Contacts of the helix formed by residues 356 - 369 (chain C) in PDB entry 3IO6
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 THR 356 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B ALA 4.4 4.2 + - - -
52B ALA 3.3 4.1 + - - -
53B THR 4.5 1.1 - - - +
54B GLY* 3.6 31.6 - - - +
268B ALA* 6.1 0.3 - - - +
269B ALA* 4.5 11.8 - - + +
350C ALA* 4.6 2.5 - - - +
355C GLN* 1.3 77.7 - - - +
357C VAL* 1.3 59.9 + - - +
358C ASP* 4.1 10.2 + - - +
359C ALA* 3.1 19.7 + - - +
360C ALA* 2.7 37.6 + - - +
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Residues in contact with VAL 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C LYS* 3.5 18.8 - - + +
192C LEU* 3.8 22.4 - - + -
193C THR* 3.4 51.6 - - + +
196C VAL* 4.5 19.3 - - + -
350C ALA* 4.6 2.8 - - - +
356C THR* 1.3 72.2 - - - +
358C ASP* 1.3 66.8 + - - +
361C LEU* 3.0 38.3 + - + +
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Residues in contact with ASP 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B SER 3.7 3.0 - - - +
74B GLY* 3.7 20.3 - - - +
268B ALA* 4.0 26.4 - - + +
269B ALA* 5.7 0.3 - - - -
189C LYS* 3.3 41.4 + - - +
356C THR* 3.3 9.2 + - - +
357C VAL* 1.3 80.0 - - - +
359C ALA* 1.3 60.9 + - + +
361C LEU* 4.4 0.3 - - - +
362C ALA* 3.3 24.8 + - - +
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Residues in contact with ALA 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ALA* 4.1 21.3 - - + +
73B SER* 3.3 18.2 - - - +
74B GLY 5.9 0.2 - - - -
75B LEU* 4.7 6.1 - - + -
355C GLN* 4.4 7.0 - - + +
356C THR* 3.1 25.3 + - - +
358C ASP* 1.3 76.4 - - - +
360C ALA* 1.3 60.4 + - - +
361C LEU 3.2 1.3 - - - -
362C ALA* 3.1 3.1 + - - +
363C ALA* 2.8 31.8 + - - +
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Residues in contact with ALA 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C LEU* 5.5 0.2 - - + -
346C ALA* 3.3 41.6 - - - +
349C ASN* 4.1 7.4 - - + -
350C ALA* 4.2 7.0 - - + +
355C GLN* 3.4 29.1 + - + +
356C THR 2.7 20.5 + - - +
357C VAL 4.4 0.4 - - - +
359C ALA* 1.3 73.0 - - - +
361C LEU* 1.3 59.9 + - - +
363C ALA* 3.8 3.5 + - - +
364C ALA* 3.3 12.3 + - - +
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Residues in contact with LEU 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C ILE* 5.1 5.8 - - + -
183C VAL* 3.4 35.0 - - + +
184C ASP* 3.8 16.5 - - - +
188C ALA* 3.7 27.8 - - + +
189C LYS* 3.8 21.5 - - + +
192C LEU* 3.8 20.9 - - + -
343C VAL* 6.1 2.5 - - + -
346C ALA* 4.6 10.3 - - + -
347C VAL* 6.3 1.3 - - + -
357C VAL* 3.0 29.2 + - + +
358C ASP* 4.4 1.6 - - - +
360C ALA* 1.3 76.1 - - - +
362C ALA* 1.3 63.2 + - - +
363C ALA 3.2 0.2 - - - -
364C ALA* 3.3 13.4 + - - +
365C GLN* 3.3 11.8 + - - +
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Residues in contact with ALA 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLN* 3.2 27.9 - - - +
73B SER* 3.7 13.5 - - - -
74B GLY* 4.0 2.9 - - - +
184C ASP* 3.6 23.0 + - - +
189C LYS* 5.8 0.2 - - - +
358C ASP 3.3 18.3 + - - +
359C ALA 3.1 2.0 + - - +
361C LEU* 1.3 75.4 - - - +
363C ALA* 1.3 63.7 + - - +
