Contacts of the helix formed by residues 370 - 388 (chain B) 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 ASP 370 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534A TYR* 2.4 43.2 + - - -
535A ASN 5.2 0.3 - - - +
260B ARG* 3.3 27.1 + - - +
367B ALA* 3.4 22.3 + - + +
368B ARG 3.4 0.2 - - - -
369B ASP* 1.3 76.9 - - - +
371B GLU* 1.3 57.4 + - - +
372B ALA 3.3 1.7 + - - -
373B ALA* 2.9 20.2 + - + +
374B ALA* 2.8 27.8 + - - +
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Residues in contact with GLU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A ILE* 3.6 38.6 - - + +
369B ASP 3.8 2.8 + - - -
370B ASP* 1.3 73.1 - - - +
372B ALA* 1.3 62.4 + - - +
374B ALA* 3.1 9.5 + - - +
375B VAL* 2.9 30.9 + - + +
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Residues in contact with ALA 372 (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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529A VAL 4.1 12.3 - - - +
530A TYR* 3.6 23.1 - - + -
531A PRO* 4.2 8.1 - - + -
534A TYR* 3.3 34.1 - - + -
370B ASP* 3.1 1.0 + - - -
371B GLU* 1.3 76.1 - - - +
373B ALA* 1.3 58.5 + - - +
375B VAL* 3.0 9.3 + - - +
376B ALA* 2.8 25.6 + - - +
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Residues in contact with ALA 373 (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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530A TYR* 4.3 4.0 - - - +
534A TYR* 4.0 4.2 + - - +
259B ILE* 4.1 7.7 - - + +
260B ARG 3.6 27.6 - - - +
366B ALA* 3.6 7.0 - - + -
370B ASP* 2.9 30.2 + - + +
372B ALA* 1.3 72.2 - - - +
374B ALA* 1.3 69.3 + - - +
376B ALA* 2.9 9.3 + - - +
377B LEU* 2.8 27.2 + - - +
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Residues in contact with ALA 374 (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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452A ILE* 4.0 28.3 - - + +
366B ALA* 3.5 15.8 - - + +
370B ASP 2.8 17.1 + - - +
371B GLU* 3.1 16.4 - - - +
373B ALA* 1.3 73.2 - - - +
375B VAL* 1.3 56.8 + - - +
377B LEU* 4.0 1.9 - - - +
378B SER* 3.0 28.2 + - - -
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Residues in contact with VAL 375 (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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452A ILE* 4.1 20.6 - - + +
453A MET 4.9 5.6 - - - +
454A ALA* 3.7 3.3 - - + +
458A GLN* 3.1 41.5 - - - +
529A VAL* 3.6 14.6 - - + +
371B GLU* 2.9 21.7 + - + +
372B ALA* 3.4 9.0 - - - +
374B ALA* 1.3 74.0 - - - +
376B ALA* 1.3 62.8 + - - +
378B SER* 3.2 7.3 + - - -
379B SER* 2.8 27.5 + - - -
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Residues in contact with ALA 376 (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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462A MET* 4.7 0.3 - - - +
525A PHE* 4.0 17.6 - - + -
529A VAL* 4.5 3.1 - - + +
530A TYR* 3.5 31.4 - - + +
259B ILE* 3.8 19.0 - - + +
372B ALA 2.8 12.4 + - - +
373B ALA* 3.4 7.0 - - - +
375B VAL* 1.3 77.3 - - - +
377B LEU* 1.3 64.0 + - - +
379B SER* 3.2 20.3 + - - -
380B LEU* 3.3 6.4 + - - +
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Residues in contact with LEU 377 (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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251B LEU* 4.0 26.9 - - + -
259B ILE* 4.1 11.3 - - + +
261B ILE* 4.0 13.7 - - + -
364B VAL* 3.9 9.2 - - + +
365B PHE* 3.7 13.5 - - - -
366B ALA* 3.5 30.1 - - + +
373B ALA 2.8 18.4 + - - +
374B ALA 4.0 2.9 - - - +
376B ALA* 1.3 73.2 - - - +
378B SER* 1.3 56.8 + - - +
380B LEU* 3.0 12.6 + - + +
381B ILE* 2.8 49.3 + - + +
417B GLU 4.9 2.0 - - - +
418B CYS* 4.8 1.3 - - - -
419B LEU* 4.2 11.9 - - + +
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Residues in contact with SER 378 (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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452A ILE 4.1 3.8 - - - -
453A MET* 3.6 0.7 - - - -
454A ALA* 2.9 29.6 + - - -
374B ALA 3.0 19.9 + - - -
375B VAL* 3.2 7.6 + - - -
377B LEU* 1.3 76.1 - - - +
379B SER* 1.3 64.2 + - - +
381B ILE* 3.3 6.4 + - - +
382B HIS* 2.9 35.0 + - - -
417B GLU* 2.7 27.8 + - - -
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Residues in contact with SER 379 (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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454A ALA* 3.6 7.8 - - - +
458A GLN* 3.8 20.1 - - - +
459A VAL* 4.2 8.8 - - - +
462A MET* 3.7 21.5 - - - +
525A PHE* 3.6 19.4 - - - -
529A VAL* 4.1 0.9 - - - +
375B VAL 2.8 18.3 + - - -
