Contacts of the helix formed by residues 321 - 336 (chain B) in PDB entry 3MDR
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 GLN 321 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317B GLU* 3.1 40.3 + - - +
318B LEU* 3.3 15.6 + - + +
319B SER 3.5 0.2 - - - -
320B ARG* 1.3 85.5 + - - +
322B PRO* 1.3 67.2 - - - +
323B GLU* 3.3 9.0 - - - +
324B ILE* 3.1 38.1 + - + +
325B VAL* 3.1 21.0 + - - +
411B PHE* 3.8 24.8 + - + +
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Residues in contact with PRO 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 4.6 0.4 - - - +
319B SER 5.1 2.2 - - - +
320B ARG* 3.5 9.6 - - - +
321B GLN* 1.3 88.9 - - - +
323B GLU* 1.3 76.5 + - + +
325B VAL* 3.3 9.4 + - + +
326B ALA* 3.1 22.3 + - - +
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Residues in contact with GLU 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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321B GLN* 4.1 8.1 - - - +
322B PRO* 1.3 92.0 - - + +
324B ILE* 1.3 64.5 + - + +
326B ALA* 3.3 7.5 + - - +
327B ARG* 3.2 25.6 + - - +
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Residues in contact with ILE 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU* 3.9 11.2 - - + -
321B GLN* 3.1 35.4 + - + +
323B GLU* 1.3 78.0 + - + +
325B VAL* 1.3 56.3 + - - +
327B ARG* 3.2 5.5 + - - +
328B LEU* 2.8 43.7 + - + +
352B TYR* 3.5 26.2 - - - +
356B VAL* 3.8 15.5 - - + -
411B PHE* 3.8 28.0 - - + +
413B PRO* 3.8 13.9 - - + -
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Residues in contact with VAL 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU* 3.3 44.6 - - + +
321B GLN 3.1 7.8 + - - +
322B PRO* 3.6 10.3 - - + +
323B GLU 3.3 0.2 - - - -
324B ILE* 1.3 77.0 - - - +
326B ALA* 1.3 51.0 + - - +
328B LEU* 3.2 10.2 + - + +
329B GLN* 2.6 60.7 + - + +
455B LEU* 4.5 9.2 - - + -
459B GLU* 5.4 2.9 - - + +
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B PRO 3.1 13.5 + - - +
323B GLU* 3.7 9.4 - - - +
324B ILE 3.3 0.4 - - - -
325B VAL* 1.3 75.9 - - - +
327B ARG* 1.3 53.4 + - + +
329B GLN* 3.1 16.0 + - - +
330B ALA* 2.7 37.1 + - - +
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Residues in contact with ARG 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B GLU 3.2 14.0 + - - +
324B ILE* 3.2 4.0 + - - +
326B ALA* 1.3 78.1 - - - +
328B LEU* 1.3 61.9 + - - +
330B ALA* 3.4 7.8 + - - +
331B GLU* 3.0 24.6 + - - +
352B TYR* 3.3 56.1 + - + +
355B GLN* 5.3 1.6 + - - +
414B ASP* 3.3 29.3 + - - -
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU* 3.7 30.5 - - + -
324B ILE* 2.8 38.2 + - + +
325B VAL* 3.5 10.3 - - - +
327B ARG* 1.3 72.7 - - - +
329B GLN* 1.3 62.4 + - - +
331B GLU* 3.3 5.7 + - - +
332B VAL* 3.0 27.5 + - - +
352B TYR* 3.5 22.0 - - + -
353B LEU* 3.6 31.9 - - + +
356B VAL* 3.6 16.2 - - + -
455B LEU* 3.7 21.8 - - + -
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Residues in contact with GLN 329 (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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325B VAL* 2.6 37.2 + - + +
326B ALA* 3.5 19.0 - - - +
328B LEU* 1.3 70.2 - - - +
330B ALA* 1.3 67.5 - - - +
332B VAL* 3.3 5.4 + - - +
333B ASP* 3.0 31.8 + - - +
455B LEU* 3.9 17.5 + - + +
458B LEU 4.8 2.2 + - - -
459B GLU* 3.5 35.2 + - - +
489B ARG* 3.7 37.7 + - - +
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Residues in contact with ALA 330 (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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326B ALA 2.7 20.9 + - - +
327B ARG* 3.6 9.4 - - - +
329B GLN* 1.3 74.8 - - - +
331B GLU* 1.3 60.9 + - - +
333B ASP* 3.3 9.4 + - - +
334B GLU* 3.2 27.9 + - + +
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Residues in contact with GLU 331 (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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327B ARG 3.0 17.5 + - - +
328B LEU* 3.8 6.3 - - - +
330B ALA* 1.3 73.8 - - - +
332B VAL* 1.3 64.7 + - + +
334B GLU* 3.4 9.4 + - - +
335B VAL* 3.2 33.4 + - + +
349B ARG 4.1 1.8 - - - +
350B LEU* 3.3 22.3 - - + +
351B GLN* 3.3 12.9 + - - +
352B TYR* 2.7 33.4 + - + +
353B LEU* 3.0 28.4 + - - +
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU 3.0 18.6 + - - +
329B GLN* 3.7 4.3 - - - +
331B GLU* 1.3 76.9 - - + +
333B ASP* 1.3 75.1 + - - +
336B ILE* 3.1 26.6 + - + +
337B GLY 3.1 17.4 + - - +
350B LEU* 4.4 11.4 - - + -
353B LEU* 5.5 2.7 - - + -
452B ALA* 3.9 22.4 - - - +
455B LEU* 4.0 16.4 - - + -
456B GLN* 3.4 39.7 - - + +
489B ARG* 4.5 0.7 - - - +
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Residues in contact with ASP 333 (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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329B GLN 3.0 12.5 + - - +
330B ALA* 3.4 11.6 - - - +
332B VAL* 1.3 78.5 - - - +
334B GLU* 1.3 63.2 + - + +
337B GLY* 3.1 31.0 - - - +
489B ARG* 2.6 44.3 + - - -
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Residues in contact with GLU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ALA* 3.2 18.3 + - - +
331B GLU* 3.4 10.0 + - - +
332B VAL 3.4 0.4 - - - -
333B ASP* 1.3 76.5 - - + +
335B VAL* 1.3 67.9 + - + +
337B GLY* 4.6 1.0 + - - -
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Residues in contact with VAL 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLU* 3.2 22.6 + - + +
334B GLU* 1.3 83.3 - - + +
336B ILE* 1.3 72.0 + - + +
339B LYS* 5.7 0.3 - - - +
346B ASP* 3.5 23.3 - - - +
349B ARG* 4.0 42.0 + - + +
350B LEU* 3.3 32.5 - - + -
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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
----------------------------------------------------------
332B VAL* 3.1 27.6 + - + +
334B GLU 5.0 0.4 - - - -
335B VAL* 1.3 90.2 - - + +
337B GLY* 1.3 58.4 - - - +
338B SER 3.7 0.2 + - - -
339B LYS* 2.9 39.1 + - + +
342B LEU* 4.0 18.8 - - + -
346B ASP* 3.8 28.5 - - + +
350B LEU* 4.7 4.5 - - + -
452B ALA* 3.9 26.0 - - + -
456B GLN* 3.6 32.3 - - - +
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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
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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