Contacts of the helix formed by residues 314 - 327 (chain D) in PDB entry 1M7X
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 THR 314 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209D GLU* 3.3 17.7 - - - +
265D TYR* 3.6 7.4 - - - -
308D PRO* 5.2 2.0 - - - -
310D ARG* 3.3 25.1 - - - +
313D GLY* 1.3 75.7 - - - -
315D ARG* 1.3 65.5 + - - +
316D ASP* 3.7 8.5 + - - +
317D ASP* 2.6 34.9 + - - +
318D PHE 3.1 16.5 + - - -
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Residues in contact with ARG 315 (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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208D PHE* 4.1 21.2 + - - +
209D GLU* 3.2 24.2 + - + +
221D CYS* 3.8 17.6 - - - +
222D GLY 2.6 46.0 + - - +
223D LEU 3.9 1.8 + - - -
224D PRO* 3.4 30.5 - - - +
308D PRO* 4.0 26.2 - - + -
314D THR* 1.3 76.8 - - - +
316D ASP* 1.3 89.2 + - - +
318D PHE* 3.2 4.5 + - - +
319D ARG* 2.8 27.6 + - - +
392D TYR* 5.0 0.6 + - - -
397D PHE* 3.7 16.7 - - + -
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Residues in contact with ASP 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D PRO* 4.8 5.4 - - - +
266D ARG* 5.0 2.8 + - - -
314D THR* 3.2 8.6 + - - +
315D ARG* 1.3 109.8 + - - +
317D ASP* 1.3 59.3 + - - +
319D ARG* 3.6 11.0 - - + +
320D TYR* 3.0 26.9 + - - +
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Residues in contact with ASP 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D SER* 6.0 1.0 - - - -
265D TYR* 3.5 24.5 - - + +
266D ARG* 3.0 36.7 + - - +
310D ARG* 5.2 0.3 + - - -
312D PHE 5.1 0.4 - - - -
313D GLY* 3.1 9.1 - - - -
314D THR* 2.6 46.2 + - - +
315D ARG 3.1 0.2 - - - -
316D ASP* 1.3 76.2 - - - +
318D PHE* 1.3 66.0 + - - +
320D TYR* 3.0 7.0 + - - +
321D PHE* 3.0 16.8 + - - +
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Residues in contact with PHE 318 (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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250D LEU* 5.0 0.4 - - + -
265D TYR* 3.4 40.3 - + + -
286D LEU* 3.9 17.9 - - + -
289D ILE* 3.7 25.8 - - + -
308D PRO* 3.8 25.8 - - + -
314D THR 3.1 4.0 + - - +
315D ARG 3.4 7.0 - - - +
317D ASP* 1.3 80.7 - - - +
319D ARG* 1.3 62.5 + - - +
321D PHE* 2.9 20.2 + + - +
322D ILE* 2.9 41.7 + - + +
334D LEU* 5.4 0.9 - - + -
393D TRP* 3.7 26.0 - + - -
397D PHE* 3.8 16.2 - + + -
399D ILE* 4.8 6.5 - - + -
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Residues in contact with ARG 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D PRO* 3.6 16.1 - - + +
225D GLU* 3.2 21.6 + - - +
226D LYS 4.5 1.8 + - - -
227D VAL* 3.0 23.9 - - - +
315D ARG 2.8 16.3 + - - +
316D ASP* 3.6 15.0 - - + +
317D ASP 3.2 0.2 - - - -
318D PHE* 1.3 78.6 - - - +
320D TYR* 1.3 56.1 + - - +
322D ILE* 3.2 3.4 + - - +
323D ASP* 2.9 54.8 + - - +
396D ARG 2.7 29.7 + - - -
397D PHE* 4.1 28.7 - - + +
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Residues in contact with TYR 320 (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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266D ARG* 3.7 58.4 + - + +
269D ALA* 4.1 19.3 - - + -
316D ASP 3.0 15.6 + - - +
317D ASP 3.0 7.8 + - - +
319D ARG* 1.3 77.5 - - - +
321D PHE* 1.3 58.5 + - - +
323D ASP* 3.8 10.1 - - + +
324D ALA* 2.9 30.3 + - + +
