Contacts of the helix formed by residues 314 - 328 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A GLU* 3.7 21.1 - - - +
265A TYR* 3.8 2.2 - - - -
308A PRO* 5.6 0.9 - - - -
310A ARG* 4.8 3.1 - - - +
313A GLY* 1.3 76.0 - - - -
315A ARG* 1.3 54.7 + - - +
316A ASP* 3.0 13.2 + - - +
317A ASP* 2.8 52.6 + - - +
318A PHE* 2.8 17.7 + - - +
632D ASP* 5.8 4.5 - - - +
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Residues in contact with ARG 315 (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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208A PHE* 3.8 27.5 + - - +
209A GLU* 2.8 30.4 + - + +
221A CYS* 3.4 19.7 - - + +
222A GLY* 3.3 43.4 + - - +
223A LEU 3.6 3.2 + - - +
224A PRO* 3.6 28.3 - - - +
308A PRO* 4.0 23.9 + - + -
314A THR* 1.3 70.6 - - - +
316A ASP* 1.3 82.8 + - - +
318A PHE* 3.6 2.5 + - - +
319A ARG* 3.0 19.4 + - - +
392A TYR* 5.2 0.4 + - - -
397A PHE* 3.3 23.8 - - + -
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Residues in contact with ASP 316 (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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224A PRO* 5.2 3.1 - - - +
266A ARG* 4.3 7.5 + - - +
314A THR* 3.0 10.1 + - - +
315A ARG* 1.3 108.7 + - - +
317A ASP* 1.3 64.2 + - - +
318A PHE 3.2 0.4 - - - -
319A ARG* 3.6 10.2 - - - +
320A TYR* 3.1 22.3 + - - +
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Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A SER* 5.9 0.7 - - - -
265A TYR* 3.4 23.8 - - + +
266A ARG* 2.8 42.7 + - - +
312A PHE 4.5 0.7 - - - +
313A GLY* 3.5 8.6 - - - -
314A THR* 2.8 46.1 + - - +
316A ASP* 1.3 76.9 - - - +
318A PHE* 1.3 56.0 + - - +
320A TYR* 3.1 8.7 - - - +
321A PHE 3.1 20.1 + - - -
632D ASP* 5.4 5.5 - - - +
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Residues in contact with PHE 318 (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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265A TYR* 3.5 41.7 - + + -
286A LEU* 4.0 22.9 - - + -
289A ILE* 3.3 34.5 - - + -
308A PRO* 3.6 16.8 - - + -
314A THR 2.8 10.8 + - - +
315A ARG 3.6 7.0 - - - +
316A ASP 3.2 0.2 - - - -
317A ASP* 1.3 73.3 - - - +
319A ARG* 1.3 64.3 + - - +
320A TYR 3.1 1.8 - - - -
321A PHE* 2.9 18.5 + + - +
322A ILE* 3.1 32.8 + - + +
334A LEU* 4.7 4.5 - - + -
393A TRP* 4.0 7.0 - + - -
397A PHE* 3.3 39.3 - + + -
399A ILE* 5.2 1.3 - - + -
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Residues in contact with ARG 319 (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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224A PRO* 3.6 16.3 - - + +
225A GLU* 3.9 16.0 - - - +
226A LYS 4.2 13.7 + - - +
227A VAL* 3.1 30.3 - - - +
315A ARG 3.0 18.9 + - - +
316A ASP* 3.6 14.6 - - - +
318A PHE* 1.3 75.3 - - - +
320A TYR* 1.3 57.4 + - - +
322A ILE* 3.2 4.3 + - - +
323A ASP* 2.9 51.1 + - - +
396A ARG 3.3 21.6 + - - -
397A PHE* 4.0 25.4 - - + +
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Residues in contact with TYR 320 (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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266A ARG* 2.9 52.0 - - + +
269A ALA* 3.6 26.7 - - + -
270A ASP* 4.7 9.2 + - - -
316A ASP 3.1 13.8 + - - +
317A ASP 3.1 12.3 - - - +
319A ARG* 1.3 77.7 - - - +
321A PHE* 1.3 54.0 + - - +
323A ASP* 3.2 12.9 + - + +
324A ALA* 2.7 38.2 + - + +
636D ARG* 5.4 9.4 + - - -
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Residues in contact with PHE 321 (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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250A LEU* 4.6 6.5 - - + -
265A TYR* 3.6 33.9 - + + +
