Contacts of the helix formed by residues 317 - 328 (chain A) in PDB entry 2MX7
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 ASP 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A THR* 2.6 52.6 + - - +
311A MET* 4.1 4.9 - - - +
312A THR* 4.2 19.5 - - + +
315A GLY 3.5 2.1 + - - +
316A ILE* 1.3 78.8 - - - +
318A THR* 1.3 56.3 + - - +
319A ALA* 3.3 29.7 + - - +
320A LYS* 3.5 17.2 + - - +
339A TRP* 4.6 1.6 - - - -
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Residues in contact with THR 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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316A ILE* 4.2 0.6 - - - +
317A ASP* 1.3 71.5 + - - +
319A ALA* 1.3 67.7 - - + +
320A LYS 3.2 0.4 - - - -
321A LEU* 2.9 25.5 + - - +
322A TYR* 3.0 44.9 + - + +
335A LEU 5.2 1.2 + - - -
339A TRP* 3.1 42.9 + - + +
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Residues in contact with ALA 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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317A ASP* 3.1 22.2 + - - +
318A THR* 1.3 81.8 - - + +
320A LYS* 1.3 60.5 + - + +
322A TYR* 3.5 15.2 - - - -
323A PRO* 3.3 18.0 - - - +
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Residues in contact with LYS 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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309A THR 4.0 6.9 + - - +
310A THR* 2.9 35.7 + - - +
311A MET 4.8 7.7 + - - -
312A THR* 4.8 10.2 - - - +
317A ASP* 3.5 13.7 + - - +
318A THR 3.2 0.4 - - - -
319A ALA* 1.3 75.0 - - + +
321A LEU* 1.3 64.4 - - - +
322A TYR 3.1 2.9 - - - -
323A PRO* 3.0 17.7 - - + +
324A ILE* 3.1 27.7 - - + +
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Residues in contact with LEU 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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306A ILE* 4.6 9.6 - - + -
309A THR* 5.3 1.8 - - + -
310A THR* 2.8 30.1 + - + +
318A THR* 3.1 26.5 - - - +
320A LYS* 1.3 77.6 - - - +
322A TYR* 1.3 63.7 + - + +
324A ILE* 4.7 1.1 - - - -
325A LEU* 3.1 52.0 + - + +
335A LEU* 4.4 16.6 - - + +
339A TRP* 3.5 44.4 - - + -
362A ILE* 4.9 4.3 - - + -
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Residues in contact with TYR 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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318A THR* 3.0 56.9 + - + +
319A ALA* 3.5 15.3 - - - -
321A LEU* 1.3 77.7 - - + +
323A PRO* 1.4 59.3 - - + +
326A MET* 2.7 52.2 + - + +
332A ARG* 4.3 18.8 - - + -
335A LEU* 4.0 14.4 - - + +
336A GLY* 4.1 23.4 - - - -
339A TRP* 6.0 0.3 - - - +
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Residues in contact with PRO 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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319A ALA 3.3 12.3 - - - +
320A LYS* 3.0 25.4 - - - +
322A TYR* 1.4 91.6 - - + +
324A ILE* 1.3 59.3 + - + +
326A MET* 3.1 18.8 - - + +
327A SER* 2.9 30.7 + - - -
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Residues in contact with ILE 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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309A THR* 3.5 43.5 - - + +
310A THR* 4.2 1.1 - - - -
320A LYS* 3.1 29.8 + - + +
321A LEU* 4.3 2.0 - - - +
322A TYR 3.3 0.8 - - - -
323A PRO* 1.3 78.7 - - + +
325A LEU* 1.3 60.9 + - + +
327A SER* 3.0 10.2 + - - -
328A SER* 2.8 23.1 + - - -
388A LEU* 3.6 27.5 - - + +
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Residues in contact with LEU 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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306A ILE* 6.0 2.5 - - + -
309A THR* 5.4 2.7 - - + -
321A LEU* 3.1 48.0 + - + +
324A ILE* 1.3 80.5 - - + +
326A MET* 1.3 60.3 + - - +
328A SER* 2.9 20.6 + - - -
330A LEU* 3.0 29.5 + - + +
335A LEU* 3.7 18.4 - - + -
362A ILE* 3.5 35.2 - - + -
366A GLN* 3.8 4.7 - - - +
388A LEU* 3.6 30.7 - - + -
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Residues in contact with MET 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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322A TYR* 2.7 37.3 + - + +
323A PRO* 3.1 27.1 - - + +
325A LEU* 1.3 73.6 - - - +
327A SER* 1.3 58.0 + - - +
329A GLY* 3.2 16.5 + - - -
330A LEU 2.9 21.5 + - - +
332A ARG* 3.6 34.5 - - + +
335A LEU* 3.6 4.2 - - + +
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Residues in contact with SER 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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323A PRO 2.9 19.7 + - - -
324A ILE* 3.2 8.3 - - - -
326A MET* 1.3 75.6 - - - +
328A SER* 1.3 54.5 + - - +
329A GLY* 2.9 8.9 + - - -
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Residues in contact with SER 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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324A ILE 2.8 9.0 + - - -
325A LEU* 2.9 21.9 + - - -
327A SER* 1.3 75.9 - - - +
329A GLY* 1.3 58.6 + - - +
330A LEU* 4.7 4.1 - - - +
366A GLN* 2.9 31.8 + - - +
387A THR 3.7 6.6 + - - -
388A LEU* 4.0 13.6 - - - +
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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