Contacts of the helix formed by residues 312 - 322 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201C ILE* 4.7 1.6 - - + -
202C ASP* 3.9 23.4 + - + +
205C MSE 3.6 43.3 - - + -
206C GLY* 3.4 30.4 + - - +
207C ASP* 3.2 10.9 + - - +
212C TYR* 3.9 24.7 - + - -
287C ASP* 3.2 23.1 + - - -
311C MSE 1.3 80.3 - - - +
313C GLY* 1.3 70.3 + - - +
314C ALA 3.8 0.7 - - - -
315C ILE* 3.5 3.1 - - - +
316C HIS* 2.8 73.6 + + + +
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Residues in contact with GLY 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C PRO 3.8 5.6 - - - -
201C ILE* 3.3 31.4 - - - +
207C ASP* 2.9 17.3 + - - -
310C ASP 4.0 1.6 + - - -
311C MSE 3.7 1.2 - - - -
312C TRP* 1.3 77.8 - - - +
314C ALA* 1.3 62.0 + - - +
316C HIS* 3.9 1.2 - - - +
317C SER* 2.9 28.1 + - - -
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Residues in contact with ALA 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C PRO* 4.0 12.5 - - + +
301C TRP* 3.6 19.0 - - + +
302C LEU 3.3 43.1 - - - +
303C GLN* 3.4 16.4 + - + +
310C ASP 4.9 1.6 + - - -
313C GLY* 1.3 72.1 - - - +
315C ILE* 1.3 58.0 + - - +
317C SER* 3.4 0.9 + - - -
318C TYR* 2.9 30.7 + - - +
333C LEU* 4.8 2.7 - - + -
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Residues in contact with ILE 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303C GLN* 3.1 17.1 + - - +
311C MSE 3.9 8.1 - - - +
312C TRP 3.5 11.7 - - - +
314C ALA* 1.3 75.7 - - - +
316C HIS* 1.3 73.6 + - + +
318C TYR* 3.5 8.5 + - + +
319C ALA* 3.1 26.9 + - + +
333C LEU* 3.7 32.5 - - + +
335C MSE 4.1 14.1 - - + -
404C TRP* 4.0 17.0 - - + +
405C PRO* 6.2 0.7 - - + -
573C THR* 3.8 20.4 - - - +
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Residues in contact with HIS 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C ASP* 3.7 15.4 - - + +
311C MSE 5.5 0.2 - - - -
312C TRP* 2.8 90.5 + + + +
313C GLY 4.0 0.7 - - - +
315C ILE* 1.3 88.5 - - + +
317C SER* 1.3 64.4 + - - +
319C ALA* 3.5 6.2 + - - +
320C ALA* 3.2 22.5 + - - +
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Residues in contact with SER 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C ILE* 3.4 29.8 - - - +
287C ASP* 3.8 10.3 - - - +
290C MSE 4.5 5.4 - - - +
301C TRP* 3.5 35.6 + - - -
313C GLY 2.9 20.2 + - - -
316C HIS* 1.3 74.0 - - - +
318C TYR* 1.3 66.7 + - - +
320C ALA* 3.3 11.3 + - - +
321C MSE 3.5 20.3 + - - +
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Residues in contact with TYR 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C TRP* 3.7 18.1 - + + -
314C ALA 2.9 18.0 + - - +
315C ILE* 3.6 10.5 - - + +
317C SER* 1.3 77.4 - - - +
319C ALA* 1.3 61.4 + - + +
321C MSE 3.3 0.9 + - - -
322C GLU* 3.0 70.3 + - + +
331C ASN* 3.0 26.3 + - - +
332C TYR 3.5 24.0 - - - -
333C LEU* 3.6 39.7 - - + -
387C PRO* 4.7 2.5 + - - +
388C VAL* 3.7 16.6 - - + +
402C LYS 5.0 0.7 + - - -
403C ALA* 4.6 2.9 - - - -
404C TRP* 3.9 25.3 + - + -
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Residues in contact with ALA 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C ILE* 3.1 16.7 + - + +
316C HIS* 3.5 7.2 + - - +
317C SER 3.3 0.2 - - - -
318C TYR* 1.3 87.9 - - + +
320C ALA* 1.3 61.4 + - - +
322C GLU* 4.1 4.3 - - - -
323C PRO* 3.3 21.8 - - - +
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Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C ASP* 3.4 27.8 - - + +
290C MSE 4.6 1.3 - - + -
291C ALA* 3.6 20.2 - - + +
316C HIS 3.2 16.9 + - - +
317C SER* 3.7 7.9 - - - +
318C TYR 3.3 0.6 - - - -
319C ALA* 1.3 75.8 - - - +
321C MSE 1.3 58.7 + - - +
323C PRO* 4.4 4.0 - - - +
324C ARG* 3.5 17.0 + - - -
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Residues in contact with MSE 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C LEU* 5.9 2.0 - - + -
290C MSE 3.6 38.8 - - + +
293C THR* 3.3 33.9 - - + +
294C PRO 4.3 4.3 - - - +
295C LEU* 3.5 37.5 - - + +
299C THR* 5.5 6.1 - - - +
301C TRP* 3.8 30.7 - - - -
317C SER 3.5 11.2 - - - +
318C TYR 3.3 1.4 + - - -
319C ALA 3.2 0.2 - - - -
320C ALA* 1.3 77.4 - - - +
322C GLU* 1.3 64.6 + - - +
323C PRO* 3.4 4.0 - - - -
324C ARG* 3.2 17.5 + - - +
331C ASN* 3.7 18.2 - - - +
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Residues in contact with GLU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C TYR* 3.0 45.8 + - + +
319C ALA* 4.5 2.5 - - - +
321C MSE 1.3 76.8 - - - +
323C PRO* 1.3 69.6 - - + +
325C ASP* 3.0 23.4 + - - +
328C ASN* 3.1 10.6 - - - +
331C ASN* 2.9 23.6 + - - +
402C LYS 4.8 3.5 - - - +
403C ALA* 5.8 2.0 - - + +
404C TRP 5.7 1.8 - - - +
638C CA 2.6 29.4 - - - -
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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