Contacts of the strand formed by residues 331 - 336 (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 ASN 331 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B LEU* 4.2 7.3 - - + +
299B THR* 3.5 3.3 - - - +
301B TRP* 3.0 26.0 + - - -
318B TYR* 3.1 38.6 + - - -
321B MSE 3.7 17.7 - - - +
322B GLU* 3.0 29.9 + - - +
325B ASP* 3.0 14.9 + - + +
330B LEU* 1.3 80.8 - - - +
332B TYR* 1.3 64.9 + - - +
387B PRO 4.3 0.3 - - - +
638B CA 2.2 30.8 - - - -
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Residues in contact with TYR 332 (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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298B PRO* 5.3 0.4 - - + -
299B THR 2.8 19.0 + - - +
300B MSE 4.0 21.8 - - + -
301B TRP* 2.9 25.6 + - - +
318B TYR* 3.5 10.9 - - - -
328B ASN 3.9 6.0 + - - -
329B THR* 3.3 49.2 + - - +
330B LEU 4.0 2.2 - - - -
331B ASN* 1.3 78.2 - - - +
333B LEU* 1.3 61.9 + - - +
334B VAL* 5.6 0.2 - - + -
371B PHE* 3.8 23.0 - + - -
375B TYR* 5.3 1.2 + - - -
385B THR* 3.4 41.4 + - + -
386B PRO 3.3 19.1 - - - +
387B PRO* 3.5 15.7 - - + +
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B TRP* 3.4 13.0 - - + +
314B ALA* 4.6 1.8 - - + +
315B ILE* 3.9 21.8 - - + +
318B TYR* 3.6 34.8 - - + -
332B TYR* 1.3 76.8 - - - +
334B VAL* 1.3 72.8 + - - +
335B MSE 3.9 28.7 - - + +
386B PRO 5.0 0.5 - - - +
387B PRO 3.2 5.7 + - - +
388B VAL* 3.4 14.1 - - + -
389B PHE 2.9 25.2 + - - -
390B ILE* 5.2 1.3 - - + -
404B TRP* 3.8 39.7 - - + -
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Residues in contact with VAL 334 (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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300B MSE 3.7 31.6 - - + -
301B TRP 2.9 7.4 + - - +
302B LEU* 3.3 29.8 - - + -
303B GLN 3.1 23.1 + - - -
332B TYR* 5.6 0.2 - - + -
333B LEU* 1.3 79.8 - - - +
335B MSE 1.3 69.4 + - - +
338B TRP* 4.2 12.3 - - + -
363B PHE* 3.9 25.8 - - + -
367B VAL* 5.0 0.7 - - + -
389B PHE* 3.2 25.4 - - + +
398B TRP* 4.6 1.3 - - + -
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Residues in contact with MSE 335 (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* 3.2 45.3 - - + +
304B GLY 4.6 2.0 - - - +
305B LEU* 4.1 19.1 - - + +
311B MSE 5.9 0.9 - - - -
315B ILE* 4.2 13.5 - - + -
333B LEU* 3.9 28.7 - - + -
334B VAL* 1.3 79.5 - - - +
336B GLY* 1.3 61.0 + - - +
389B PHE 3.0 8.4 + - - -
390B ILE* 3.4 23.8 - - + +
391B TYR* 3.0 25.1 + - - +
398B TRP* 3.7 1.5 - - - -
404B TRP* 4.7 0.4 - - - -
573B THR* 3.8 39.5 - - + +
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Residues in contact with GLY 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLN 3.3 8.5 + - - -
304B GLY* 3.6 0.7 - - - -
305B LEU* 2.9 27.1 + - - +
335B MSE 1.3 73.5 - - - +
337B PRO* 1.3 68.2 - - - +
338B TRP* 2.9 30.9 + - - -
391B TYR* 4.2 0.2 - - - -
398B TRP* 3.6 13.0 - - - -
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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