Contacts of the helix formed by residues 312 - 322 (chain D) in PDB entry 1MPX
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 TRP 312 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201D ILE* 4.6 1.8 - - + -
202D ASP* 3.9 21.0 + - + +
205D MSE 3.5 43.7 - - + -
206D GLY* 3.5 31.6 + - - -
207D ASP* 3.1 10.8 + - - +
212D TYR* 3.6 26.5 - + - -
287D ASP* 3.3 22.5 + - - -
311D MSE 1.3 80.8 - - - +
313D GLY* 1.3 69.5 + - - +
314D ALA 3.8 0.2 - - - -
315D ILE* 3.5 2.1 - - - +
316D HIS* 2.8 72.5 + + + -
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Residues in contact with GLY 313 (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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199D PRO 3.8 5.2 - - - -
201D ILE* 3.3 34.9 - - - +
207D ASP* 2.9 13.3 + - - -
310D ASP 4.1 1.6 + - - -
311D MSE 3.7 1.0 - - - -
312D TRP* 1.3 77.7 - - - +
314D ALA* 1.3 62.0 + - - +
316D HIS* 4.0 0.9 - - - +
317D SER* 3.0 29.2 + - - -
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Residues in contact with ALA 314 (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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199D PRO* 4.1 10.8 - - + +
301D TRP* 3.6 17.4 - - + +
302D LEU* 3.3 44.4 - - - +
303D GLN* 3.3 18.1 + - + +
310D ASP 5.0 1.2 + - - -
313D GLY* 1.3 72.4 - - - +
315D ILE* 1.3 58.2 + - - +
317D SER 3.9 0.5 - - - -
318D TYR* 3.0 31.2 + - - +
333D LEU* 4.8 2.7 - - + -
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Residues in contact with ILE 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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303D GLN* 3.0 19.0 + - - +
311D MSE 3.9 9.0 - - - +
312D TRP 3.5 12.1 - - - +
314D ALA* 1.3 75.7 - - - +
316D HIS* 1.3 79.1 + - + +
318D TYR* 3.5 8.3 + - + +
319D ALA* 3.2 23.3 + - + +
333D LEU* 3.9 31.6 - - + +
335D MSE 3.9 15.7 - - + -
404D TRP* 4.0 17.3 - - + +
405D PRO* 6.3 0.7 - - + -
573D THR* 3.8 19.1 - - - +
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Residues in contact with HIS 316 (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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287D ASP* 3.8 15.3 - - + +
312D TRP* 2.8 87.9 + + + +
313D GLY 4.1 1.1 - - - +
315D ILE* 1.3 92.2 - - + +
317D SER* 1.3 61.2 + - - +
319D ALA* 3.5 5.9 + - - +
320D ALA* 3.1 26.2 + - - +
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Residues in contact with SER 317 (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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201D ILE* 3.4 28.6 - - - +
287D ASP* 3.8 9.6 - - - +
290D MSE 4.6 5.2 - - - +
301D TRP* 3.5 34.1 + - - -
313D GLY 3.0 18.4 + - - -
316D HIS* 1.3 74.7 - - - +
318D TYR* 1.3 64.9 + - - +
320D ALA* 3.3 11.4 + - - +
321D MSE 3.4 21.3 + - - +
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Residues in contact with TYR 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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301D TRP* 3.7 18.1 - - + -
314D ALA 3.0 17.8 + - - +
315D ILE* 3.7 11.2 - - + +
317D SER* 1.3 78.4 - - - +
319D ALA* 1.3 63.6 + - + +
321D MSE 3.3 0.5 + - - -
322D GLU* 2.9 70.1 + - + +
331D ASN* 3.0 27.0 + - - +
332D TYR 3.4 24.2 - - - -
333D LEU* 3.6 40.4 - - + -
387D PRO* 4.6 2.1 + - - +
388D VAL* 3.6 17.4 - - + +
402D LYS 5.0 0.7 + - - -
403D ALA* 4.5 2.9 - - - -
404D TRP* 4.0 24.6 + - + -
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Residues in contact with ALA 319 (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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315D ILE* 3.2 17.4 + - + +
316D HIS* 3.8 7.6 - - + +
317D SER 3.3 0.2 - - - -
318D TYR* 1.3 86.8 - - + +
320D ALA* 1.3 61.4 + - - +
322D GLU* 4.1 4.3 - - - -
323D PRO* 3.3 21.0 - - - +
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Residues in contact with ALA 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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287D ASP* 3.4 26.7 - - + +
290D MSE 4.5 2.2 - - + -
291D ALA* 3.7 20.4 - - + +
316D HIS 3.1 16.5 + - - +
317D SER* 3.6 8.7 - - - +
318D TYR 3.2 0.6 - - - -
319D ALA* 1.3 76.9 - - - +
321D MSE 1.3 59.4 + - - +
323D PRO* 4.3 4.4 - - - +
324D ARG* 3.5 16.3 + - - -
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Residues in contact with MSE 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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184D LEU* 5.9 2.0 - - + -
290D MSE 3.6 49.1 - - + +
293D THR* 3.5 34.1 - - + +
294D PRO 4.6 3.6 - - - +
295D LEU* 3.4 35.9 - - + +
299D THR* 5.5 5.6 - - - -
301D TRP* 3.8 17.5 - - - -
317D SER 3.5 11.4 - - - +
318D TYR 3.3 1.6 + - - -
319D ALA 3.2 0.2 - - - -
320D ALA* 1.3 77.6 - - - +
322D GLU* 1.3 62.7 + - - +
323D PRO* 3.4 4.0 - - - -
324D ARG* 3.2 18.3 + - - +
331D ASN* 3.6 23.3 - - - +
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Residues in contact with GLU 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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318D TYR* 2.9 46.1 + - + +
319D ALA* 4.6 2.7 - - - +
321D MSE 1.3 77.1 - - - +
323D PRO* 1.3 69.0 - - + +
325D ASP* 3.1 22.6 + - - +
328D ASN* 3.1 10.9 - - - +
331D ASN* 2.9 24.5 + - - +
402D LYS 4.8 3.6 - - - +
403D ALA* 5.8 2.6 - - + +
404D TRP 5.7 1.6 - - - +
638D CA 2.5 31.1 - - - -
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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