Contacts of the helix formed by residues 313 - 325 (chain B) in PDB entry 3EWJ
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 313 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B TYR 2.9 8.1 + - - -
305B PRO* 3.6 23.8 - - + +
312B TRP* 1.3 72.8 - - - +
314B VAL* 1.3 64.4 + - - +
315B LYS* 3.1 13.3 + - - +
316B MET* 3.1 37.0 + - + +
317B LEU 3.0 18.2 + - - -
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Residues in contact with VAL 314 (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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312B TRP 3.3 4.4 + - - -
313B ASP* 1.3 73.7 + - - +
315B LYS* 1.3 72.4 + - + +
317B LEU* 3.3 2.6 + - - +
318B LEU* 3.1 18.4 + - - +
343B PHE* 3.8 47.7 - - + +
347B THR* 4.2 22.0 - - + +
349B GLY 4.5 0.7 - - - +
350B LEU* 3.7 32.1 - - + +
384B LEU* 4.2 7.4 - - + +
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Residues in contact with LYS 315 (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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313B ASP* 3.1 10.1 + - - +
314B VAL* 1.3 86.4 - - + +
316B MET* 1.3 66.1 + - + +
318B LEU* 3.3 4.2 + - - +
319B GLU* 3.1 22.4 + - - +
350B LEU* 3.6 24.0 - - + +
352B TYR* 4.6 1.6 + - - -
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Residues in contact with MET 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LYS* 4.4 9.2 - - - +
304B TYR* 2.9 39.0 - - + -
305B PRO* 4.0 15.3 - - - -
312B TRP* 3.8 10.6 - - + -
313B ASP* 3.1 32.6 + - + +
315B LYS* 1.3 77.8 - - + +
317B LEU* 1.3 57.7 + - - +
319B GLU* 3.3 7.2 + - - +
320B GLN* 2.9 30.5 + - - +
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B TYR* 3.9 26.5 - - + +
312B TRP* 3.5 37.8 - - + +
313B ASP 3.0 15.9 + - - +
314B VAL 3.6 5.4 - - - +
315B LYS 3.2 0.2 - - - -
316B MET* 1.3 78.3 - - - +
318B LEU* 1.3 57.2 + - - +
320B GLN* 3.3 0.9 + - - +
321B PHE* 2.8 27.9 + - - +
337B LEU* 4.5 11.9 - - + -
339B THR* 4.6 1.8 - - + -
341B GLN* 3.4 29.2 - - - +
343B PHE* 3.7 24.5 - - + -
384B LEU* 4.0 13.5 - - + -
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Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B VAL 3.1 15.4 + - - +
315B LYS 3.9 1.1 - - - +
317B LEU* 1.3 76.2 - - - +
319B GLU* 1.3 58.0 + - - +
321B PHE* 3.4 9.0 + - + +
322B SER* 2.9 32.4 + - - -
350B LEU* 3.8 39.0 - - + +
351B ALA* 3.9 9.9 - - - -
352B TYR* 3.4 35.9 - - + +
382B SER* 3.9 9.0 - - - +
383B GLY* 3.8 32.8 - - - +
384B LEU* 3.9 14.1 - - + +
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Residues in contact with GLU 319 (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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315B LYS 3.1 16.7 + - - +
316B MET* 3.8 6.5 - - - +
318B LEU* 1.3 77.8 - - - +
320B GLN* 1.3 57.0 + - - +
322B SER* 3.3 6.1 + - - -
323B PHE* 3.0 28.1 + - + +
352B TYR* 3.4 12.5 + - - +
371B SER* 4.8 9.2 + - - -
378B ILE* 6.5 0.9 - - + -
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Residues in contact with GLN 320 (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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296B LYS* 3.5 49.0 + - - +
297B HIS 3.9 0.2 - - - -
298B TYR* 3.5 15.3 - - + +
312B TRP* 3.6 18.7 - - + -
316B MET 2.9 16.8 + - - +
317B LEU 3.3 4.5 + - - +
319B GLU* 1.3 76.1 - - - +
321B PHE* 1.3 63.7 + - - +
323B PHE* 3.0 19.4 + - - +
324B ASP* 2.9 61.1 + - - +
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Residues in contact with PHE 321 (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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230B VAL* 4.0 21.3 - - + -
298B TYR* 3.7 47.9 - + + +
317B LEU 2.8 20.9 + - - +
318B LEU* 3.6 20.2 - - + +
320B GLN* 1.3 73.3 - - - +
322B SER* 1.3 58.4 - - - +
324B ASP* 3.4 0.5 + - - +
325B ILE* 2.9 54.0 + - + +
335B ALA* 4.2 16.8 - - + -
336B HIS 4.0 7.2 - - - -
337B LEU* 3.8 45.8 - - + -
382B SER* 4.3 6.5 - - - -
383B GLY 4.2 4.3 - - - -
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Residues in contact with SER 322 (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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318B LEU 2.9 17.4 + - - -
319B GLU* 3.5 8.1 - - - -
320B GLN 3.2 0.2 - - - -
321B PHE* 1.3 77.3 - - - +
323B PHE* 1.3 63.2 + - - +
325B ILE* 3.9 7.8 - - - +
326B ALA* 3.1 24.3 + - - +
329B ALA* 5.5 1.0 - - - +
352B TYR* 3.6 9.1 - - - -
378B ILE* 4.3 12.4 - - - +
379B TYR 3.6 19.7 + - - +
380B LEU* 5.3 0.9 - - - -
382B SER* 2.7 27.8 + - - -
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Residues in contact with PHE 323 (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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319B GLU* 3.0 15.6 + - + +
320B GLN* 3.0 22.2 + - - +
322B SER* 1.3 79.8 - - - +
324B ASP* 1.3 78.9 + - - +
326B ALA 3.3 4.7 + - - -
371B SER* 5.3 1.8 - - - -
374B GLY* 3.7 35.9 - - - -
376B LYS* 2.8 55.6 + - + -
378B ILE* 3.9 17.7 - - + +
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Residues in contact with ASP 324 (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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296B LYS 4.6 1.4 - - - +
297B HIS* 3.4 25.0 - - - +
298B TYR* 3.0 51.8 + - + -
320B GLN* 2.9 32.7 + - - +
323B PHE* 1.3 88.5 - - - +
325B ILE* 1.3 59.6 + - - +
326B ALA 3.7 0.7 + - - -
327B GLU* 3.7 10.0 - - - +
376B LYS* 4.8 1.5 + - - +
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Residues in contact with ILE 325 (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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228B LEU* 3.6 22.9 - - + -
230B VAL* 4.0 17.5 - - + -
283B ARG* 3.6 27.4 - - - +
298B TYR* 3.7 20.4 - - + +
321B PHE* 2.9 45.6 + - + +
322B SER* 4.0 7.6 - - - +
324B ASP* 1.3 75.6 - - - +
326B ALA* 1.3 60.8 + - - +
327B GLU* 3.3 2.9 - - - -
328B GLU* 3.1 11.3 + - + +
329B ALA* 2.8 40.4 + - + -
335B ALA* 4.6 3.4 - - + -
382B SER* 5.8 1.1 - - - -
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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
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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