Contacts of the helix formed by residues 314 - 328 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209B GLU* 3.7 23.1 - - - +
265B TYR* 3.7 5.3 - - - -
308B PRO* 5.5 1.3 - - - -
310B ARG* 4.0 12.8 - - - +
313B GLY* 1.3 77.4 - - - -
315B ARG* 1.3 64.5 + - - +
316B ASP* 3.0 11.1 + - - +
317B ASP* 3.0 40.8 + - - +
318B PHE 3.0 9.4 + - - -
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Residues in contact with ARG 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B PHE* 3.7 33.5 + - - +
209B GLU* 3.6 21.4 + - + +
221B CYS* 3.9 16.6 - - + +
222B GLY 3.1 34.8 + - - +
223B LEU 3.9 3.0 + - - -
224B PRO* 3.4 32.7 - - - +
308B PRO* 3.7 27.5 + - + +
314B THR* 1.3 74.2 - - - +
316B ASP* 1.3 81.8 + - - +
318B PHE* 3.6 2.5 + - - +
319B ARG* 3.1 20.1 + - - +
392B TYR* 5.1 0.8 + - - -
397B PHE* 3.4 21.7 - - - -
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Residues in contact with ASP 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B PRO* 5.0 5.7 - - - +
266B ARG* 3.9 7.4 + - - +
314B THR* 3.0 9.5 + - - +
315B ARG* 1.3 106.2 + - - +
317B ASP* 1.3 61.6 + - - +
318B PHE 3.2 0.2 - - - -
319B ARG* 3.4 8.4 + - - +
320B TYR* 2.9 26.5 + - - +
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Residues in contact with ASP 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B SER* 6.0 0.5 - - - -
265B TYR* 3.3 25.4 - - + +
266B ARG* 3.3 36.9 + - + +
310B ARG* 4.9 0.7 + - - -
312B PHE 4.7 0.7 - - - +
313B GLY* 3.4 8.1 - - - -
314B THR* 3.0 38.2 + - - +
316B ASP* 1.3 78.5 - - - +
318B PHE* 1.3 62.4 + - - +
320B TYR* 3.2 6.9 + - - +
321B PHE 3.1 16.3 + - - -
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Residues in contact with PHE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B TYR* 3.4 42.8 - + + -
286B LEU* 4.4 9.6 - - + -
289B ILE* 3.8 26.9 - - + -
308B PRO* 3.7 15.9 - - + -
314B THR 3.0 6.6 + - - +
315B ARG 3.6 7.4 - - - +
317B ASP* 1.3 75.7 - - - +
319B ARG* 1.3 59.1 + - - +
321B PHE* 2.9 27.3 + + - +
322B ILE* 3.0 40.7 + - + +
334B LEU* 5.4 0.2 - - + -
393B TRP* 3.8 18.6 - + - -
397B PHE* 3.4 39.9 - + + -
399B ILE* 4.5 8.5 - - + -
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Residues in contact with ARG 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B PRO* 3.7 18.7 - - + +
225B GLU* 4.1 14.3 - - - +
226B LYS 4.2 10.1 + - - +
227B VAL* 3.1 26.4 - - - +
315B ARG 3.1 13.8 + - - +
316B ASP* 3.4 11.0 + - - +
318B PHE* 1.3 79.0 - - - +
320B TYR* 1.3 62.8 + - - +
322B ILE* 3.2 3.2 + - - +
323B ASP* 2.8 61.8 + - - +
396B ARG 3.2 20.0 + - - -
397B PHE* 3.9 33.2 - - + +
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Residues in contact with TYR 320 (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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647A GLU* 4.8 8.3 + - - -
266B ARG* 3.3 55.6 - - + +
269B ALA* 4.0 22.7 - - + -
270B ASP* 4.4 14.2 + - - -
316B ASP 2.9 13.8 + - - +
317B ASP 3.2 9.4 - - - +
319B ARG* 1.3 77.1 - - - +
321B PHE* 1.3 57.6 + - - +
323B ASP* 3.5 8.7 + - + +
324B ALA* 2.9 34.1 + - + +
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Residues in contact with PHE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B LEU* 4.3 9.9 - - + -
265B TYR* 3.7 18.6 - + + +
268B LEU* 3.7 30.7 - - + -