268A LEU* 3.9 26.2 - - + -
269A ALA* 3.7 11.7 - - - -
272A LEU* 3.9 13.0 - - + -
273A VAL* 4.0 12.5 - - + +
284A LEU* 3.7 25.4 - - + -
286A LEU* 3.9 27.4 - - + -
317A ASP 3.1 6.7 + - - +
318A PHE* 2.9 20.8 + + - +
320A TYR* 1.3 86.2 - - - +
322A ILE* 1.3 75.9 + - + +
324A ALA* 3.3 3.1 + - - +
325A ALA* 3.0 23.3 + - + +
332A VAL* 5.3 0.9 - - + -
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Residues in contact with ILE 322 (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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286A LEU* 4.6 0.4 - - + -
318A PHE* 3.1 41.2 + - + +
319A ARG* 3.6 7.4 - - - +
321A PHE* 1.3 81.6 - - + +
323A ASP* 1.3 70.1 + - - +
325A ALA* 3.0 7.0 + - - +
326A HIS* 3.0 44.6 + - + +
332A VAL* 3.4 36.8 - - + -
397A PHE* 3.2 28.7 - - + +
398A GLY 4.3 4.3 - - - -
399A ILE* 4.6 5.8 - - + +
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Residues in contact with ASP 323 (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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227A VAL* 4.9 6.2 - - - +
319A ARG* 2.9 48.7 + - - +
320A TYR* 3.2 14.7 + - + +
322A ILE* 1.3 77.6 - - - +
324A ALA* 1.3 63.7 + - - +
326A HIS* 3.1 13.8 + - - +
327A ALA* 2.9 23.0 + - - +
397A PHE 4.9 1.9 - - - +
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Residues in contact with ALA 324 (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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269A ALA* 3.9 27.1 - - + +
273A VAL* 3.8 7.4 - - + +
320A TYR* 2.7 28.6 + - + +
321A PHE 3.5 5.8 - - - +
323A ASP* 1.3 72.5 - - - +
325A ALA* 1.3 61.8 + - - +
327A ALA* 3.1 9.6 + - - +
328A ALA* 3.0 23.9 + - - +
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Residues in contact with ALA 325 (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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273A VAL* 3.7 22.4 - - + +
284A LEU* 4.6 6.7 - - + -
321A PHE* 3.0 15.1 + - + +
322A ILE 3.0 9.2 + - - +
324A ALA* 1.3 74.8 - - - +
326A HIS* 1.3 54.7 + - - +
328A ALA* 3.3 2.9 + - - +
329A GLY 3.2 4.0 + - - -
330A LEU* 2.7 42.4 + - + +
332A VAL* 3.6 26.2 - - + -
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Residues in contact with HIS 326 (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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227A VAL* 5.2 3.5 - - + +
233A ARG* 3.3 37.7 + - + +
322A ILE* 3.0 35.2 + - + +
323A ASP* 3.5 12.0 + - - +
325A ALA* 1.3 72.3 - - - +
327A ALA* 1.3 59.0 + - - +
328A ALA 3.0 4.9 - - - -
329A GLY* 2.8 20.6 + - - -
330A LEU 3.0 29.2 - - - +
332A VAL* 4.4 3.2 + - + -
397A PHE 4.7 0.2 - - - -
398A GLY* 3.1 24.7 - - - -
400A ASP* 2.7 22.9 + - - -
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Residues in contact with ALA 327 (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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277A LYS* 5.4 1.2 + - - -
323A ASP 2.9 13.4 + - - +
324A ALA* 3.1 12.8 + - - +
326A HIS* 1.3 76.2 - - - +
328A ALA* 1.3 58.1 + - - +
329A GLY 3.3 0.4 + - - -
235B LYS* 5.4 5.4 + - - -
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Residues in contact with ALA 328 (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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273A VAL* 3.2 35.9 - - + -
274A PRO* 5.4 0.4 - - + -
277A LYS* 3.7 42.8 - - + +
324A ALA 3.0 4.2 + - - +
325A ALA 3.5 4.3 - - - +
326A HIS 3.0 1.0 - - - -
327A ALA* 1.3 79.7 - - - +
329A GLY* 1.3 59.6 + - - +
330A LEU* 4.4 5.7 - - + +
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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