Contacts of the strand formed by residues 299 - 304 (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 THR 299 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C LEU* 3.6 29.3 - - + +
194C ALA* 3.3 4.2 - - - +
196C PRO* 3.7 18.6 - - + -
297C VAL 2.9 17.9 + - - -
298C PRO* 1.3 72.8 + - - +
300C MSE 1.3 62.0 + - - +
301C TRP* 3.6 34.0 + - + +
321C MSE 5.5 4.6 - - - -
330C LEU 2.9 10.9 + - - -
331C ASN* 3.5 5.9 - - - +
332C TYR* 2.8 30.0 + - - +
371C PHE* 4.4 1.1 - - - -
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Residues in contact with MSE 300 (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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194C ALA 3.0 7.9 + - - -
195C VAL* 3.4 22.8 - - + +
196C PRO* 3.2 19.1 - - - +
299C THR* 1.3 72.0 - - - +
301C TRP* 1.3 61.1 + - - +
302C LEU* 3.5 2.5 + - + -
332C TYR* 3.7 16.8 - - + -
334C VAL* 3.7 21.8 - - + -
363C PHE* 3.7 32.3 - - + -
367C VAL* 3.8 12.6 - - + -
368C LEU* 4.9 3.1 - - - -
371C PHE* 3.5 37.7 - - + -
385C THR* 3.4 32.5 - - + -
386C PRO 5.5 0.4 - - - +
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Residues in contact with TRP 301 (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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181C VAL* 3.6 33.0 - - + -
184C LEU* 4.5 3.4 - - + -
196C PRO* 3.7 18.2 - - + -
199C PRO* 4.2 5.8 - - + -
290C MSE 4.0 17.0 - - + -
299C THR* 3.6 20.8 - - + +
300C MSE 1.3 69.8 - - - +
302C LEU* 1.3 59.4 + - - +
314C ALA* 3.6 29.8 - - + +
317C SER* 3.5 35.0 - - - -
318C TYR* 3.7 19.1 - - + +
321C MSE 3.8 23.3 - - - -
331C ASN* 3.0 27.4 + - - -
332C TYR 2.9 17.4 + - - +
333C LEU* 3.4 5.6 - - + +
334C VAL* 2.9 25.1 + - - +
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Residues in contact with LEU 302 (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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195C VAL* 4.7 1.6 - - + -
196C PRO 3.1 11.9 + - - +
197C GLU* 3.5 31.0 - - + +
198C SER* 2.7 32.4 + - - +
300C MSE 4.4 4.9 - - - +
301C TRP* 1.3 75.4 - - - +
303C GLN* 1.3 66.7 + - - +
314C ALA* 3.3 8.7 - - - +
334C VAL* 3.2 27.6 - - + +
338C TRP* 3.9 7.2 - - + -
343C VAL* 3.9 25.8 - - + -
363C PHE* 3.2 42.4 - - + -
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Residues in contact with GLN 303 (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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198C SER* 3.6 18.6 - - - +
302C LEU* 1.3 80.7 - - - +
304C GLY* 1.3 74.1 + - - +
307C ASP* 4.0 3.8 - - - +
310C ASP 4.0 2.9 + - - +
311C MSE 2.8 44.8 + - - +
314C ALA* 3.4 14.1 + - + +
315C ILE* 3.1 26.4 + - - +
334C VAL 3.1 5.9 + - - +
335C MSE 3.3 54.7 - - + +
336C GLY 3.4 4.2 + - - -
338C TRP* 3.8 8.5 - - - -
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Residues in contact with GLY 304 (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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198C SER* 4.1 0.4 + - - -
303C GLN* 1.3 96.5 + - - +
305C LEU* 1.3 64.9 + - - -
306C TRP 3.1 2.0 - - - -
307C ASP* 3.2 22.2 + - - +
335C MSE 5.1 0.2 - - - -
336C GLY 3.7 5.2 - - - -
338C TRP* 3.4 27.6 - - - -
339C ARG 4.7 1.3 + - - -
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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