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Residues in contact with PHE 321 (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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250D LEU* 4.3 10.1 - - + -
265D TYR* 3.6 28.9 - + + +
268D LEU* 3.7 28.3 - - + -
269D ALA* 3.6 18.8 - - - -
272D LEU* 4.0 12.1 - - + -
273D VAL* 3.8 10.3 - - + +
284D LEU* 3.8 26.0 - - + -
286D LEU* 4.2 18.2 - - + -
317D ASP 3.0 9.9 + - - +
318D PHE* 2.9 20.9 + + - +
320D TYR* 1.3 75.5 - - - +
322D ILE* 1.3 86.5 + - + +
324D ALA* 3.1 2.6 + - - +
325D ALA* 2.9 23.7 + - + +
332D VAL* 5.3 1.1 - - + -
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Residues in contact with ILE 322 (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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286D LEU* 4.6 0.2 - - + -
318D PHE* 2.9 54.8 + - + +
319D ARG* 3.6 7.9 - - - +
321D PHE* 1.3 86.6 - - + +
323D ASP* 1.3 64.1 + - - +
325D ALA* 3.0 8.3 + - - +
326D HIS* 2.9 45.3 + - + +
332D VAL* 3.9 27.6 - - + -
397D PHE* 3.1 27.8 - - + +
398D GLY 4.2 4.9 - - - +
399D ILE* 4.4 6.7 - - + +
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Residues in contact with ASP 323 (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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227D VAL* 4.9 4.2 - - - +
319D ARG* 2.9 54.6 + - - +
320D TYR* 3.8 9.7 - - + +
322D ILE* 1.3 78.8 - - - +
324D ALA* 1.3 57.4 + - - +
326D HIS* 3.3 14.1 + - - +
327D ALA* 2.9 29.3 + - - +
397D PHE 4.6 1.0 - - - +
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Residues in contact with ALA 324 (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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269D ALA* 3.9 30.1 - - + +
273D VAL* 3.8 4.7 - - + +
320D TYR* 2.9 28.1 + - + +
321D PHE 3.4 5.6 - - - +
322D ILE 3.1 0.4 - - - -
323D ASP* 1.3 73.3 - - - +
325D ALA* 1.3 66.5 + - - +
327D ALA* 3.2 8.6 + - - +
328D ALA* 3.2 20.8 + - - +
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Residues in contact with ALA 325 (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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273D VAL* 3.9 21.9 - - + +
284D LEU* 4.8 7.6 - - + -
321D PHE* 2.9 14.7 + - + +
322D ILE* 3.2 9.4 - - - +
324D ALA* 1.3 76.7 - - - +
326D HIS* 1.3 54.1 + - - +
328D ALA* 2.7 28.6 + - - +
329D GLY 3.3 4.7 + - - -
330D LEU* 3.4 16.2 + - + +
332D VAL* 3.6 25.8 - - + -
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Residues in contact with HIS 326 (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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227D VAL* 4.8 5.2 - - + +
233D ARG* 3.4 46.5 + - - +
322D ILE* 2.9 33.2 + - + +
323D ASP* 3.5 15.1 + - - +
325D ALA* 1.3 76.4 - - - +
327D ALA* 1.3 60.1 + - - +
329D GLY* 3.3 12.6 + - - -
330D LEU 3.6 9.9 - - - -
332D VAL* 4.2 5.6 - - + +
398D GLY* 2.8 29.5 + - - -
400D ASP* 2.8 30.2 + - - -
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Residues in contact with ALA 327 (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 LYS* 5.7 0.5 + - - -
323D ASP 2.9 16.6 + - - +
324D ALA* 3.6 9.9 - - - +
325D ALA 3.1 0.2 - - - -
326D HIS* 1.3 76.3 - - - +
328D ALA* 1.3 59.2 + - - +
329D GLY 3.2 0.6 + - - -
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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