Contacts of the strand formed by residues 336 - 341 (chain B) in PDB entry 1MK9
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 CYS 336 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B ILE* 3.8 0.7 - - - -
333B THR* 3.0 45.2 + - - +
335B GLU* 1.3 81.2 - - + +
337B VAL* 1.3 76.0 + - - +
338B MET* 3.9 30.1 - - - -
350B GLU* 4.3 14.4 - - - +
351B TRP 3.0 15.7 - - - +
352B SER* 4.7 0.2 - - - -
353B LEU* 4.0 5.0 - - - +
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Residues in contact with VAL 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU* 4.0 17.0 - - + -
331B GLY 3.4 3.6 - - - +
332B ILE* 3.4 27.8 - - + -
336B CYS* 1.3 78.8 - - - +
338B MET* 1.3 63.8 + - - +
350B GLU* 3.4 4.0 - - - +
351B TRP* 2.8 55.8 + - + +
353B LEU* 4.5 9.6 - - + -
356B ILE* 3.9 28.5 - - + -
368B LEU* 4.1 14.1 - - + -
370B PHE* 4.6 2.2 - - + -
392B ILE* 4.9 2.0 - - + -
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Residues in contact with MET 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LYS* 3.5 29.2 - - + +
307B THR* 4.9 0.4 - - - -
310B VAL* 4.1 22.7 - - + -
312B PHE* 4.3 3.4 - - - -
329B LEU 3.6 0.5 - - - +
330B LEU* 3.5 10.2 - - - +
331B GLY* 2.8 54.9 + - - +
333B THR* 5.4 2.0 - - + -
336B CYS* 3.9 22.0 - - - -
337B VAL* 1.3 75.8 - - - +
339B ARG* 1.3 64.8 + - - +
340B VAL* 4.0 19.5 - - + -
347B VAL* 4.0 12.8 - - + -
349B GLN 3.3 11.2 - - - +
350B GLU* 4.2 19.1 - - + +
351B TRP* 4.8 0.2 - - - -
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Residues in contact with ARG 339 (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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317B GLU* 2.8 37.0 + - - +
319B MET* 4.4 7.4 - - - +
328B ARG* 4.0 16.2 - - + +
329B LEU 3.7 3.1 - - - -
330B LEU* 5.1 0.7 - - - +
338B MET* 1.3 71.8 - - - +
340B VAL* 1.3 57.3 + - - +
347B VAL* 3.6 1.6 - - - -
348B ILE* 2.6 60.3 + - + +
349B GLN* 3.0 45.3 + - + +
351B TRP* 3.2 39.9 - - + -
378B TYR* 3.5 19.8 - - + +
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Residues in contact with VAL 340 (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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229B PRO* 5.5 0.4 - - + -
307B THR* 4.7 5.8 - - + -
312B PHE* 3.7 25.1 - - + -
328B ARG* 3.1 5.1 - - - +
329B LEU* 2.8 60.3 + - + +
338B MET* 4.0 20.4 - - + -
339B ARG* 1.3 77.7 - - - +
341B ASP* 1.3 74.4 + - - +
345B LYS* 3.7 24.9 - - + +
346B GLU 3.6 2.2 - - - -
347B VAL* 4.3 13.9 - - + -
348B ILE* 3.7 3.8 - - - -
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Residues in contact with ASP 341 (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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328B ARG* 3.4 19.4 + - - +
329B LEU* 3.4 4.7 - - - +
340B VAL* 1.3 72.9 - - - +
342B GLU* 1.3 63.9 + - - +
343B LYS* 3.1 11.5 + - - +
344B THR* 2.6 51.9 + - - +
345B LYS* 2.9 28.2 + - - +
346B GLU* 3.2 16.2 + - + +
348B ILE* 3.3 16.8 - - + +
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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