Contacts of the helix formed by residues 330 - 346 (chain B) in PDB entry 3E88
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 ALA 330 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B GLU* 4.6 0.7 - - - +
328B GLY* 3.2 3.0 - - - +
329B ARG* 1.3 79.5 - - - +
331B VAL* 1.3 64.9 + - - +
332B ASP 3.1 0.4 - - - -
333B TRP* 2.9 26.2 + - + +
334B TRP 3.2 8.8 + - - -
389B PRO* 4.0 17.7 - - + +
392B ARG* 3.3 24.1 + - - +
395B GLY* 4.1 24.5 - - - +
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Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B VAL* 4.1 8.7 - - + -
274B ARG* 4.0 30.3 - - + +
316B TYR 5.4 0.5 - - - +
318B ALA* 4.1 11.3 + - + +
320B GLU* 3.5 17.5 - - - +
321B VAL* 3.7 16.2 - - + -
327B TYR* 3.6 20.9 - - + -
328B GLY 3.2 20.4 - - - +
329B ARG 3.0 1.0 - - - -
330B ALA* 1.3 77.7 - - - +
332B ASP* 1.3 63.4 + - - +
334B TRP* 3.4 6.8 + - - +
335B GLY* 3.0 23.0 + - - -
392B ARG* 3.9 5.8 - - - +
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Residues in contact with ASP 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 4.0 20.7 - - + +
267B HIS* 2.7 36.2 + - + +
272B VAL* 3.6 7.4 - - - +
273B TYR* 2.9 29.9 + - - +
274B ARG* 2.7 31.8 + - - -
275B ASP 4.5 0.3 + - - -
276B ILE* 4.3 8.2 - - + +
329B ARG 3.3 3.8 + - - +
330B ALA 3.1 0.6 - - - -
331B VAL* 1.3 81.9 - - - +
333B TRP* 1.3 57.2 + - + +
335B GLY* 3.1 3.7 + - - +
336B LEU* 2.9 26.0 + - - +
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Residues in contact with TRP 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B VAL* 4.0 17.7 - - + -
263B LEU* 3.6 37.0 - - + -
264B GLU 4.6 0.4 - - - -
267B HIS* 3.9 11.3 - + - -
329B ARG 5.1 0.2 - - - -
330B ALA* 2.9 20.8 + - - +
332B ASP* 1.3 73.5 - - - +
334B TRP* 1.3 61.6 + - - +
336B LEU* 3.4 33.8 + - + +
337B GLY 3.0 21.5 + - - -
384B LEU* 3.6 14.3 - - + +
392B ARG* 4.3 4.0 - - - -
393B LEU 3.6 18.6 - - - +
394B GLY 3.3 25.2 + - - -
399B ASP* 3.3 26.1 + - - -
400B ALA* 3.6 38.6 - - + -
403B VAL* 3.9 13.9 - - + -
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Residues in contact with TRP 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B GLU 5.4 0.6 + - - -
316B TYR 3.1 28.7 + - - -
317B LEU 3.4 6.6 + - - -
318B ALA* 3.5 13.2 - - + -
319B PRO* 3.5 33.0 - - + -
330B ALA 3.2 4.8 + - - -
331B VAL 3.5 9.0 - - - +
333B TRP* 1.3 72.3 - - - +
335B GLY* 1.3 66.1 + - - +
337B GLY* 3.0 11.3 + - - -
338B VAL* 3.0 22.8 + - + +
350B PHE* 3.9 29.4 - + - -
362B ILE* 3.9 17.0 - - + -
384B LEU 3.5 10.1 - - - -
385B LEU* 3.3 53.7 - - + +
386B LYS 4.0 4.3 - - - -
387B LYS* 4.2 4.0 - - + -
392B ARG* 3.5 32.0 - - - +
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Residues in contact with GLY 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ILE* 3.9 24.8 - - - +
316B TYR* 4.3 6.8 - - - -
331B VAL 3.0 14.2 + - - -
332B ASP* 3.1 5.8 + - - -
334B TRP* 1.3 78.7 - - - +
336B LEU* 1.3 66.2 + - - +
338B VAL* 3.2 14.7 + - - +
339B VAL* 3.2 14.7 + - - +
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B GLY 4.4 3.4 - - - +
259B ILE* 3.7 31.4 - - + -
260B VAL* 3.5 28.3 - - + -
263B LEU* 4.5 5.6 - - + -
276B ILE* 4.0 4.7 - - - +
332B ASP 2.9 12.6 + - - +
333B TRP* 3.5 29.2 - - + +
334B TRP 3.3 0.2 - - - -
335B GLY* 1.3 72.8 - - - +
337B GLY* 1.3 53.6 + - - +
339B VAL* 2.8 30.6 - - + +
340B MET* 2.8 44.2 + - + +
384B LEU* 4.1 13.7 - - + -
403B VAL* 4.3 4.3 - - + -
409B PHE* 5.7 2.2 - - + -
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Residues in contact with GLY 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B TRP 3.0 11.3 + - - -
334B TRP 3.0 6.0 + - - -
336B LEU* 1.3 75.8 - - - +
338B VAL* 1.3 55.9 + - - +
340B MET* 4.3 0.9 - - - -
341B TYR* 2.8 30.1 + - - +
381B LEU* 3.6 7.1 - - - +
384B LEU* 3.6 29.1 - - - +
385B LEU* 3.6 13.0 - - - +
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Residues in contact with VAL 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B GLU 4.5 4.9 - - - +
316B TYR* 3.6 29.2 - - + -
334B TRP* 3.0 36.9 + - + +
335B GLY 3.2 6.0 + - - +
