Contacts of the helix formed by residues 304 - 319 (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 HIS 304 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B THR* 4.2 22.6 - - + +
188B ALA* 3.3 31.2 - - + +
189B MET* 3.7 33.8 - - + +
192B LEU* 4.2 4.5 - - + -
215B VAL* 4.1 27.3 - - + +
300B PHE 2.6 27.4 + - - -
301B ILE* 3.3 18.3 + - + -
303B GLY* 1.3 80.4 - - - +
305B GLU* 1.3 76.2 + - + +
306B THR 3.5 1.6 - - - -
307B SER* 4.0 3.8 - - - -
308B ALA* 3.0 26.3 + - + +
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Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B THR* 5.3 6.1 + - - +
215B VAL* 5.0 0.3 - - - +
219B LEU* 3.5 27.3 - - + +
301B ILE* 2.9 28.2 + - + +
302B ALA 4.4 0.4 - - - -
304B HIS* 1.3 93.8 + - + +
306B THR* 1.3 58.6 + - - +
308B ALA* 3.6 3.7 - - - +
309B ASN* 3.0 50.8 + - - +
473B GLN* 5.8 0.9 - - - +
474B ALA* 5.9 0.8 - - + +
475B THR* 3.6 21.4 + - + +
477B LYS* 2.7 30.8 + - - +
506B GJZ 4.4 7.6 - - + -
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Residues in contact with THR 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ILE 4.7 0.2 + - - -
302B ALA 3.6 3.3 + - - -
305B GLU* 1.3 78.3 - - - +
307B SER* 1.3 57.0 + - - +
309B ASN* 3.5 5.7 + - - -
310B HIS* 3.0 29.6 + - - +
366B PRO* 3.6 21.9 - - + +
367B ALA* 4.2 4.7 - - + -
475B THR* 4.0 16.4 - - + -
505B HEM 3.1 44.3 - - + +
506B GJZ 3.5 37.1 - - + -
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Residues in contact with SER 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ALA* 4.5 4.9 - - - -
303B GLY 4.1 1.1 + - - -
304B HIS 3.6 10.0 + - - -
305B GLU 3.3 0.6 - - - -
306B THR* 1.3 81.0 + - - +
308B ALA* 1.3 62.0 + - - +
310B HIS* 3.4 2.3 + - - +
311B LEU* 3.1 31.2 + - - +
443B ALA* 4.1 2.4 - - - +
446B GLU* 2.7 35.7 + - - -
447B VAL* 4.3 7.0 - - - +
505B HEM 3.5 34.0 - - - +
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLN* 5.2 2.1 - - - +
184B LEU* 3.9 7.3 - - - +
185B THR* 3.7 39.7 - - + +
188B ALA* 3.9 9.5 - - + +
304B HIS* 3.0 18.6 + - + +
305B GLU* 3.6 6.3 - - - +
307B SER* 1.3 74.4 - - - +
309B ASN* 1.3 67.7 + - - +
311B LEU* 3.4 7.2 + - - +
312B ALA* 3.0 24.5 + - - +
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Residues in contact with ASN 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLN* 4.2 4.8 + - - -
185B THR* 5.9 0.4 + - - -
305B GLU* 3.0 44.4 + - - +
306B THR* 3.6 5.8 - - - +
308B ALA* 1.3 76.9 - - - +
310B HIS* 1.3 58.3 + - - +
312B ALA* 3.2 6.5 + - - +
313B PHE* 2.9 37.0 + - + -
366B PRO* 3.7 11.8 - - + +
475B THR* 2.7 27.6 + - - -
476B LEU 3.3 19.3 - - - +
477B LYS* 3.5 24.8 - - + +
478B PRO* 4.6 0.2 - - - +
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Residues in contact with HIS 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B THR 3.0 19.2 + - - +
307B SER 3.7 3.8 - - - +
309B ASN* 1.3 76.1 - - - +
311B LEU* 1.3 57.3 + - - +
313B PHE* 3.4 4.8 + - - +
314B THR* 2.7 45.2 + - - -
357B LEU* 3.3 43.7 + - + +
360B SER* 3.9 8.0 + - - -
361B LEU* 3.3 29.0 + - + +
364B TYR 5.3 1.0 + - - -
366B PRO* 4.0 11.7 - - + -
430B PHE* 5.7 0.4 - + - -
447B VAL* 3.9 23.5 - - + +
505B HEM 3.7 24.5 - - + -
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 3.7 29.2 - - + +
187B THR* 6.0 1.6 - - + -
188B ALA* 5.3 5.4 - - + +
307B SER* 3.1 26.5 + - - +
308B ALA* 3.6 8.5 - - - +
310B HIS* 1.3 77.4 - - - +
312B ALA* 1.3 57.1 + - - +
314B THR* 3.3 5.4 + - - -
315B VAL* 2.9 33.6 + - - +
357B LEU* 5.8 1.3 - - + -
446B GLU* 5.9 2.2 - - + -
447B VAL* 3.9 27.4 - - + +
450B VAL* 3.9 29.6 - - + -
451B MET* 3.7 32.9 - - + +
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLN* 3.8 33.9 - - - +
184B LEU* 3.7 16.7 - - + +
