Contacts of the helix formed by residues 345 - 358 (chain D) in PDB entry 5MR4
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 ASN 345 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271D PHE* 4.8 0.4 - - - -
275D CYS* 2.8 28.5 + - - +
276D ARG* 4.4 1.4 - - - +
277D ALA* 3.5 13.3 - - - +
340D ARG 3.6 6.1 - - - +
341D ASP* 2.8 36.8 + - - +
344D GLU* 1.3 74.2 - - - +
346D PRO* 1.3 67.6 - - - +
347D CYS* 2.8 21.7 + - - +
348D LEU* 3.7 17.1 - - + +
349D ARG* 2.9 23.6 + - - +
501D FMT 3.6 8.6 + - - +
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Residues in contact with PRO 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D ALA* 3.9 18.4 - - + -
279D TYR* 6.4 2.0 - - + -
284D SER* 4.0 19.1 - - - +
344D GLU 3.4 10.3 - - - +
345D ASN* 1.3 86.5 - - - +
347D CYS* 1.3 56.5 + - - +
349D ARG* 4.1 12.8 - - + -
350D ASN* 2.9 41.7 + - - +
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Residues in contact with CYS 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D CYS* 3.4 31.6 - - - +
277D ALA* 4.2 1.3 - - - -
283D THR 4.1 4.9 - - - -
284D SER* 3.4 19.2 - - - +
285D CYS* 2.0 57.1 - - - -
286D PRO* 4.1 1.6 - - - -
293D CYS* 4.0 8.5 - - - -
345D ASN* 2.8 17.7 + - - +
346D PRO* 1.3 72.1 - - - +
348D LEU* 1.3 59.9 + - - +
350D ASN* 3.2 1.7 + - - +
351D ALA* 2.8 26.0 + - - +
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Residues in contact with LEU 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D PHE* 4.3 5.2 - - + -
275D CYS* 4.4 2.7 - - + -
293D CYS* 3.9 24.9 - - - -
294D LEU* 5.1 2.7 - - + -
297D TYR* 3.6 34.5 - - + -
319D VAL* 3.7 18.2 - - + -
341D ASP 4.2 4.9 - - - +
342D PHE* 3.6 31.6 - - - +
345D ASN* 3.3 19.1 + - + +
347D CYS* 1.3 79.1 - - - +
349D ARG* 1.3 63.6 + - - +
351D ALA* 3.3 1.2 + - - +
352D ILE* 3.0 47.7 + - + +
501D FMT 4.3 2.5 - - - +
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Residues in contact with ARG 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D ILE* 5.9 5.8 - - + +
345D ASN 2.9 18.1 + - - +
346D PRO* 3.7 10.8 - - + +
348D LEU* 1.3 78.9 - - - +
350D ASN* 1.3 82.6 + - - +
352D ILE* 4.0 3.9 - - - +
353D GLN* 3.0 59.6 + - - +
501D FMT 4.1 16.7 + - - +
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Residues in contact with ASN 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282D VAL 5.0 1.0 - - - +
283D THR* 2.8 24.8 - - - +
284D SER* 4.5 2.3 + - - -
290D TYR* 3.4 22.8 + - + +
346D PRO* 2.9 27.1 + - - +
347D CYS 3.7 3.4 - - - +
349D ARG* 1.3 108.1 - - - +
351D ALA* 1.3 57.7 + - - +
353D GLN* 3.8 4.3 + - - +
354D ALA* 2.8 33.3 + - - +
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Residues in contact with ALA 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D CYS* 4.6 0.4 - - - -
290D TYR* 3.5 34.2 - - + +
293D CYS* 4.5 7.4 - - - -
294D LEU* 3.9 26.1 - - + +
347D CYS 2.8 17.3 + - - +
348D LEU* 3.8 7.0 - - - +
349D ARG 3.3 0.2 - - - -
350D ASN* 1.3 78.5 - - - +
352D ILE* 1.3 61.7 + - - +
354D ALA* 3.4 1.6 + - - +
355D PHE* 3.1 23.6 + - - +
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Residues in contact with ILE 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D PHE* 3.7 38.7 - - + +
294D LEU* 3.9 12.3 - - + -
297D TYR* 5.0 3.1 - - + -
309D TYR* 3.9 17.5 - - - +
317D ILE* 4.0 28.5 - - + -
319D VAL* 4.5 22.9 - - + -
348D LEU* 3.0 39.2 + - + +
349D ARG* 4.0 4.0 - - - +
351D ALA* 1.3 74.4 - - - +
353D GLN* 1.3 63.8 + - - +
355D PHE* 3.4 4.9 + - - +
356D GLY* 3.3 17.5 + - - -
501D FMT 5.8 1.8 - - - -
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Residues in contact with GLN 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D SER* 5.8 0.3 - - - -
317D ILE* 5.8 5.4 - - + -
349D ARG* 3.0 57.3 + - - +
350D ASN* 3.9 4.7 - - - +
352D ILE* 1.3 79.3 - - - +
354D ALA* 1.3 60.8 + - - +
356D GLY* 3.5 2.4 + - - -
357D ASN* 3.1 46.4 + - - +
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Residues in contact with ALA 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D TYR* 3.5 32.3 - - + +
350D ASN 2.8 21.9 + - - +
351D ALA 4.0 0.9 - - - +
352D ILE 3.4 0.2 - - - -
353D GLN* 1.3 69.6 - - - +
355D PHE* 1.3 68.1 + - - +
357D ASN* 3.6 7.0 + - - +
358D GLY* 3.4 13.3 + - - -
359D THR 3.6 25.1 + - - +
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Residues in contact with PHE 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D SER 4.8 3.1 - - - -
214D GLU* 5.5 3.6 - - - -
217D TYR* 3.5 47.6 - + + -
218D ARG* 3.7 16.4 - - + -
221D PHE* 3.8 21.1 - + + -
222D CYS* 5.5 0.9 - - - -
291D GLN* 4.1 12.6 - - - -
294D LEU* 3.9 23.6 - - + -
351D ALA 3.1 17.2 + - - +
352D ILE 3.7 5.2 - - - +
353D GLN 3.3 0.2 - - - -
354D ALA* 1.3 78.0 - - - +
356D GLY* 1.3 63.6 + - - +
358D GLY* 3.2 14.6 + - - -
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Residues in contact with GLY 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D HIS* 4.4 9.5 + - - -
221D PHE 3.7 17.2 + - - -
222D CYS* 4.6 1.3 - - - -
223D SER* 3.3 32.7 + - - -
352D ILE 3.3 8.8 + - - -
353D GLN* 3.9 2.7 - - - -
355D PHE* 1.3 80.9 - - - +
357D ASN* 1.3 61.4 + - - +
358D GLY 3.5 0.3 + - - -
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Residues in contact with ASN 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D SER* 4.8 7.6 + - - -
353D GLN* 3.1 41.2 + - - +
354D ALA* 4.0 8.0 - - - +
355D PHE 3.2 0.4 - - - -
356D GLY* 1.3 77.0 - - - +
358D GLY* 1.3 59.6 - - - +
359D THR* 3.3 9.3 + - - +
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Residues in contact with GLY 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D ALA 3.4 0.6 + - - -
355D PHE 3.2 15.1 + - - -
356D GLY 3.3 1.6 - - - -
357D ASN* 1.3 76.1 - - - +
359D THR* 1.3 63.1 + - - +
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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