Contacts of the helix formed by residues 325 - 344 (chain B) in PDB entry 5M4G
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 TRP 325 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B GLY 3.5 2.8 + - - -
324B VAL* 1.3 76.2 - - - +
326B TRP* 1.3 66.2 + - - +
327B PRO* 3.5 24.3 - - + +
328B ASP* 2.9 51.9 + - - +
329B MET 3.5 2.4 + - - -
331B ARG* 3.6 22.7 - - - -
389B ILE* 3.9 22.4 - - + -
400B ALA* 2.9 29.8 + - + -
401B ARG 3.8 2.0 - - - -
402B HIS* 3.4 37.3 - + + +
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Residues in contact with TRP 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B VAL* 4.3 0.2 - - + -
320B MET* 3.6 35.9 - - + -
324B VAL* 3.6 3.2 + - - -
325B TRP* 1.3 70.7 - - - +
327B PRO* 1.3 68.2 - - + +
329B MET* 2.9 39.1 + - + +
330B HIS* 3.1 9.4 + - - +
368B LEU* 3.7 20.4 - - + -
369B GLY* 3.0 31.7 + - - -
397B LEU* 3.7 17.2 - - + +
399B THR* 3.5 35.9 - - + +
401B ARG 3.1 20.3 + - - +
403B LEU* 4.0 14.4 - - + -
409B LEU* 3.6 21.7 - - + +
410B THR 3.6 23.1 - - - -
411B VAL* 4.2 4.5 - - + -
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Residues in contact with PRO 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B TRP* 3.5 38.4 - - + +
326B TRP* 1.3 94.3 - - + +
328B ASP* 1.3 56.1 + - - +
330B HIS* 3.2 3.6 + - - +
331B ARG* 3.0 36.3 + - - +
389B ILE* 3.6 28.5 - - + -
394B LEU* 3.8 7.5 - - + +
397B LEU* 3.9 17.7 - - + -
400B ALA* 3.9 18.6 - - + -
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Residues in contact with ASP 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B VAL* 5.3 0.4 - - + -
325B TRP* 2.9 42.1 + - - +
327B PRO* 1.3 77.0 - - - +
329B MET* 1.3 68.8 + - + +
331B ARG* 2.6 34.4 + - - +
332B LEU* 2.9 27.4 + - - +
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Residues in contact with MET 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B VAL* 3.7 19.7 - - + +
319B ALA* 3.7 31.9 - - + +
320B MET* 4.2 4.9 - - + -
324B VAL* 3.6 34.1 - - + -
325B TRP 3.5 0.2 + - - -
326B TRP* 2.9 30.3 + - + +
328B ASP* 1.3 86.5 - - + +
330B HIS* 1.3 65.7 + - - +
332B LEU* 3.2 17.2 + - + +
333B ALA 3.1 18.4 + - - -
368B LEU* 3.4 24.2 - - + +
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Residues in contact with HIS 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B TRP 3.1 6.0 + - - +
327B PRO 3.2 8.9 + - - +
329B MET* 1.3 76.7 - - - +
331B ARG* 1.3 62.1 + - + +
333B ALA* 3.2 5.5 + - - +
334B ASP* 3.0 37.2 + - - +
361B ALA* 6.2 0.2 - - - -
364B MET* 3.6 16.9 + - + +
366B HIS 3.2 27.4 - - - -
367B GLY* 3.7 4.0 - - - -
368B LEU* 3.1 35.5 + - + +
392B PRO 5.1 0.4 + - - -
393B GLY* 3.7 23.8 - - - -
394B LEU* 3.6 24.7 - - + -
397B LEU* 3.7 14.9 - - + +
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Residues in contact with ARG 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B TRP* 3.6 25.5 - - - -
327B PRO* 3.0 16.1 + - - +
328B ASP* 2.6 42.0 + - - +
330B HIS* 1.3 77.3 - - + +