308B ALA 3.0 18.1 + - - +
309B ASN 3.7 3.6 - - - +
311B LEU* 1.3 72.3 - - - +
313B PHE* 1.3 61.2 + - - +
315B VAL* 4.0 2.0 - - - +
316B MET* 3.0 30.8 + - - +
478B PRO* 4.2 10.3 - - + -
482B VAL* 4.0 8.9 - - + +
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Residues in contact with PHE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B ASN* 2.9 27.1 + - + +
310B HIS* 3.6 6.1 - - - +
312B ALA* 1.3 77.2 - - - +
314B THR* 1.3 58.5 + - - +
316B MET* 3.5 18.5 + - + +
317B GLU* 3.0 30.0 + - - +
360B SER* 4.1 5.8 + - - +
364B TYR* 3.4 52.0 - + + +
366B PRO* 4.6 2.7 - - + -
470B LEU* 3.6 34.5 - - + -
476B LEU* 3.5 24.7 - - + -
477B LYS* 3.3 26.9 - - - -
478B PRO* 3.7 17.3 - - + -
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Residues in contact with THR 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B HIS* 2.7 29.4 + - - -
311B LEU* 3.5 6.7 - - - -
312B ALA 3.2 0.2 - - - -
313B PHE* 1.3 74.3 - - - +
315B VAL* 1.3 60.3 + - - +
317B GLU* 3.3 2.9 + - - +
318B LEU* 2.9 56.8 + - + +
356B VAL* 4.5 9.9 - - + -
357B LEU* 3.8 22.7 - - + +
360B SER* 2.9 24.1 + - - +
411B PHE* 5.9 0.7 - - + -
451B MET* 4.0 12.6 - - + -
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Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B MET* 4.2 28.9 - - + -
184B LEU* 4.1 15.5 - - + -
311B LEU 2.9 19.6 + - - +
312B ALA* 4.1 3.4 - - - +
314B THR* 1.3 74.3 - - - +
316B MET* 1.3 63.8 + - - +
318B LEU* 3.4 6.7 + - - +
319B SER* 3.3 21.5 + - - -
451B MET* 4.1 21.5 - - + -
454B LEU* 4.3 14.1 - - + -
460B PHE* 4.5 20.9 - - + +
482B VAL* 4.3 6.1 - - + -
484B CYS* 4.6 4.3 - - - -
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Residues in contact with MET 316 (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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312B ALA 3.0 19.9 + - - +
313B PHE* 3.7 33.0 - - + +
315B VAL* 1.3 77.5 - - - +
317B GLU* 1.3 62.7 + - - +
319B SER* 2.9 25.9 + - - -
364B TYR* 4.2 17.5 - - + -
462B LEU* 5.1 7.0 - - + -
467B ARG 4.1 7.6 - - - +
468B PHE* 3.3 62.4 - - + +
469B GLY 4.7 0.2 - - - +
478B PRO* 4.1 21.5 - - - -
482B VAL* 3.8 22.6 - - + +
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Residues in contact with GLU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B PHE 3.0 18.4 + - - +
314B THR* 3.3 4.2 + - - +
316B MET* 1.3 76.9 - - + +
318B LEU* 1.3 63.3 + - - +
320B ARG* 2.9 52.3 + - - +
321B GLN* 3.1 37.4 + - - +
360B SER* 5.6 0.2 - - - +
363B LEU* 5.9 0.4 - - - -
364B TYR* 2.8 35.1 + - + -
411B PHE* 3.5 45.2 - - + +
468B PHE* 4.6 2.9 - - - -
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Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B THR* 2.9 39.9 + - + +
315B VAL* 4.0 4.7 - - - +
316B MET 3.3 0.2 - - - -
317B GLU* 1.3 76.8 - - + +
319B SER* 1.3 60.5 + - - +
320B ARG 3.2 0.9 + - - -
321B GLN* 3.3 15.6 + - + +
322B PRO* 5.1 0.3 - - - +
324B ILE* 3.9 28.7 - - + -
325B VAL* 3.3 27.8 - - + +
328B LEU* 3.7 22.4 - - + -
353B LEU* 6.1 0.2 - - + -
356B VAL* 3.9 12.1 - - + -
411B PHE* 4.3 11.9 - - + -
451B MET* 3.9 17.3 - - + -
455B LEU* 5.3 3.1 - - + -
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Residues in contact with SER 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B VAL* 3.3 11.1 + - - -
316B MET 2.9 18.3 + - - -
317B GLU 3.1 0.6 + - - -
318B LEU* 1.3 76.8 - - - +
320B ARG* 1.3 58.2 + - - +
321B GLN 3.5 1.1 + - - -
322B PRO* 5.1 3.0 - - - +
460B PHE* 4.9 17.5 - - - +
461B ARG* 5.4 0.7 - - - -
462B LEU* 3.8 37.5 + - - +
468B PHE* 3.9 9.9 - - - -
484B CYS* 5.7 2.0 - - - -
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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