Contacts of the helix formed by residues 360 - 374 (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 ALA 360 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335B ILE* 3.9 9.4 - - + +
348B ALA 4.8 4.0 - - - +
349B LEU* 5.3 0.4 - - - -
352B ALA* 3.9 20.0 - - + -
357B LEU 5.5 0.2 - - - +
358B ALA* 3.8 0.6 - - - +
359B GLY* 1.3 78.6 - - - +
361B GLU* 1.3 53.4 + - - +
362B GLU* 3.2 2.7 - - - -
363B LEU* 2.7 45.4 + - + +
364B PHE* 3.2 34.6 + - + -
388B PRO* 5.6 2.4 - - + +
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Residues in contact with GLU 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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358B ALA* 4.0 8.3 - - - +
359B GLY* 3.0 34.5 + - - +
360B ALA* 1.3 75.2 - - - +
362B GLU* 1.3 63.9 + - - +
364B PHE* 3.3 11.0 + - - +
365B ALA* 3.1 21.7 + - - +
388B PRO* 6.2 1.5 - - + +
391B ILE* 4.0 37.0 - - + +
392B LEU* 6.1 0.2 - - - +
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Residues in contact with GLU 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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174A GLN* 5.0 2.2 - - - +
359B GLY 5.2 1.5 + - - +
360B ALA 3.2 0.8 - - - -
361B GLU* 1.3 80.2 + - - +
363B LEU* 1.3 59.5 + - + +
365B ALA* 3.3 9.4 + - - +
366B ARG* 2.8 72.5 + - - +
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Residues in contact with LEU 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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339B THR* 3.6 38.8 - - + +
345B PRO* 3.8 29.6 - - + +
348B ALA* 4.1 15.5 - - + -
349B LEU* 4.4 17.3 - - + -
359B GLY 5.4 0.4 - - - +
360B ALA* 2.7 28.9 + - + +
362B GLU* 1.3 72.4 - - + +
364B PHE* 1.3 58.9 + - - +
366B ARG* 3.2 24.2 + - + +
367B LYS* 2.8 34.5 + - + +
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Residues in contact with PHE 364 (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* 3.7 37.7 - - + -
352B ALA* 4.4 4.5 - - + -
353B VAL* 4.9 5.6 - - + -
360B ALA* 3.2 43.8 + - + -
361B GLU* 3.3 9.8 + - - +
363B LEU* 1.3 76.2 - - - +
365B ALA* 1.3 64.5 + - - +
367B LYS* 4.0 4.5 - - - +
368B PHE* 3.0 24.8 + - - +
383B VAL* 4.0 23.6 - - + +
386B ASN 4.0 17.5 - - - -
387B ALA* 4.8 2.7 - - + -
388B PRO* 3.6 32.3 - - + -
391B ILE* 5.6 4.7 - - + -
392B LEU* 3.5 19.9 - - + +
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Residues in contact with ALA 365 (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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361B GLU 3.1 13.1 + - - +
362B GLU* 3.5 14.8 - - - +
364B PHE* 1.3 76.5 - - - +
366B ARG* 1.3 55.3 + - - +
368B PHE* 3.2 5.7 + - - +
369B ASN* 2.7 48.7 + - - +
392B LEU* 4.5 12.2 - - + +
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Residues in contact with ARG 366 (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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174A GLN* 3.7 46.9 + - - +
176A ARG* 5.5 9.9 - - - +
362B GLU* 2.8 49.8 + - - +
363B LEU* 3.4 26.9 - - + +
365B ALA* 1.3 77.3 - - - +
367B LYS* 1.3 58.0 + - + +
369B ASN* 3.9 6.4 - - - +
370B ALA* 3.0 32.5 + - - +
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Residues in contact with LYS 367 (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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223A GLN* 3.8 26.4 - - - +
345B PRO* 6.1 0.7 - - - -
346B ASP* 4.0 12.5 + - - -
349B LEU* 3.8 33.2 - - + -
363B LEU* 2.8 22.3 + - + +
364B PHE* 4.0 5.4 - - - +
366B ARG* 1.3 76.3 - - + +
368B PHE* 1.3 61.9 + - - +
370B ALA* 4.0 4.9 - - - +
371B LEU* 3.3 37.2 + - + +
383B VAL* 4.3 16.8 - - + -
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Residues in contact with PHE 368 (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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364B PHE 3.0 19.5 + - - +
365B ALA* 3.5 6.3 - - - +
366B ARG 3.2 0.2 - - - -
367B LYS* 1.3 75.8 - - - +
369B ASN* 1.3 62.0 + - - +
371B LEU* 3.2 5.5 + - - +
372B PHE* 2.9 39.5 + + - +
380B ALA* 3.3 34.3 - - + +
383B VAL* 4.5 4.9 - - + +
384B ALA* 3.8 22.9 - - + -
392B LEU* 4.2 18.4 - - + -
397B THR* 3.7 16.4 - - + -
400B ARG* 3.6 33.7 - - + -
401B PHE* 3.6 31.0 - + - -
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Residues in contact with ASN 369 (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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365B ALA* 2.7 39.2 + - - +
366B ARG* 4.0 6.2 - - - +
368B PHE* 1.3 76.1 - - - +
370B ALA* 1.3 56.8 + - - +
372B PHE* 3.6 1.2 - - - +
373B ALA* 3.0 29.5 + - - +
400B ARG* 2.7 35.8 + - - +
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Residues in contact with ALA 370 (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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366B ARG 3.0 19.3 + - - +
367B LYS* 4.0 7.0 - - + +
369B ASN* 1.3 77.4 - - - +
371B LEU* 1.3 58.1 + - + +
373B ALA* 3.5 6.0 + - - +
374B GLN* 2.9 35.1 + - - +
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Residues in contact with LEU 371 (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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367B LYS* 3.3 25.4 + - + +
368B PHE 3.2 1.8 + - - +
370B ALA* 1.3 76.8 - - + +
372B PHE* 1.3 63.9 + - - +
374B GLN* 3.3 11.1 + - + -
376B ASN* 3.1 58.8 + - + +
379B GLU* 3.8 19.1 - - + +
380B ALA* 3.7 21.5 - - + +
383B VAL* 3.7 26.2 - - + -
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Residues in contact with PHE 372 (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* 2.9 27.1 + + - +
369B ASN 3.6 2.2 - - - +
371B LEU* 1.3 78.1 - - - +
373B ALA* 1.3 62.8 + - - +
375B GLY* 3.3 12.6 + - - -
376B ASN 5.5 0.7 - - - -
377B TYR* 5.8 4.7 - - + +
380B ALA* 4.3 6.0 - - + +
400B ARG* 3.3 76.5 - - + +
401B PHE* 4.0 30.3 - + - -
403B SER* 5.8 1.3 - - - -
404B VAL* 3.7 20.9 - - + -
413B PRO* 5.9 0.4 - - + -
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Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B ASN 3.0 17.7 + - - +
370B ALA* 3.8 6.1 - - - +
372B PHE* 1.3 79.2 - - - +
374B GLN* 1.3 59.7 + - - +
375B GLY* 3.2 1.7 + - - -
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Residues in contact with GLN 374 (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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370B ALA* 2.9 22.7 + - - +
371B LEU* 3.5 16.6 - - + +
372B PHE 3.1 0.6 - - - -
373B ALA* 1.3 77.6 - - - +
375B GLY* 1.3 55.3 + - - +
376B ASN* 3.0 16.0 + - + +
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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