Contacts of the helix formed by residues 378 - 393 (chain B) in PDB entry 3EIJ
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 SER 378 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B THR 5.0 4.7 - - - -
377B GLU* 1.3 77.8 - - - +
379B THR* 1.3 59.6 + - - -
380B PHE 3.3 0.4 - - - -
381B LYS* 4.1 7.6 - - - +
382B MET* 2.8 49.1 + - - +
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Residues in contact with THR 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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339B LEU* 4.3 23.3 - - + +
370B MET 3.3 24.2 - - - +
371B VAL* 3.9 0.9 - - - -
374B SER* 3.4 22.6 - - - +
377B GLU 2.5 10.5 + - - -
378B SER* 1.3 80.6 + - - +
380B PHE* 1.3 55.5 + - - +
382B MET* 4.3 4.5 - - - -
383B ILE* 2.8 60.1 + - + +
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Residues in contact with PHE 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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371B VAL* 3.6 22.2 - - + +
374B SER* 4.4 2.6 + - - +
376B GLY 4.4 4.5 - - - +
377B GLU* 3.4 37.1 + - - +
378B SER 3.3 0.2 - - - -
379B THR* 1.3 79.9 - - - +
381B LYS* 1.3 65.3 + - + +
384B LEU* 3.2 28.0 + - + +
425B VAL* 4.3 10.8 - - + -
428B ARG* 3.9 22.2 - - + -
429B PHE* 3.4 58.6 - + + -
432B GLU* 3.8 29.6 - - + -
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Residues in contact with LYS 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B GLU* 4.3 14.6 - - + +
378B SER* 3.5 14.5 + - - +
380B PHE* 1.3 82.7 - - + +
382B MET* 1.3 69.1 + - - +
384B LEU* 3.1 12.9 + - + +
385B ASP* 3.0 47.9 + - - +
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Residues in contact with MET 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B TYR* 2.6 42.0 + - + +
339B LEU* 3.4 38.8 - - + +
340B LEU 5.1 0.4 - - - -
341B SER 4.4 1.1 - - - +
342B GLY* 3.2 36.6 - - - +
378B SER* 2.8 32.6 + - - +
379B THR 4.1 2.2 - - - +
381B LYS* 1.3 77.3 - - + +
383B ILE* 1.3 61.6 + - - +
385B ASP* 3.4 8.1 + - - +
386B LEU 3.1 7.6 + - - -
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Residues in contact with ILE 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B LEU* 6.0 2.5 - - + -
338B TYR* 4.4 3.1 - - + -
339B LEU* 4.0 16.2 - - + -
367B ALA* 3.2 43.3 - - + +
370B MET* 4.0 7.6 - - + -
371B VAL* 3.1 23.1 - - + +
379B THR* 2.8 47.3 + - + +
382B MET* 1.3 77.2 - - - +
384B LEU* 1.3 57.7 + - - +
386B LEU* 3.2 11.2 + - + +
387B LEU* 3.1 30.4 + - + +
429B PHE* 4.2 9.9 - - + -
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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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380B PHE* 3.2 26.3 + - + +
381B LYS* 3.1 13.3 + - + +
383B ILE* 1.3 75.6 - - - +
385B ASP* 1.3 63.1 + - - +
387B LEU* 3.5 2.2 + - - +
388B LYS* 2.9 51.9 + - + +
429B PHE* 3.8 11.0 - - + -
432B GLU* 4.2 29.8 - - + +
433B CYS* 3.4 46.0 - - - +
436B ALA* 5.8 0.4 - - + -
438B ILE* 4.8 1.3 - - + -
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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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338B TYR* 4.0 6.5 - - - +
344B ILE* 4.4 13.1 - - + +
381B LYS* 3.0 49.5 + - - +
382B MET* 3.5 11.1 - - - +
384B LEU* 1.3 79.1 - - - +
386B LEU* 1.3 57.2 + - - +
388B LYS* 3.4 24.8 + - - +
389B SER* 2.9 32.3 + - - -
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Residues in contact with LEU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LEU* 5.4 0.9 - - + -
335B LEU* 3.7 30.3 - - + -
338B TYR* 3.7 38.5 + - + -
