Contacts of the helix formed by residues 312 - 322 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B ILE* 4.7 2.0 - - + -
202B ASP* 4.0 21.5 - - + +
205B MSE 3.6 38.8 - - + -
206B GLY* 3.4 34.7 + - - +
207B ASP* 3.1 10.5 + - - +
212B TYR* 3.8 25.1 - + - -
287B ASP* 3.3 22.3 + - - -
288B LYS* 6.4 0.4 - - - -
311B MSE 1.3 80.5 - - - +
313B GLY* 1.3 69.1 - - - +
314B ALA 3.8 0.7 - - - -
315B ILE* 3.5 2.8 - - - +
316B HIS* 2.9 72.8 + + + -
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Residues in contact with GLY 313 (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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199B PRO 3.8 5.2 - - - -
201B ILE* 3.3 31.6 - - - -
207B ASP* 2.9 16.9 + - - -
310B ASP 4.0 2.0 + - - -
311B MSE 3.7 1.0 - - - -
312B TRP* 1.3 76.6 - - - +
314B ALA* 1.3 58.6 + - - +
316B HIS* 3.9 1.0 - - - +
317B SER* 2.8 33.8 + - - -
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Residues in contact with ALA 314 (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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199B PRO* 4.1 11.0 - - + +
301B TRP* 3.6 18.6 - - + +
302B LEU 3.3 43.1 - - - +
303B GLN* 3.3 18.4 + - + +
310B ASP 5.0 1.4 + - - -
313B GLY* 1.3 71.7 - - - +
315B ILE* 1.3 58.0 + - - +
317B SER* 3.9 0.3 - - - -
318B TYR* 2.9 30.9 + - - +
333B LEU* 4.8 2.5 - - + -
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Residues in contact with ILE 315 (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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303B GLN* 3.0 17.1 + - - +
311B MSE 3.9 9.2 - - - +
312B TRP 3.5 11.9 - - - +
314B ALA* 1.3 75.3 - - - +
316B HIS* 1.3 73.3 + - + +
318B TYR* 3.6 9.0 - - + +
319B ALA* 3.1 27.9 + - + +
333B LEU* 3.9 30.7 - - + +
335B MSE 4.2 12.6 - - + -
404B TRP* 4.1 16.8 - - + +
405B PRO* 6.1 1.8 - - + -
573B THR* 3.7 22.2 - - - +
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Residues in contact with HIS 316 (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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287B ASP* 3.8 15.5 - - + +
312B TRP* 2.9 90.9 + + + +
313B GLY 4.1 0.7 - - - +
315B ILE* 1.3 86.5 - - + +
317B SER* 1.3 64.2 + - - +
319B ALA* 3.5 6.0 + - - +
320B ALA* 3.2 22.0 + - - +
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Residues in contact with SER 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ILE* 3.5 28.4 - - - +
287B ASP* 4.0 9.0 - - - +
290B MSE 4.5 5.0 - - - +
301B TRP* 3.5 34.7 - - - -
313B GLY 2.8 21.1 + - - -
316B HIS* 1.3 74.3 - - - +
318B TYR* 1.3 65.3 + - - +
320B ALA* 3.2 14.2 + - - +
321B MSE 3.4 18.2 + - - +
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Residues in contact with TYR 318 (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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301B TRP* 3.6 18.3 - - + +
314B ALA 2.9 18.9 + - - +
315B ILE* 3.6 11.4 - - + +
317B SER* 1.3 77.6 - - - +
319B ALA* 1.3 62.3 + - + +
321B MSE 3.2 1.4 + - - -
322B GLU* 3.0 71.3 + - + +
328B ASN* 5.4 0.2 + - - -
331B ASN* 3.1 25.5 + - - +
332B TYR 3.5 24.9 - - - -
333B LEU* 3.6 39.5 - - + -
387B PRO* 4.7 1.7 + - - +
388B VAL* 3.7 18.0 - - + +
402B LYS 5.1 0.5 + - - -
403B ALA* 4.6 2.4 - - - -
404B TRP 3.9 24.9 + - - -
638B CA 4.5 0.2 - - - -
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Residues in contact with ALA 319 (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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315B ILE* 3.1 19.7 + - + +
316B HIS* 3.9 8.3 - - + +
317B SER 3.3 0.2 - - - -
318B TYR* 1.3 83.9 - - + +
320B ALA* 1.3 61.9 + - - +
322B GLU* 4.6 3.4 - - - +
323B PRO* 3.3 21.3 - - - +
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ASP* 3.4 26.5 - - + +
290B MSE 4.4 2.0 - - + -
291B ALA* 3.7 20.7 - - + +
316B HIS 3.2 14.0 + - - +
317B SER* 3.2 12.5 + - - +
319B ALA* 1.3 78.3 - - - +
321B MSE 1.3 58.0 + - - +
323B PRO* 4.4 3.9 - - - +
324B ARG* 3.3 16.8 + - - -
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Residues in contact with MSE 321 (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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184B LEU* 5.9 2.5 - - + -
290B MSE 3.7 46.4 - - + +
293B THR* 3.4 34.3 - - + +
294B PRO 4.3 4.5 - - - +
295B LEU* 3.5 33.6 - - + +
299B THR* 5.5 5.2 - - - +
301B TRP* 3.8 21.8 - - - -
317B SER 3.4 10.1 + - - +
318B TYR 3.2 1.4 + - - -
319B ALA 3.2 0.2 - - - -
320B ALA* 1.3 80.8 - - - +
322B GLU* 1.3 63.6 + - - +
323B PRO* 3.3 4.0 - - - -
324B ARG* 3.1 19.5 + - - +
331B ASN* 3.7 20.2 - - - +
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Residues in contact with GLU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B TYR* 3.0 46.7 + - + +
319B ALA* 4.6 2.7 - - - +
321B MSE 1.3 76.4 - - - +
323B PRO* 1.3 68.8 - - + +
325B ASP* 3.0 22.9 + - - +
328B ASN* 3.0 12.5 + - - +
331B ASN* 3.0 23.6 + - - +
402B LYS 4.7 3.1 - - - +
403B ALA* 5.8 2.2 - - + +
404B TRP 5.6 1.3 - - - +
638B CA 2.6 30.4 - - - -
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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