Contacts of the helix formed by residues 350 - 364 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A GLU* 3.3 28.9 - - + +
332A VAL* 4.3 18.6 - - + -
335A VAL* 3.3 25.1 - - + -
336A ILE* 4.9 2.7 - - + -
342A LEU* 4.2 13.7 - - + -
346A ASP 3.7 14.8 - - - +
347A LEU* 3.1 20.3 + - + +
348A GLY 4.4 1.3 - - - -
349A ARG* 1.3 75.5 - - - +
351A GLN* 1.3 56.1 + - - +
353A LEU* 4.1 15.3 - - + -
354A SER* 3.1 20.4 + - - -
448A LYS* 3.4 16.0 - - - +
452A ALA* 4.1 24.2 - - + -
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Residues in contact with GLN 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLU* 3.1 3.6 + - - +
348A GLY 4.7 9.0 - - - +
349A ARG 2.9 13.9 + - - +
350A LEU* 1.3 69.1 - - - +
352A TYR* 1.3 61.1 + - - +
353A LEU 3.3 1.8 - - - -
354A SER* 3.3 14.0 + - - -
355A GLN* 2.7 57.7 + - - +
358A LYS* 5.5 4.0 + - - -
416A PHE 4.7 2.8 + - - +
418A PRO* 3.9 22.8 - - - +
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Residues in contact with TYR 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A ILE* 3.5 35.0 - - - +
327A ARG* 3.3 73.7 + - + +
328A LEU* 3.7 15.5 - - + -
331A GLU* 2.7 25.4 + - + +
351A GLN* 1.3 70.8 - - - +
353A LEU* 1.3 58.6 + - - +
355A GLN* 3.3 24.0 + - - +
356A VAL* 3.0 43.9 + - + +
413A PRO* 3.7 21.7 - - + +
414A ASP* 4.3 3.5 + - - -
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Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A THR* 5.9 0.2 - - + -
328A LEU* 3.7 23.2 - - + +
331A GLU* 3.0 18.4 + - - +
332A VAL* 5.6 2.0 - - + -
350A LEU* 3.8 22.9 - - + +
352A TYR* 1.3 73.1 - - - +
354A SER* 1.3 66.2 + - - +
356A VAL* 3.2 5.1 + - + +
357A LEU* 3.0 46.5 + - + +
448A LYS* 3.8 36.6 - - + +
451A MET* 3.9 19.1 - - + -
452A ALA* 4.2 12.1 - - - +
455A LEU* 4.2 9.6 - - + -
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Residues in contact with SER 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU 3.1 16.0 + - - -
351A GLN* 3.3 21.8 + - - -
353A LEU* 1.3 76.9 - - - +
355A GLN* 1.3 57.3 + - - +
357A LEU* 3.5 7.0 + - - +
358A LYS* 3.0 50.3 + - - +
448A LYS* 3.8 21.5 + - - +
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Residues in contact with GLN 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ARG* 5.4 1.4 + - - +
351A GLN* 2.7 43.0 + - - +
352A TYR* 3.5 29.2 - - - +
353A LEU 3.3 0.2 - - - -
354A SER* 1.3 75.5 - - - +
356A VAL* 1.3 56.5 + - - +
358A LYS* 3.4 4.4 + - + +
359A GLU* 3.0 29.6 + - - +
413A PRO* 3.0 30.8 + - + +
414A ASP* 4.1 6.1 + - - +
416A PHE* 3.3 29.5 - - + +
417A GLY* 3.5 18.7 - - - -
418A PRO* 3.7 7.0 - - - +
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Residues in contact with VAL 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A THR* 4.5 6.7 - - + -
318A LEU* 3.9 28.7 - - + -
324A ILE* 3.9 4.5 - - + -
328A LEU* 3.7 13.7 - - + -
352A TYR* 3.0 44.7 + - + +
353A LEU* 3.2 7.2 + - + +
355A GLN* 1.3 73.1 - - - +
357A LEU* 1.3 61.5 + - - +
359A GLU* 3.3 1.5 + - - +
360A SER* 2.9 26.3 + - - -
411A PHE* 3.8 20.1 - - + -
413A PRO* 3.7 20.6 - - + -
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Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A HIS* 3.3 34.6 - - + +
311A LEU* 5.6 1.1 - - + -
314A THR* 3.7 29.8 - - + +
353A LEU* 3.0 42.1 + - + +
354A SER* 3.9 4.9 - - - +
356A VAL* 1.3 72.3 - - + +
358A LYS* 1.3 66.0 + - + +
360A SER* 3.3 1.6 + - - -
361A LEU* 3.0 21.7 + - - +
447A VAL* 3.8 24.9 - - + -
448A LYS* 3.9 19.1 - - + +
451A MET* 4.1 11.9 - - + -