344B ILE* 4.5 14.4 - - + +
347B ALA* 3.9 27.1 - - + -
363B LEU* 4.6 8.3 - - + -
367B ALA* 5.3 3.8 - - + -
382B MET 3.1 3.4 + - - -
383B ILE* 3.4 11.9 - - + +
384B LEU 3.2 0.4 - - - -
385B ASP* 1.3 79.8 - - - +
387B LEU* 1.3 59.2 + - + +
389B SER* 3.7 1.4 - - - -
390B LEU* 2.9 57.3 + - + +
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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
----------------------------------------------------------
363B LEU* 4.2 25.4 - - + -
364B VAL* 4.5 17.7 - - + -
367B ALA* 4.8 5.4 - - + -
368B ILE* 5.1 4.9 - - + -
383B ILE* 3.1 20.0 + - + +
384B LEU* 4.1 2.0 - - - +
386B LEU* 1.3 78.3 - - + +
388B LYS* 1.3 67.4 + - - +
390B LEU* 4.0 4.4 - - + +
391B TRP* 2.9 26.9 + - - +
396B ILE* 4.3 13.6 - - + +
401B MET* 4.2 9.8 - - + +
405B TYR* 3.8 26.9 - - + +
429B PHE* 4.0 23.8 - - + -
433B CYS* 4.9 0.4 - - - -
438B ILE* 3.9 15.0 - - + +
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Residues in contact with LYS 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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384B LEU* 2.9 40.4 + - + +
385B ASP* 3.5 20.8 + - - +
387B LEU* 1.3 77.4 - - - +
389B SER* 1.3 64.0 + - - +
391B TRP* 3.2 2.3 + - - +
392B LYS* 3.1 47.3 + - - +
436B ALA* 3.9 21.7 - - + +
438B ILE* 3.9 28.9 - - + +
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Residues in contact with SER 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ILE* 3.2 33.6 - - - +
348B GLU* 4.7 6.6 + - - -
385B ASP 2.9 20.2 + - - -
386B LEU 3.7 1.6 - - - -
388B LYS* 1.3 72.6 - - - +
390B LEU* 1.3 63.0 + - - +
392B LYS* 3.3 11.5 + - - +
393B SER* 3.1 26.1 + - - -
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Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ILE* 5.9 0.9 - - + -
347B ALA* 6.0 1.1 - - + +
348B GLU* 3.7 36.8 - - + +
351B LEU* 4.5 8.7 - - + -
363B LEU* 4.2 13.0 - - + -
386B LEU* 2.9 45.2 + - + +
387B LEU* 4.0 3.4 - - - +
389B SER* 1.3 74.4 - - - +
391B TRP* 1.3 62.0 + - - +
393B SER* 3.5 4.0 + - - -
395B THR* 3.0 50.8 + - + +
396B ILE* 3.3 35.0 + - + -
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Residues in contact with TRP 391 (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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177A GLU 4.8 4.0 - - - -
178A HIS* 6.1 0.2 - - - -
387B LEU 2.9 17.5 + - - +
388B LYS 3.5 3.1 - - - +
390B LEU* 1.3 77.1 - - - +
392B LYS* 1.3 74.8 + - + +
394B SER* 3.0 16.5 + - - -
396B ILE* 3.7 21.0 - - - +
397B THR* 4.5 0.7 - - - -
398B VAL* 3.7 45.3 - - + -
401B MET* 4.8 13.9 - - + -
437B GLY 3.6 16.8 + - - -
438B ILE* 3.6 46.7 - - + -
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Residues in contact with LYS 392 (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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388B LYS* 3.1 46.8 + - - +
389B SER* 3.3 7.2 + - - +
391B TRP* 1.3 86.0 - - + +
393B SER* 1.3 57.2 + - - +
394B SER* 3.1 7.8 + - - -
436B ALA* 4.5 14.6 + - - +
438B ILE* 4.8 3.4 - - - +
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Residues in contact with SER 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B GLU* 3.5 24.0 + - - +
352B LYS* 5.1 4.0 + - - -
389B SER* 3.1 17.8 + - - -
390B LEU* 3.5 5.4 + - - -
392B LYS* 1.3 74.9 - - - +
394B SER* 1.3 67.8 + - - +
395B THR* 2.9 25.6 + - - -
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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
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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