332B LEU* 1.3 63.8 + - - +
334B ASP* 3.3 12.2 + - - +
335B ARG* 3.0 23.9 + - - +
355B VAL* 5.8 8.9 - - + +
389B ILE* 4.7 2.4 - - - +
391B GLU* 4.8 6.6 + - - -
394B LEU* 3.8 32.6 - - + +
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Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ALA* 4.1 28.7 - - + +
316B VAL* 4.3 8.1 - - + -
319B ALA* 4.3 6.5 - - + -
328B ASP 2.9 17.6 + - - +
329B MET* 3.2 25.5 + - + +
331B ARG* 1.3 74.1 - - - +
333B ALA* 1.3 65.3 + - - +
335B ARG* 3.3 11.1 + - + +
336B ILE* 3.1 48.2 + - + +
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Residues in contact with ALA 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B SER* 4.1 22.7 - - - -
316B VAL* 4.3 6.5 - - + +
329B MET 3.1 12.3 + - - +
330B HIS 3.2 8.3 + - - +
332B LEU* 1.3 76.0 - - - +
334B ASP* 1.3 64.1 + - - +
336B ILE* 3.2 2.2 + - - +
337B HIS* 2.9 40.2 + - + -
364B MET* 4.4 3.8 - - + -
368B LEU* 4.0 22.9 - - + -
413B PRO* 4.4 0.7 - - + -
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Residues in contact with ASP 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B HIS* 3.0 32.5 + - - +
331B ARG* 3.5 14.7 - - - +
332B LEU 3.3 0.2 - - - -
333B ALA* 1.3 76.1 - - - +
335B ARG* 1.3 62.4 + - - +
337B HIS* 3.3 8.0 + - - +
338B LEU* 2.9 33.3 + - + +
355B VAL* 5.8 2.9 - - + -
360B GLY* 3.7 34.1 - - - +
361B ALA* 4.7 2.3 + - - +
364B MET* 3.5 19.6 - - - +
392B PRO 5.4 3.5 - - - +
393B GLY* 5.8 0.2 - - - -
394B LEU* 5.9 0.3 - - - +
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Residues in contact with ARG 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ARG 3.0 16.7 + - - +
332B LEU* 3.6 12.1 - - + +
333B ALA 3.3 0.2 - - - -
334B ASP* 1.3 76.2 - - - +
336B ILE* 1.3 60.8 + - + +
338B LEU* 3.3 4.4 + - - +
339B GLU* 2.9 51.4 + - - +
351B VAL* 4.0 19.7 - - + +
352B ASP* 2.9 30.5 + - - +
355B VAL* 3.8 38.3 - - + +
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Residues in contact with ILE 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ALA 4.2 4.0 - - - +
311B ARG* 3.8 43.1 - - + +
312B SER* 3.8 29.2 - - - +
315B ALA* 3.3 34.5 - - + -
332B LEU* 3.1 33.2 + - + +
333B ALA* 3.7 4.0 - - - +
335B ARG* 1.3 75.6 - - + +
337B HIS* 1.3 65.9 + - - +
339B GLU* 3.3 8.7 + - - +
340B GLU* 2.9 25.2 + - + +
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Residues in contact with HIS 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ALA 4.0 8.5 - - - -
309B VAL* 4.3 4.2 - - - -
312B SER* 2.8 30.6 + - - -
333B ALA 2.9 21.7 + - - -
334B ASP* 3.6 10.3 + - - +
336B ILE* 1.3 77.2 - - - +
338B LEU* 1.3 59.2 + - + +
340B GLU* 3.2 3.5 + - - +
341B LEU* 2.8 40.2 + - + +
360B GLY* 5.6 3.7 + - - +
363B PHE* 5.6 3.9 - - + +
364B MET* 3.8 18.7 - - - +
413B PRO* 3.7 17.9 - - + +
414B GLY 3.4 26.3 + - - -
415B ILE* 3.7 30.0 - - + +
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Residues in contact with LEU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ASP* 2.9 23.7 + - + +