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Residues in contact with LYS 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A GLN* 5.5 3.8 + - - -
354A SER* 3.0 37.8 + - - +
355A GLN* 3.7 5.6 - - + +
356A VAL 3.3 0.2 - - - -
357A LEU* 1.3 78.3 - - + +
359A GLU* 1.3 55.3 + - - +
361A LEU* 3.2 4.1 + - + -
362A ARG 3.1 18.2 + - - -
416A PHE* 3.8 37.5 + - + +
422A LYS* 5.7 6.5 - - - +
427A TYR* 2.8 35.3 + - + +
444A GLN* 5.1 14.6 - - - +
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Residues in contact with GLU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A GLN 3.0 18.3 + - - +
356A VAL 3.8 4.5 - - - +
357A LEU 3.3 0.2 - - - -
358A LYS* 1.3 74.3 - - - +
360A SER* 1.3 63.5 + - - +
362A ARG* 2.8 46.1 + - - -
363A LEU* 3.5 19.6 + - - +
410A THR 3.2 0.5 - - - +
411A PHE* 3.5 20.3 - - + -
412A ASN 2.6 44.2 + - - +
413A PRO* 3.9 9.6 - - + -
415A ARG* 2.9 11.9 + - - -
416A PHE* 3.6 10.7 - - + -
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Residues in contact with SER 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A HIS* 3.9 6.7 + - - -
313A PHE* 4.1 6.8 - - - +
314A THR* 2.8 42.3 + - - -
317A GLU* 5.6 0.2 - - - +
356A VAL 2.9 16.9 + - - -
357A LEU* 3.5 7.6 - - - -
358A LYS 3.3 0.2 - - - -
359A GLU* 1.3 76.8 - - - +
361A LEU* 1.3 52.7 + - - +
363A LEU 3.5 0.3 + - - -
364A TYR* 2.7 46.1 + - - +
411A PHE* 3.7 14.7 - - - -
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Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A HIS* 3.3 42.0 - - + +
357A LEU 3.0 12.3 + - - +
358A LYS* 3.2 10.1 + - + +
360A SER* 1.3 75.4 - - - +
362A ARG* 1.3 63.5 + - - +
364A TYR 4.1 2.2 - - - +
365A PRO* 3.2 26.4 - - + +
366A PRO* 3.6 28.3 - - + -
395A THR* 5.2 0.9 + - - -
427A TYR* 3.7 12.7 - - - +
429A PRO* 3.8 21.7 - - + +
430A PHE* 3.7 32.3 - - + -
444A GLN* 6.1 0.9 - - + +
505A HEM 4.3 7.4 - - + -
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Residues in contact with ARG 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A LYS 3.1 7.4 + - - +
359A GLU* 2.8 49.4 + - - +
360A SER 3.3 0.4 - - - -
361A LEU* 1.3 81.0 - - - +
363A LEU* 1.3 76.7 + - - +
365A PRO* 3.6 8.1 - - - +
395A THR* 4.4 5.3 - - - +
396A TYR 4.7 3.5 - - - +
399A GLY* 2.6 55.1 + - - -
400A ARG* 5.2 0.3 + - - -
405A PHE* 3.6 33.4 - - + +
408A PRO* 2.9 33.3 + - - +
410A THR 3.1 11.5 + - - -
415A ARG* 3.3 14.6 - - - +
416A PHE* 4.6 4.0 - - + -
427A TYR* 3.5 29.1 - - + -
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Residues in contact with LEU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A GLU* 5.4 0.2 - - - +
359A GLU 3.5 7.1 + - - +
362A ARG* 1.3 103.5 - - - +
364A TYR* 1.3 84.8 + - + +
365A PRO* 3.5 5.6 - - - +
396A TYR* 3.9 2.9 - - - -
400A ARG* 2.8 61.1 + - + +
408A PRO 3.5 18.4 - - - +
409A LEU* 4.2 16.4 - - + +
411A PHE* 4.0 35.0 - - + -
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Residues in contact with TYR 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A HIS* 5.2 1.2 + - - -
313A PHE* 3.4 49.8 - + + +
316A MET* 4.3 12.9 - - + +
317A GLU* 2.7 40.4 + - + -
320A ARG* 3.6 11.4 + - - -
360A SER* 2.7 33.6 + - - +
361A LEU* 3.7 3.3 - - - +
363A LEU* 1.3 101.5 - - + +
365A PRO* 1.3 63.1 - - - +
366A PRO* 3.3 9.9 - - - +
400A ARG* 3.7 15.3 - - - -
411A PHE* 4.7 1.8 - + - -
468A PHE 4.8 2.8 + - - -
470A LEU* 3.8 30.5 - - + -
476A LEU* 5.6 0.2 - - - -
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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