337B GLY* 1.3 74.2 - - - +
339B VAL* 1.3 58.7 + - - +
341B TYR* 3.2 7.6 + - - +
342B GLU* 2.8 27.8 + - - +
348B LEU* 3.5 31.2 - - + -
349B PRO* 3.7 16.4 - - + -
350B PHE* 6.0 0.7 - - + -
385B LEU* 3.9 8.5 - - + -
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Residues in contact with VAL 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ILE* 4.6 3.6 - - + -
276B ILE* 4.0 11.2 - - + -
277B LYS* 3.7 19.1 - - - -
278B LEU* 3.9 14.3 - - + +
281B LEU* 4.2 15.9 - - + -
316B TYR* 3.7 23.6 - - + -
335B GLY 3.2 9.4 + - - +
336B LEU* 2.8 39.7 - - + +
338B VAL* 1.3 72.5 - - - +
340B MET* 1.3 60.8 + - + +
342B GLU* 3.6 9.4 - - - +
343B MET* 2.9 40.3 + - + +
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Residues in contact with MET 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ALA* 3.8 17.9 - - + +
256B GLY* 3.7 21.3 - - - -
336B LEU* 2.8 41.0 + - + +
337B GLY* 3.6 2.0 - - - +
339B VAL* 1.3 73.5 - - - +
341B TYR* 1.3 63.4 + - - +
343B MET* 3.4 22.1 + - + +
344B MET* 3.2 53.0 + - + +
380B LEU* 4.3 7.6 - - + -
381B LEU* 3.6 17.9 - - + -
384B LEU* 4.2 9.4 - - + -
408B PHE* 4.0 19.3 - - + -
409B PHE* 5.0 3.6 - - + -
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Residues in contact with TYR 341 (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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337B GLY 2.8 19.3 + - - +
338B VAL* 3.3 9.0 - - - +
340B MET* 1.3 77.4 - - - +
342B GLU* 1.3 52.9 + - - +
345B CYS* 2.8 69.1 + - + +
347B ARG* 3.1 52.3 + - + -
348B LEU 3.9 2.9 - - - -
349B PRO* 3.4 37.3 + - + +
367B ILE* 4.6 5.2 - - + -
368B ARG 2.5 31.3 + - - -
369B PHE* 4.3 9.1 - + - -
370B PRO* 5.0 1.6 - - - +
381B LEU* 3.6 20.2 - - + -
385B LEU* 4.2 12.8 - - + -
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Residues in contact with GLU 342 (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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241B LEU* 3.7 20.8 - - + +
278B LEU* 3.5 13.0 - - + +
316B TYR* 2.7 26.0 + - - -
338B VAL 2.8 22.4 + - - +
339B VAL* 3.6 8.3 - - - +
341B TYR* 1.3 70.8 - - - +
343B MET* 1.3 60.8 + - - +
346B GLY* 2.8 28.9 + - - -
347B ARG* 3.5 28.3 - - - +
348B LEU* 3.1 23.0 + - + +
4D ARG* 2.8 31.9 + - - -
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Residues in contact with MET 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LEU* 4.3 11.2 - - - -
241B LEU* 3.8 9.0 - - + -
246B VAL* 3.4 2.8 - - - +
247B PHE* 2.7 53.6 + - + +
252B ALA* 4.0 18.6 - - + +
255B TYR* 4.0 35.7 - - + -
256B GLY* 4.6 1.6 - - - +
259B ILE* 4.9 4.3 - - + -
278B LEU* 4.5 13.0 - - + -
339B VAL* 2.9 30.4 + - + +
340B MET* 3.4 37.5 - - + +
342B GLU* 1.3 77.0 - - - +
344B MET* 1.3 57.7 + - - +
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Residues in contact with MET 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B VAL* 3.2 16.0 - - - +
247B PHE 4.0 5.5 - - - +
249B GLU* 3.9 28.9 - - + -
252B ALA* 3.5 21.5 - - + -
340B MET* 3.2 40.4 + - + +
341B TYR 4.4 0.2 - - - +
343B MET* 1.3 78.8 - - - +
345B CYS* 1.3 63.3 + - - +
346B GLY 3.6 0.4 - - - -
370B PRO* 5.2 1.7 - - - +
373B LEU* 4.2 21.5 - - + +
377B ALA* 4.3 10.5 - - + +
380B LEU* 5.2 2.7 - - + -
381B LEU* 4.1 24.0 - - + -
408B PHE* 4.0 23.8 - - + -
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Residues in contact with CYS 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B VAL* 4.5 2.2 - - - -
341B TYR* 2.8 58.3 + - + +
344B MET* 1.3 76.2 - - - +
346B GLY* 1.3 63.1 + - - +
347B ARG* 3.2 11.4 + - + +
370B PRO* 3.7 36.0 - - + +
373B LEU* 4.0 16.8 - - - -
381B LEU* 4.2 4.9 - - - -
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Residues in contact with GLY 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 5.4 2.7 - - - -
245B ARG 3.3 24.6 - - - +
246B VAL* 4.1 6.0 - - - +
342B GLU* 2.8 20.1 + - - -
344B MET 3.6 1.8 - - - -
345B CYS* 1.3 76.7 - - - +
347B ARG* 1.3 59.3 + - - +
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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