335B ARG 3.7 3.1 - - - +
336B ILE 3.2 0.2 - - - -
337B HIS* 1.3 77.3 - - + +
339B GLU* 1.3 63.0 + - - +
341B LEU* 3.3 2.2 + - + +
342B ALA* 3.0 24.4 + - - +
347B LEU* 3.7 27.6 - - + +
351B VAL* 4.2 13.3 - - + +
354B MET* 4.1 16.5 - - + +
355B VAL* 3.9 29.6 - - + +
359B LEU* 4.0 16.6 - - + +
360B GLY* 3.8 33.7 - - - +
363B PHE* 4.6 7.0 - - + -
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Residues in contact with GLU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ARG* 3.0 34.8 + - - +
335B ARG* 2.9 38.2 + - - +
336B ILE* 3.6 8.9 - - - +
338B LEU* 1.3 76.2 - - - +
340B GLU* 1.3 58.6 + - - +
342B ALA* 3.3 3.3 + - - +
343B HIS* 2.9 42.4 + - - +
351B VAL* 4.0 26.1 - - + +
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Residues in contact with GLU 340 (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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307B GLU 5.9 0.4 - - - -
308B ALA* 3.5 33.5 - - + -
311B ARG* 2.5 45.1 + - - +
336B ILE* 2.9 20.5 + - + +
337B HIS 4.0 1.3 - - - +
339B GLU* 1.3 74.1 - - - +
341B LEU* 1.3 66.2 + - - +
343B HIS* 3.2 25.7 + - - +
344B MET* 3.0 29.1 + - + +
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B VAL* 5.4 1.3 - - + -
308B ALA* 5.9 0.9 - - + -
337B HIS* 2.8 27.6 + - + +
338B LEU* 4.7 1.1 - - + -
340B GLU* 1.3 74.8 - - - +
342B ALA* 1.3 60.9 + - - +
344B MET* 3.3 14.1 + - - +
345B GLY 3.3 2.9 + - - -
346B ILE* 3.0 54.6 + - + +
347B LEU* 3.3 21.7 + - + -
363B PHE* 3.6 43.7 - - + -
415B ILE* 4.3 28.5 - - + -
417B PHE* 4.4 6.7 - - + -
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Residues in contact with ALA 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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338B LEU 3.0 17.3 + - - +
339B GLU* 3.5 7.2 - - - +
341B LEU* 1.3 73.8 - - - +
343B HIS* 1.3 64.0 + - + +
344B MET 3.0 4.9 - - - -
345B GLY* 3.0 13.0 + - - -
347B LEU* 3.3 31.0 - - + +
348B SER* 5.0 1.3 - - - -
349B GLY 5.6 1.3 - - - +
351B VAL* 4.6 7.9 - - + -
354B MET* 4.6 10.1 - - + -
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Residues in contact with HIS 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ARG* 5.3 0.4 + - - -
339B GLU* 2.9 33.1 + - + +
340B GLU* 3.2 35.7 + - - +
342B ALA* 1.3 77.6 - - + +
344B MET* 1.3 58.5 + - + +
345B GLY 3.8 0.2 + - - -
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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
----------------------------------------------------------
301B ASP* 4.4 1.3 - - - +
304B ALA* 3.7 40.6 - - + +
305B VAL* 3.8 14.6 - - + -
308B ALA* 5.6 2.0 - - - -
340B GLU* 3.0 18.3 + - + +
341B LEU* 3.5 17.3 - - - +
342B ALA 3.0 0.4 - - - -
343B HIS* 1.3 77.1 - - + +
345B GLY* 1.3 60.7 + - - +
346B ILE* 3.5 16.1 + - + +
439B VAL* 4.0 11.3 - - - +
442B ARG* 5.1 4.5 + - - +
443B PHE* 3.2 41.3 - - + -
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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