Contacts of the helix formed by residues 272 - 283 (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 ASN 272 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C ILE 4.0 1.4 + - - -
3C GLU 3.1 24.7 + - - -
4C GLU* 3.3 19.1 - - - +
5C GLY 3.2 20.3 + - - +
6C LYS 3.5 11.9 + - - -
7C LEU* 4.4 6.5 - - + -
58C ASP* 3.3 18.6 + - - +
266C ILE* 5.6 0.2 - - - -
270C SER* 3.1 10.2 + - - +
271C PRO* 1.3 78.2 - - - +
273C LYS* 1.3 63.6 + - - +
274C GLU* 3.3 3.4 - - - +
275C LEU* 3.2 26.9 + - + +
276C ALA* 3.1 23.4 + - - +
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Residues in contact with LYS 273 (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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77C ALA* 4.3 22.5 - - + +
266C ILE* 4.2 28.7 - - + +
267C ASN 4.3 2.0 - - - +
268C ALA 4.0 13.9 + - - +
270C SER 3.3 23.6 - - - +
271C PRO* 3.4 9.1 + - - -
272C ASN* 1.3 77.5 - - - +
274C GLU* 1.3 67.1 + - - +
276C ALA* 3.7 1.7 + - - +
277C LYS* 3.0 29.4 + - - +
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Residues in contact with GLU 274 (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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271C PRO 4.2 7.1 - - - +
272C ASN* 3.3 0.4 - - - -
273C LYS* 1.3 89.8 + - - +
275C LEU* 1.3 65.5 + - + +
277C LYS* 3.5 11.3 - - + +
278C GLU* 3.2 23.9 + - - +
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Residues in contact with LEU 275 (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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4C GLU* 5.7 1.8 - - - +
5C GLY* 3.6 26.7 - - - +
7C LEU* 3.8 17.4 - - + +
33C ILE* 3.8 33.2 - - + -
272C ASN* 3.2 29.1 + - + +
274C GLU* 1.3 81.0 - - + +
276C ALA* 1.3 55.1 + - - +
277C LYS 3.2 1.1 - - - -
278C GLU* 3.2 6.8 + - + +
279C PHE* 2.8 34.0 + - - +
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Residues in contact with ALA 276 (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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7C LEU* 3.7 12.2 - - + +
58C ASP* 5.4 1.1 - - + +
59C ILE* 3.7 26.9 - - + -
266C ILE* 4.0 22.2 - - + -
270C SER* 6.1 0.2 - - - +
272C ASN 3.1 15.8 + - - +
273C LYS 4.0 3.8 - - - +
275C LEU* 1.3 71.7 - - - +
277C LYS* 1.3 66.7 + - - +
279C PHE* 3.1 5.2 + - - +
280C LEU* 3.0 32.6 + - + +
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Residues in contact with LYS 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ILE* 6.4 0.2 - - - -
80C THR* 4.0 30.7 - - + +
106C TYR* 2.9 21.3 + - - +
266C ILE* 4.9 8.7 - - + +
273C LYS 3.0 20.6 + - - +
274C GLU* 3.5 14.1 - - + +
276C ALA* 1.3 76.9 - - - +
278C GLU* 1.3 60.8 - - - +
280C LEU* 4.9 0.2 - - - +
281C GLU* 2.6 54.2 + - - +
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Residues in contact with GLU 278 (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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27C PHE* 4.5 2.2 - - + -
31C THR* 5.5 14.5 - - + +
274C GLU 3.2 12.9 + - - +
275C LEU* 3.5 10.1 - - + +
276C ALA 3.2 0.2 - - - -
277C LYS* 1.3 78.6 - - - +
279C PHE* 1.3 67.2 + - - +
281C GLU* 5.2 0.4 - - - -
282C ASN* 3.3 49.9 + - - +
283C TYR* 3.7 20.4 + - + +
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Residues in contact with PHE 279 (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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7C LEU* 4.5 16.8 - - + -
9C ILE* 3.6 25.1 - - + -
20C LEU* 4.6 13.9 - - + -
23C VAL* 5.1 0.7 - - + -
24C GLY* 4.1 7.9 - - - -
27C PHE* 2.9 73.5 - + + -
35C VAL* 4.0 22.2 - - + -
37C VAL* 6.1 0.2 - - + -
59C ILE* 4.2 5.8 - - + -
275C LEU 2.8 20.2 + - - +
276C ALA* 3.1 10.3 + - - +
278C GLU* 1.3 75.4 - - - +
280C LEU* 1.3 84.9 + - + +
283C TYR 3.6 1.2 + - - -
284C LEU* 3.4 22.2 + - + -
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Residues in contact with LEU 280 (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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59C ILE* 3.8 24.5 - - + -
61C PHE* 4.1 4.3 - - + -
106C TYR* 3.7 36.8 - - + -
108C ILE* 5.6 0.9 - - + -
264C ALA* 3.9 27.8 - - + +
266C ILE* 4.4 10.1 - - + -
276C ALA 3.0 22.6 + - - +
279C PHE* 1.3 99.9 - - + +
281C GLU* 1.3 58.3 + - - +
284C LEU* 3.7 17.2 - - + +
285C LEU* 3.0 39.9 + - + +
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Residues in contact with GLU 281 (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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81C PRO* 3.2 27.7 - - - +
82C ASP* 4.4 4.2 - - - +
85C PHE* 3.4 63.5 - - + +
106C TYR* 3.2 10.2 + - + -
277C LYS* 2.6 47.3 + - - +
278C GLU* 5.2 0.4 - - - -
280C LEU* 1.3 80.0 - - - +
282C ASN* 1.3 74.7 + - - +
283C TYR 3.4 0.2 + - - -
285C LEU* 4.0 10.0 + - - +
286C THR* 4.4 2.1 - - - +
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Residues in contact with ASN 282 (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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85C PHE* 6.3 0.4 - - - -
278C GLU* 3.3 28.1 + - - +
281C GLU* 1.3 89.1 + - - +
283C TYR* 1.3 80.9 + - + +
286C THR* 3.4 17.1 + - - +
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Residues in contact with TYR 283 (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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23C VAL* 4.7 3.6 - - + -
26C LYS* 4.2 21.5 - - + -
27C PHE* 2.9 51.1 - + + -
30C ASP* 2.8 43.6 + - + +
31C THR* 5.2 5.2 - - - +
278C GLU* 3.7 20.1 + - + -
279C PHE 3.6 1.4 + - - -
281C GLU 3.3 0.4 - - - -
282C ASN* 1.3 102.1 - - + +
284C LEU* 1.3 63.1 + - - +
285C LEU 3.3 1.3 - - - -
286C THR* 2.6 24.9 + - - -
289C GLY* 3.6 10.7 + - - -
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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