365C GLN* 3.6 13.5 + - - +
366C THR* 3.8 12.0 + - - +
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Residues in contact with ALA 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B SER* 5.3 3.7 - - - +
355C GLN* 4.6 11.7 - - - +
359C ALA 2.8 16.7 + - - +
360C ALA* 3.9 9.2 - - - +
362C ALA* 1.3 76.2 - - - +
364C ALA* 1.3 60.5 + - - +
366C THR* 2.6 25.4 + - - +
367C ASN* 3.0 22.4 - - - +
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Residues in contact with ALA 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C VAL* 4.8 12.1 - - + -
342C ALA* 3.3 39.2 - - + +
343C VAL 4.6 0.2 - - - +
346C ALA* 3.8 7.4 - - + -
360C ALA 3.3 11.8 + - - +
361C LEU* 3.3 11.3 + - - +
363C ALA* 1.3 78.4 - - - +
365C GLN* 1.3 62.7 + - - +
367C ASN* 3.1 11.0 + - - +
368C ALA* 3.0 20.6 + - - +
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Residues in contact with GLN 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLN* 5.2 5.7 + - - +
181C VAL* 4.0 41.0 + - + +
183C VAL* 5.7 4.4 - - + +
184C ASP* 4.5 23.1 - - + +
361C LEU 3.3 9.3 + - - +
362C ALA* 3.7 11.4 - - - +
363C ALA 3.2 0.8 - - - -
364C ALA* 1.3 79.9 - - - +
366C THR* 1.3 68.4 + - - +
368C ALA* 3.6 5.8 + - - +
369C ALA* 3.5 20.9 + - - +
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Residues in contact with THR 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLN* 3.5 25.4 - - - +
376B LYS* 6.0 1.0 - - - -
380B ALA* 4.8 5.7 - - - +
362C ALA 3.8 8.9 + - - +
363C ALA* 2.6 25.7 + - - -
365C GLN* 1.3 83.0 - - - +
367C ASN* 1.3 62.9 + - - +
369C ALA* 3.4 9.9 + - - +
370C ALA* 3.1 24.8 + - - +
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Residues in contact with ASN 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B ALA* 4.9 5.0 - - - +
383B SER* 5.7 0.9 + - - -
384B LEU* 3.4 40.0 - - + +
338C ALA 5.6 0.2 - - - +
341C TYR* 6.6 0.2 - - + -
342C ALA* 4.3 15.6 + - + +
345C THR* 5.7 5.1 - - - +
363C ALA* 3.0 28.3 + - - +
364C ALA* 3.1 11.6 + - - +
366C THR* 1.3 82.1 + - - +
368C ALA* 1.3 58.6 + - - +
370C ALA* 3.3 8.6 - - - +
371C MET* 2.9 33.9 + - + +
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Residues in contact with ALA 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C PHE* 5.9 4.7 - - + -
181C VAL* 5.1 18.2 - - + -
338C ALA* 3.7 27.7 - - + +
339C PHE* 4.6 7.4 - - + +
342C ALA* 4.1 10.9 - - + +
364C ALA 3.0 10.6 + - - +
365C GLN* 3.8 10.5 - - - +
366C THR 3.3 0.2 - - - -
367C ASN* 1.3 73.4 - - - +
369C ALA* 1.3 56.8 + - - +
370C ALA 2.9 10.6 + - - -
371C MET 3.5 8.1 + - - -
372C ALA 3.7 3.3 + - - -
373C THR* 3.8 7.9 - - - +
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Residues in contact with ALA 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B LYS* 4.4 17.6 - - - -
377B LEU* 4.3 7.8 - - - +
179C LYS* 5.6 9.0 - - - +
365C GLN* 3.5 16.2 + - - +
366C THR* 3.4 13.1 + - - +
368C ALA* 1.3 74.1 - - - +
370C ALA* 1.3 52.6 + - - +
373C THR* 2.7 30.3 + - + -
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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