Contacts of the strand formed by residues 357 - 363 (chain B) in PDB entry 1MWT
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 LEU 357 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B THR* 2.7 21.8 + - - +
328B ILE* 3.1 16.3 + - + +
348B THR* 6.5 0.2 - - - -
349B ALA 3.8 5.4 - - - +
350B ILE* 3.8 27.8 - - + -
356B GLU* 1.3 70.7 - - - +
358B LEU* 1.3 61.6 + - - +
359B ALA 3.4 0.7 - - - -
360B LEU* 4.0 20.9 - - + -
498B PHE* 3.8 29.6 - - + -
529B VAL* 4.0 24.5 - - + -
532B LEU* 6.4 0.4 - - + -
547B PRO* 4.1 2.7 - - + -
548B HIS* 2.9 39.9 + - - +
549B LEU* 4.0 14.6 - - + +
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Residues in contact with LEU 358 (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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157B ARG* 3.9 23.6 - - - +
327B THR 3.8 16.8 - - - +
328B ILE* 3.6 3.6 - - - +
329B ASP* 2.9 34.6 + - + +
332B VAL* 4.0 5.1 - - + +
349B ALA* 2.9 18.2 + - + +
350B ILE 3.8 14.1 - - - +
351B HIS* 4.0 15.5 - - + +
356B GLU* 3.3 4.0 + - + +
357B LEU* 1.3 73.9 - - - +
359B ALA* 1.3 63.1 + - - +
626B ASN 3.5 24.7 - - - +
627B MET* 3.8 14.1 - - + -
664B TYR* 4.3 3.8 - - - +
666B ILE* 3.8 20.4 - - + -
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Residues in contact with ALA 359 (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 ILE* 3.6 3.1 - - - -
332B VAL* 3.4 27.6 - - + -
333B GLN* 3.3 17.5 - - - +
336B ILE* 4.0 9.9 - - + -
347B GLY 4.2 0.7 - - - -
348B THR* 3.4 4.7 - - - -
349B ALA* 3.0 30.4 + - + +
357B LEU 3.4 2.8 - - - -
358B LEU* 1.3 82.2 - - - +
360B LEU* 1.3 72.4 + - - +
361B VAL* 4.1 2.5 - - + -
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Residues in contact with LEU 360 (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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248B ALA 4.6 0.3 - - - +
249B THR* 5.5 0.7 - - - -
252B LEU* 4.2 21.8 + - + +
328B ILE* 3.9 8.5 - - + +
333B GLN* 3.0 23.5 + - - -
347B GLY 3.8 1.8 - - - -
348B THR* 3.9 8.5 - - + -
357B LEU* 4.0 24.2 - - + -
359B ALA* 1.3 81.3 - - - +
361B VAL* 1.3 60.4 + - - +
395B PHE* 3.3 42.9 - - + -
496B TYR* 5.3 0.4 - - + -
498B PHE* 4.5 5.6 - - + -
529B VAL* 3.8 28.0 - - + -
549B LEU* 4.0 26.5 - - + -
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Residues in contact with VAL 361 (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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248B ALA 4.2 5.6 - - - +
333B GLN* 3.6 42.2 - - - +
336B ILE* 3.8 19.5 - - + -
337B TYR* 4.0 28.9 - - + -
340B MET* 5.4 1.3 - - - -
346B SER* 3.3 7.4 - - - -
347B GLY 2.7 41.8 + - - +
359B ALA* 4.9 1.1 - - + -
360B LEU* 1.3 77.5 - - - +
362B SER* 1.3 64.9 + - - +
363B THR* 4.1 16.8 - - + -
395B PHE* 3.6 6.2 - - - -
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Residues in contact with SER 362 (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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247B LYS 5.1 0.3 - - - +
248B ALA 5.7 0.2 + - - -
251B HIS* 3.2 43.1 + - - -
337B TYR* 5.0 0.2 - - - -
345B GLY 3.7 4.3 - - - -
346B SER* 4.5 0.2 - - - +
361B VAL* 1.3 78.1 - - - +
363B THR* 1.3 67.2 + - - +
365B SER* 3.8 9.0 - - - -
392B LEU 3.1 22.3 + - - -
394B LYS* 3.2 26.5 + - - +
395B PHE* 4.0 8.5 - - - -
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Residues in contact with THR 363 (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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337B TYR* 3.9 20.4 - - + -
340B MET* 3.0 47.3 + - + +
341B LYS* 3.8 9.0 - - - -
343B ASP 2.9 16.7 + - - -
345B GLY 2.9 32.1 + - - +
346B SER* 4.9 0.2 - - - +
361B VAL* 4.1 6.5 - - + -
362B SER* 1.3 80.5 + - - +
364B PRO* 1.3 63.3 - - + +
394B LYS* 2.7 22.2 + - - -
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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