Contacts of the helix formed by residues 376 - 386 (chain B) in PDB entry 5ODS
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 376 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B LEU* 3.1 31.2 + - + +
374B GLN* 3.0 13.6 + - + +
375B GLY* 1.3 75.5 - - - +
377B TYR* 1.3 58.8 + - - +
378B SER* 3.6 8.3 + - - -
379B GLU* 3.2 39.2 + - - +
380B ALA* 3.3 14.4 + - - +
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Residues in contact with TYR 377 (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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371B LEU 4.9 0.4 - - - -
372B PHE* 5.8 5.4 - - + +
375B GLY* 2.9 32.5 + - - -
376B ASN* 1.3 71.3 - - - +
378B SER* 1.3 66.0 + - - +
379B GLU 3.4 0.2 - - - -
380B ALA* 3.7 8.4 - - - +
381B ALA* 3.1 23.0 + - - +
401B PHE* 4.2 11.9 - - + -
410B GLN* 3.9 17.4 - - + +
411B THR* 3.6 25.7 + - - -
412B SER 5.0 0.4 - - - -
413B PRO* 3.8 45.0 - - + +
416B GLN* 3.4 34.4 - - + +
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Residues in contact with SER 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ASN* 3.3 7.4 - - - -
377B TYR* 1.3 85.3 - - - +
379B GLU* 1.3 61.0 + - - +
381B ALA* 3.6 9.5 + - - +
382B LYS* 3.4 32.2 + - - +
416B GLN* 3.5 36.6 + - - +
420B ILE* 3.7 3.8 - - - +
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Residues in contact with GLU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LEU* 3.8 21.2 - - + +
376B ASN* 3.2 24.4 + - - +
378B SER* 1.3 78.1 - - - +
380B ALA* 1.3 66.2 + - - +
381B ALA 3.2 2.0 - - - -
382B LYS* 3.1 48.7 + - - +
383B VAL* 3.2 18.4 + - - +
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Residues in contact with ALA 380 (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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368B PHE* 3.3 37.5 - - + +
371B LEU* 3.7 29.7 - - + +
372B PHE* 4.3 6.3 - - + +
376B ASN 3.3 18.2 + - - +
377B TYR* 3.7 10.8 - - - +
378B SER 3.4 0.2 - - - -
379B GLU* 1.3 78.5 - - - +
381B ALA* 1.3 60.4 - - - +
383B VAL* 3.4 9.7 + - - +
384B ALA 3.4 1.4 + - - -
401B PHE* 4.6 5.6 - - + -
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Residues in contact with ALA 381 (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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377B TYR 3.1 16.8 + - - +
378B SER* 3.7 7.0 - - - +
379B GLU 3.2 0.2 - - - -
380B ALA* 1.3 74.7 - - - +
382B LYS* 1.3 59.5 + - - +
384B ALA* 3.2 5.3 + - - +
385B ALA* 2.9 29.0 + - - +
401B PHE* 4.3 5.5 - - + -
416B GLN 4.7 0.2 - - - -
417B TYR* 3.8 45.8 - - + +
420B ILE* 3.8 12.6 - - + -
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Residues in contact with LYS 382 (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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378B SER* 3.4 31.8 + - - +
379B GLU* 3.1 42.4 + - - +
381B ALA* 1.3 75.3 - - - +
383B VAL* 1.3 58.5 + - + +
385B ALA* 3.3 6.7 + - - -
386B ASN* 3.0 41.1 + - - +
420B ILE* 4.3 25.7 - - + +
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Residues in contact with VAL 383 (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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349B LEU* 6.1 0.2 - - + -
364B PHE* 4.0 38.7 - - + +
367B LYS* 4.3 16.4 - - + +
368B PHE* 4.5 5.2 - - + +
371B LEU* 3.7 22.2 - - + -
379B GLU* 3.3 16.6 - - - +
380B ALA* 3.5 8.3 - - - +
381B ALA 3.2 0.6 - - - -
382B LYS* 1.3 80.4 - - + +
384B ALA* 1.3 62.2 + - - +
386B ASN* 3.5 10.3 + - - -
387B ALA* 3.6 10.0 + - - -
392B LEU* 4.2 7.0 - - + +
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Residues in contact with ALA 384 (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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368B PHE* 3.8 20.6 - - + -
380B ALA 3.4 1.8 + - - -
381B ALA 3.2 8.2 + - - +
383B VAL* 1.3 79.7 - - - +
385B ALA* 1.3 62.7 + - - +
387B ALA* 3.6 16.3 + - - +
390B GLY* 5.8 0.2 - - - -
392B LEU* 3.7 38.5 - - + +
393B ARG* 4.4 6.6 + - - +
397B THR* 4.4 1.1 - - + -
417B TYR* 3.7 22.2 - - + -
421B LEU* 5.6 0.2 - - - -
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Residues in contact with ALA 385 (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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381B ALA 2.9 17.5 + - - +
382B LYS* 3.6 9.4 - - - +
383B VAL 3.3 0.2 - - - -
384B ALA* 1.3 77.6 - - - +
386B ASN* 1.3 63.8 + - - +
387B ALA* 3.3 6.1 + - - +
393B ARG* 5.1 9.1 + - - -
417B TYR* 4.9 0.8 - - - +
420B ILE* 4.7 14.1 - - + +
421B LEU* 4.1 32.1 - - + +
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Residues in contact with ASN 386 (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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353B VAL* 3.5 28.4 - - + +
364B PHE* 4.0 10.4 - - - -
382B LYS* 3.0 30.1 + - - +
383B VAL* 3.7 7.1 - - - +
384B ALA 3.4 0.6 - - - -
385B ALA* 1.3 81.9 + - - +
387B ALA* 1.3 63.4 + - - +
388B PRO 3.8 0.3 - - - -
420B ILE* 6.1 0.5 - - - +
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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