Contacts of the strand formed by residues 299 - 304 (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 THR 299 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D LEU* 3.6 35.4 - - + +
194D ALA* 3.3 4.1 - - - +
196D PRO* 3.7 12.8 - - + -
297D VAL 2.8 17.6 + - - -
298D PRO* 1.3 72.2 + - - +
300D MSE 1.3 63.9 + - - +
301D TRP* 3.6 33.7 - - + +
321D MSE 5.5 4.5 - - - -
330D LEU 2.9 11.0 + - - -
331D ASN* 3.5 5.7 - - - +
332D TYR* 2.8 27.9 + - - +
371D PHE* 4.5 3.1 - - - -
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Residues in contact with MSE 300 (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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194D ALA 2.9 7.7 + - - -
195D VAL* 3.5 22.3 - - + +
196D PRO* 3.2 18.6 - - - +
299D THR* 1.3 73.3 - - - +
301D TRP* 1.3 60.7 - - - +
302D LEU* 3.5 2.4 + - + -
332D TYR* 3.8 17.9 - - + -
334D VAL* 3.7 21.3 - - + -
363D PHE* 3.7 32.8 - - + -
367D VAL* 3.8 12.8 - - + -
368D LEU* 4.8 3.1 - - - -
371D PHE* 3.7 36.8 - - + -
385D THR* 3.4 32.8 - - + -
386D PRO 5.3 1.1 - - - +
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Residues in contact with TRP 301 (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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181D VAL* 3.5 32.3 - - + -
184D LEU* 4.5 2.5 - - + -
196D PRO* 3.7 19.5 - - + -
199D PRO* 4.1 13.5 - - + -
290D MSE 4.0 17.5 - - + -
299D THR* 3.6 22.5 - - + +
300D MSE 1.3 70.6 - - - +
302D LEU* 1.3 58.0 + - - +
314D ALA* 3.6 22.2 - - + +
317D SER* 3.5 35.9 - - - -
318D TYR* 3.7 17.6 - - + +
321D MSE 3.8 22.4 - - - -
331D ASN* 3.1 27.4 + - - -
332D TYR 2.9 16.8 + - - +
333D LEU* 3.4 5.1 - - + +
334D VAL* 2.9 26.2 + - - +
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Residues in contact with LEU 302 (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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195D VAL* 4.8 1.8 - - + -
196D PRO 3.1 11.3 + - - +
197D GLU* 3.5 26.5 - - + +
198D SER* 2.6 32.1 + - - +
300D MSE 4.4 4.9 - - - +
301D TRP* 1.3 76.4 - - - +
303D GLN* 1.3 68.5 + - - +
314D ALA* 3.3 9.5 - - - +
334D VAL* 3.2 27.4 - - + +
338D TRP* 3.9 15.5 - - + -
343D VAL* 4.0 18.8 - - + -
363D PHE* 3.2 42.6 - - + -
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Residues in contact with GLN 303 (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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198D SER* 3.6 19.1 - - - +
302D LEU* 1.3 84.1 - - - +
304D GLY* 1.3 73.5 + - - +
307D ASP* 3.9 3.8 - - - +
310D ASP 4.1 2.9 + - - +
311D MSE 2.9 44.4 + - - +
314D ALA* 3.3 14.9 + - + +
315D ILE* 3.0 26.0 + - - +
334D VAL 3.1 5.7 + - - +
335D MSE 3.2 55.1 - - + +
336D GLY 3.3 4.2 + - - -
338D TRP* 3.8 4.6 - - - -
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Residues in contact with GLY 304 (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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198D SER* 4.1 0.4 + - - -
303D GLN* 1.3 97.9 + - - +
305D LEU* 1.3 66.2 + - - -
306D TRP 3.1 2.5 - - - -
307D ASP* 3.3 19.8 + - - +
335D MSE 5.2 0.4 - - - -
336D GLY 3.6 7.0 - - - -
338D TRP* 3.4 26.7 - - - -
339D ARG 4.9 1.1 + - - -
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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