Contacts of the helix formed by residues 350 - 364 (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 LEU 350 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLU* 3.3 27.5 - - + +
332B VAL* 4.4 16.8 - - + -
335B VAL* 3.3 26.5 - - + -
336B ILE* 4.7 2.2 - - + -
342B LEU* 4.1 15.0 - - + -
346B ASP 3.7 14.8 - - - +
347B LEU* 3.1 21.2 + - + +
348B GLY 4.5 1.6 - - - -
349B ARG* 1.3 74.4 - - - +
351B GLN* 1.3 55.9 + - - +
353B LEU* 4.2 14.4 - - + -
354B SER* 3.1 21.2 + - - -
448B LYS* 3.4 15.7 - - + +
452B ALA* 4.0 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLU* 3.3 4.2 + - - +
348B GLY 4.8 8.3 - - - +
349B ARG 2.8 15.3 + - - +
350B LEU* 1.3 68.8 - - - +
352B TYR* 1.3 61.8 + - - +
353B LEU 3.3 0.2 - - - -
354B SER* 3.3 14.2 + - - -
355B GLN* 2.6 57.3 + - - +
358B LYS* 5.7 2.4 + - - -
416B PHE 4.6 2.6 + - - +
418B PRO* 3.9 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B ILE* 3.5 34.3 - - + +
327B ARG* 3.3 73.6 + - + +
328B LEU* 3.5 22.2 - - + -
331B GLU* 2.7 26.5 + - + +
351B GLN* 1.3 73.8 - - - +
353B LEU* 1.3 56.4 + - - +
355B GLN* 3.2 25.3 + - - +
356B VAL* 2.9 46.4 + - + +
413B PRO* 3.8 21.4 - - + +
414B ASP* 4.2 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 3.6 18.2 - - + +
331B GLU* 3.0 16.8 + - - +
332B VAL* 5.5 2.5 - - + -
350B LEU* 3.9 21.1 - - + +
351B GLN 3.3 0.2 - - - -
352B TYR* 1.3 73.9 - - - +
354B SER* 1.3 65.0 + - - +
356B VAL* 3.2 5.1 + - + +
357B LEU* 3.0 44.9 + - + +
448B LYS* 3.9 36.3 - - + +
451B MET* 3.9 22.4 - - + -
452B ALA* 4.2 11.9 - - - +
455B LEU* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU 3.1 17.1 + - - -
351B GLN* 3.3 21.0 + - - -
353B LEU* 1.3 77.2 - - - +
355B GLN* 1.3 55.6 + - - -
357B LEU* 3.6 6.7 + - - +
358B LYS* 3.1 50.0 + - - +
444B GLN* 5.9 0.3 + - - -
448B LYS* 3.7 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ARG* 5.3 1.5 + - - +
351B GLN* 2.6 42.8 + - - +
352B TYR* 3.3 30.4 + - - +
353B LEU 3.2 0.4 - - - -
354B SER* 1.3 71.8 - - - +
356B VAL* 1.3 61.6 + - - +
358B LYS* 3.6 3.9 + - + +
359B GLU* 3.1 27.9 + - - +
413B PRO* 3.1 32.2 + - + +
414B ASP* 4.1 5.7 + - - +
416B PHE* 3.4 28.9 - - + +
417B GLY* 3.5 18.1 - - - -
418B PRO* 3.7 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B THR* 4.5 8.1 - - + -
318B LEU* 3.9 35.7 - - + -
324B ILE* 3.8 17.9 - - + -
328B LEU* 3.6 23.1 - - + -
352B TYR* 2.9 28.4 + - + +
353B LEU* 3.2 7.4 + - + +
355B GLN* 1.3 76.2 - - - +
357B LEU* 1.3 59.0 + - + +
359B GLU 3.3 0.9 + - - -
360B SER* 2.9 27.2 + - - -
411B PHE* 3.6 13.4 - - + -
413B PRO* 3.8 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B HIS* 3.3 32.0 - - + +
311B LEU* 5.8 1.3 - - + -
314B THR* 3.8 29.8 - - + +
353B LEU* 3.0 42.1 + - + +
354B SER* 3.8 5.6 - - - +
356B VAL* 1.3 73.4 - - - +
358B LYS* 1.3 64.7 + - - +
360B SER* 3.3 1.1 + - - -
361B LEU* 3.0 23.7 + - + +