269B ALA* 3.6 27.1 - - - -
272B LEU* 3.8 20.2 - - + -
273B VAL* 4.0 9.4 - - + +
284B LEU* 3.9 18.8 - - + -
286B LEU* 3.9 24.7 - - + -
317B ASP 3.1 10.2 + - - +
318B PHE* 2.9 20.5 + + - +
320B TYR* 1.3 76.1 - - - +
322B ILE* 1.3 79.4 + - + +
324B ALA* 3.2 3.1 + - - +
325B ALA* 3.0 22.6 + - + +
332B VAL* 5.4 1.6 - - + -
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Residues in contact with ILE 322 (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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286B LEU* 4.7 0.4 - - + -
318B PHE* 3.0 50.2 + - + +
319B ARG* 3.2 7.6 + - - +
321B PHE* 1.3 85.5 - - + +
323B ASP* 1.3 64.0 + - - +
325B ALA* 3.3 6.2 + - - +
326B HIS* 3.1 44.2 + - + +
332B VAL* 4.3 20.4 - - + -
397B PHE* 3.0 29.4 - - + +
398B GLY 4.3 3.6 - - - -
399B ILE* 4.0 15.3 - - + -
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Residues in contact with ASP 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B VAL* 4.8 7.8 - - - +
319B ARG* 2.8 55.3 + - - +
320B TYR* 3.8 9.0 - - + +
322B ILE* 1.3 74.4 - - - +
324B ALA* 1.3 65.3 + - - +
326B HIS* 3.4 14.1 + - - +
327B ALA* 3.0 25.7 + - - +
397B PHE 4.8 1.2 - - - +
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Residues in contact with ALA 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ALA* 3.6 31.9 - - + +
273B VAL* 3.8 4.8 - - + +
320B TYR* 2.9 26.2 + - + +
321B PHE 3.3 7.0 - - - +
323B ASP* 1.3 76.7 - - - +
325B ALA* 1.3 62.2 + - - +
327B ALA* 3.2 7.6 + - - +
328B ALA* 3.0 22.3 + - - +
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B VAL* 3.7 22.3 - - + +
284B LEU* 4.7 7.2 - - + -
321B PHE* 3.0 14.5 + - + +
322B ILE 3.3 9.2 + - - +
324B ALA* 1.3 75.9 - - - +
326B HIS* 1.3 56.8 + - - +
328B ALA* 3.0 13.5 + - - +
329B GLY 3.1 0.5 + - - -
330B LEU* 2.9 32.9 + - + +
332B VAL* 3.7 24.7 - - + -
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Residues in contact with HIS 326 (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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227B VAL* 5.1 2.0 - - + +
233B ARG* 3.4 48.5 + - - +
322B ILE* 3.1 32.7 + - + +
323B ASP* 3.7 13.7 + - - +
325B ALA* 1.3 77.0 - - - +
327B ALA* 1.3 57.2 + - - +
329B GLY* 3.1 16.1 + - - -
330B LEU 3.3 19.7 - - - -
332B VAL* 4.2 5.0 - - + +
398B GLY* 3.0 27.3 + - - -
400B ASP* 2.5 25.7 + - - -
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Residues in contact with ALA 327 (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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235A LYS* 5.8 1.6 + - - -
614A LYS* 5.7 2.8 + - - -
323B ASP 3.0 17.7 + - - +
324B ALA* 3.2 7.6 + - - +
326B HIS* 1.3 75.0 - - - +
328B ALA* 1.3 60.0 + - - +
329B GLY 3.1 2.6 + - - -
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Residues in contact with ALA 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B VAL* 3.1 36.1 - - + -
274B PRO* 5.7 0.7 - - + -
277B LYS* 3.2 46.6 - - + +
324B ALA 3.0 5.6 + - - +
325B ALA 3.0 5.8 + - - +
327B ALA* 1.3 77.3 - - - +
329B GLY* 1.3 59.6 + - - +
330B LEU* 3.5 1.8 - - + -
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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
------------------------------------------------------------
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