLU* 5.7 0.4 - - - -
430A PRO* 4.2 9.2 - - + -
431A GLY* 3.2 48.9 - - - +
432A PHE* 3.5 17.4 - - + -
438B LEU* 5.0 8.5 - - + -
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Residues in contact with ILE 387 (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 SER* 3.0 37.2 + - - +
384A ALA 3.4 7.0 - - - +
385A LEU 3.0 0.2 - - - -
386A LEU* 1.3 81.2 - - + +
388A LYS* 1.3 58.7 + - + +
390A LEU* 3.8 7.3 - - + +
391A GLU* 3.2 41.2 + - + +
439B LYS* 5.7 14.6 - - + -
446B PRO* 4.0 22.4 - - + -
451B LEU* 4.2 19.5 - - + -
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Residues in contact with LYS 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ALA 2.8 13.7 + - - +
385A LEU 3.8 0.2 - - - +
387A ILE* 1.3 73.9 - - - +
389A CYS* 1.3 60.2 + - - +
390A LEU 3.2 1.8 - - - -
391A GLU* 2.9 33.3 + - + +
392A LYS* 2.9 36.0 + - + +
451B LEU* 3.3 47.0 - - + +
452B ASN* 4.5 7.9 + - - -
454B VAL* 3.6 19.7 - - + -
455B ASP* 3.4 30.4 + - + +
458B ILE* 3.4 22.9 - - + -
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Residues in contact with CYS 389 (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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350A PHE* 4.0 20.9 - - - -
385A LEU* 2.7 25.4 + - - +
386A LEU 4.3 0.2 - - - +
388A LYS* 1.3 73.6 - - - +
390A LEU* 1.3 57.1 + - - +
393A GLU* 2.8 25.1 + - - -
394A VAL* 3.0 36.3 + - - +
396A ALA* 4.9 4.5 - - - -
415A PRO* 3.7 18.7 - - + +
432A PHE* 4.1 16.8 - - + -
458B ILE* 4.0 15.5 - - - -
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Residues in contact with LEU 390 (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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386A LEU* 3.1 38.3 + - + +
387A ILE* 3.8 7.2 - - + +
388A LYS 3.2 0.2 - - - -
389A CYS* 1.3 76.7 - - - +
391A GLU* 1.3 65.5 + - + +
393A GLU* 3.4 16.6 + - - +
415A PRO* 3.8 32.3 - - + +
417A GLU* 4.2 42.6 - - + +
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Residues in contact with GLU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ILE* 3.2 28.0 + - + +
388A LYS* 2.9 41.7 + - - +
390A LEU* 1.3 82.0 - - + +
392A LYS* 1.3 62.0 + - + +
393A GLU* 3.6 4.2 + - - +
451B LEU* 5.8 2.1 - - - +
455B ASP* 4.4 2.9 - - - +
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Residues in contact with LYS 392 (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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352A PRO* 5.8 0.5 - - - +
388A LYS* 2.9 20.3 + - + +
391A GLU* 1.3 79.8 - - + +
393A GLU* 1.3 73.3 + - - +
394A VAL* 3.4 16.0 + - + +
455B ASP* 2.6 54.8 + - - +
458B ILE* 3.6 20.5 - - + +
459B ASP* 2.9 35.1 + - - +
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Residues in contact with GLU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PRO* 3.6 5.9 - - - +
353A LEU* 3.1 38.8 + - + +
354A VAL* 6.0 0.5 - - - +
389A CYS 2.8 10.8 + - - -
390A LEU* 3.4 11.8 + - - +
391A GLU 3.4 4.6 - - - +
392A LYS* 1.3 81.3 - - - +
394A VAL* 1.3 56.6 + - - +
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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