444B GLN 5.4 0.2 - - - +
447B VAL* 4.0 22.7 - - + +
448B LYS* 4.0 18.4 - - + -
451B MET* 4.2 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B GLN* 5.7 2.4 + - - -
354B SER* 3.1 32.5 + - - +
355B GLN* 3.8 2.7 - - + +
357B LEU* 1.3 74.6 - - + +
359B GLU* 1.3 56.7 + - - +
361B LEU* 3.4 3.7 + - + -
362B ARG* 3.1 17.8 + - - +
416B PHE* 3.7 42.3 + - + +
422B LYS* 5.6 7.7 - - - +
427B TYR* 2.7 35.4 + - + +
444B GLN* 5.0 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLN 3.1 18.1 + - - +
356B VAL 3.7 4.3 - - - +
358B LYS* 1.3 73.2 - - - +
360B SER* 1.3 65.8 + - - +
362B ARG* 2.8 43.7 + - - +
363B LEU* 3.4 12.1 + - - +
410B THR 3.3 0.2 - - - +
411B PHE* 3.7 19.0 - - + -
412B ASN 2.6 45.2 + - - +
413B PRO* 3.8 9.0 - - + -
415B ARG* 2.8 23.4 + - - -
416B PHE* 3.6 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B HIS* 3.9 8.7 + - - -
313B PHE* 4.1 7.3 - - - +
314B THR* 2.9 40.3 + - - -
356B VAL 2.9 17.4 + - - -
357B LEU* 3.5 6.7 - - - -
359B GLU* 1.3 78.0 - - - +
361B LEU* 1.3 51.8 + - - +
364B TYR* 2.7 45.1 + - - +
411B PHE* 3.6 16.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B HIS* 3.3 40.2 - - + +
357B LEU 3.0 14.7 + - - +
358B LYS* 3.7 6.5 - - + +
359B GLU 3.3 0.2 - - - -
360B SER* 1.3 74.1 - - - +
362B ARG* 1.3 63.4 + - - +
364B TYR 4.0 2.9 - - - +
365B PRO* 3.2 25.5 - - - +
366B PRO* 3.5 30.7 - - + -
395B THR* 5.3 1.2 - - - +
427B TYR* 3.7 8.4 - - - +
429B PRO* 3.7 25.3 - - + +
430B PHE* 3.7 34.5 - - + -
444B GLN* 6.0 1.1 - - + +
505B HEM 4.3 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B LYS 3.1 9.1 + - - +
359B GLU* 2.8 49.0 + - - +
360B SER 3.3 0.6 - - - -
361B LEU* 1.3 77.4 - - - +
363B LEU* 1.3 75.9 - - - +
365B PRO* 3.7 6.4 - - - +
395B THR* 4.2 13.1 - - - +
396B TYR 4.8 2.6 - - - +
399B GLY* 2.8 47.7 + - - -
400B ARG* 5.2 0.3 + - - -
405B PHE* 3.6 33.4 - - + +
408B PRO* 2.8 33.1 + - - +
410B THR 3.0 13.1 + - - -
415B ARG* 3.1 15.1 - - - +
416B PHE* 4.7 4.7 - - + -
427B TYR* 3.5 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B GLU* 5.7 0.4 - - - +
359B GLU 3.4 6.2 + - - +
362B ARG* 1.3 105.8 - - - +
364B TYR* 1.3 80.6 + - + +
365B PRO* 3.4 7.6 - - - +
396B TYR* 3.8 2.9 - - - -
400B ARG* 2.7 57.9 + - + +
408B PRO 3.4 21.5 - - - +
409B LEU* 4.3 16.4 - - + +
411B PHE* 4.0 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B HIS* 5.3 1.2 + - - -
313B PHE* 3.4 58.1 - + + +
316B MET* 4.2 14.3 - - + +
317B GLU* 2.8 43.4 + - + -
320B ARG* 3.6 10.2 + - - -
360B SER* 2.7 33.8 + - - +
361B LEU* 3.7 4.2 - - - +
363B LEU* 1.3 98.3 - - + +
365B PRO* 1.3 63.7 - - - +
366B PRO* 3.2 10.0 - - - +
400B ARG* 3.8 14.8 - - - -
411B PHE* 4.8 2.2 - + - -
468B PHE 4.7 3.0 + - - -
470B LEU* 3.8 22.7 - - + -
476B LEU* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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