376B ALA 3.2 7.8 + - - -
378B SER* 1.3 76.2 - - - +
380B LEU* 1.3 53.1 + - - -
382B HIS* 3.6 1.4 - - - +
383B ALA* 2.6 36.7 + - - +
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Residues in contact with LEU 380 (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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462A MET* 3.3 30.2 - - + +
466A VAL* 4.3 2.2 - - + -
251B LEU* 4.0 34.8 - - + -
253B ILE* 4.6 8.7 - - + -
259B ILE* 5.1 4.0 - - + -
342B VAL* 5.6 1.6 - - + -
345B PHE* 3.8 20.9 - - + -
376B ALA 3.3 6.6 + - - +
377B LEU* 3.0 14.3 + - + +
379B SER* 1.3 77.7 - - - +
381B ILE* 1.3 58.1 + - + +
383B ALA* 3.0 3.3 + - - +
384B LEU* 2.8 56.8 + - + +
391B ALA* 5.8 2.2 - - + -
419B LEU* 4.2 13.9 - - + -
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Residues in contact with ILE 381 (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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377B LEU* 2.8 36.3 + - + +
378B SER* 3.6 6.3 - - - +
380B LEU* 1.3 73.3 - - + +
382B HIS* 1.3 67.0 + - + +
384B LEU* 3.2 2.4 + - - -
385B ASP* 3.0 18.5 + - - +
410B PRO* 3.3 19.0 - - + +
412B ILE* 3.8 27.4 - - + -
417B GLU* 3.6 16.8 - - + +
418B CYS* 3.2 41.7 - - - +
419B LEU* 3.8 24.0 - - + +
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Residues in contact with HIS 382 (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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453A MET* 3.7 18.4 - - + +
454A ALA 5.1 1.3 - - - -
459A VAL* 3.7 24.5 - - + -
378B SER* 2.9 41.3 + - - +
381B ILE* 1.3 73.7 - - + +
383B ALA* 1.3 67.3 + - - +
385B ASP* 4.3 7.3 + - - -
386B ASP* 2.8 35.5 + - - +
412B ILE* 3.8 24.4 - - + +
417B GLU* 2.5 32.4 + - - -
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Residues in contact with ALA 383 (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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459A VAL* 4.0 4.2 - - - +
462A MET* 3.7 26.7 - - + -
463A LYS* 3.9 25.1 - - + +
466A VAL* 4.4 6.1 - - + -
379B SER 2.6 23.3 + - - +
380B LEU* 3.1 7.2 - - - +
382B HIS* 1.3 74.4 - - - +
384B LEU* 1.3 57.4 + - - +
386B ASP* 3.6 0.9 - - - +
387B LEU* 3.0 34.2 + - - +
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Residues in contact with LEU 384 (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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466A VAL* 4.0 17.5 - - + -
345B PHE* 3.6 27.1 - - + -
380B LEU* 2.8 30.6 + - + +
381B ILE 3.6 5.4 - - - +
382B HIS 3.1 0.2 - - - -
383B ALA* 1.3 76.0 - - - +
385B ASP* 1.3 59.9 + - - +
386B ASP 3.1 1.6 - - - -
387B LEU* 4.9 0.4 - - - -
388B ASP* 2.9 25.5 + - - -
389B MET* 2.9 15.9 + - + +
390B VAL* 4.1 16.2 - - - +
391B ALA* 4.4 5.8 - - + +
408B ALA 4.1 9.9 - - - +
410B PRO* 3.6 21.3 - - + +
419B LEU* 3.9 24.9 - - + -
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Residues in contact with ASP 385 (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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381B ILE 3.0 16.5 + - - +
382B HIS* 3.8 6.2 + - - +
384B LEU* 1.3 76.4 - - - +
386B ASP* 1.3 69.6 + - - +
388B ASP* 3.7 9.7 + - - +
410B PRO* 3.6 14.6 - - + +
412B ILE* 3.6 30.3 - - + +
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Residues in contact with ASP 386 (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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459A VAL* 4.7 2.6 - - - +
463A LYS* 2.6 42.3 + - - +
382B HIS* 2.8 32.5 + - - +
383B ALA 3.6 1.6 - - - +
385B ASP* 1.3 84.1 - - - +
387B LEU* 1.3 59.7 + - - +
388B ASP* 2.8 13.8 + - - +
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Residues in contact with LEU 387 (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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463A LYS* 4.0 29.2 - - + +
466A VAL* 3.5 37.9 - - + -
467A GLU* 3.3 35.0 - - + +
470A ARG* 5.2 5.1 + - - +
383B ALA 3.0 21.8 + - - +
384B LEU* 4.8 0.7 - - - +
386B ASP* 1.3 77.5 - - - +
388B ASP* 1.3 68.6 + - - +
389B MET* 3.4 21.0 + - + +
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Residues in contact with ASP 388 (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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347B LYS* 4.0 4.0 - - - +
348B SER* 3.2 31.3 + - - -
349B SER* 5.1 4.5 + - - -
384B LEU 2.9 9.5 + - - -
385B ASP* 3.9 7.7 - - - +
386B ASP 2.8 10.7 - - - +
387B LEU* 1.3 81.4 - - - +
389B MET* 1.3 60.2 + - - +
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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