Contacts of the helix formed by residues 270 - 284 (chain C) in PDB entry 3EU9
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 270 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B ILE* 4.5 5.1 - - - +
56B TYR* 3.5 13.5 - - - -
238C THR* 4.5 7.5 - - - +
265C ALA 3.4 5.6 + - - +
268C ARG* 3.3 2.2 - - - +
269C LYS* 1.3 76.4 - - - +
271C VAL* 1.3 56.9 + - - +
272C TRP* 3.0 14.6 + - - +
273C MET* 3.0 44.0 + - + +
274C ILE* 2.9 31.4 + - - +
452C SO4 2.8 46.0 + - - +
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Residues in contact with VAL 271 (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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56B TYR* 2.9 27.5 + - + +
68B GLY 3.8 8.1 - - - +
69B ILE* 3.7 22.2 - - + -
70B TYR 5.0 1.6 - - - +
71B GLU* 6.5 2.0 - - + -
269C LYS 4.7 4.0 - - - +
270C ASN* 1.3 69.1 - - - +
272C TRP* 1.3 61.5 + - - +
274C ILE* 4.2 12.3 - - + -
275C ASN* 2.9 50.3 + - - +
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Residues in contact with TRP 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A SO4 4.8 4.0 + - - -
53B ILE* 3.1 36.8 - - + +
56B TYR* 3.8 18.7 - - + -
59B TRP* 3.9 24.0 - + - -
67B TYR* 4.0 16.1 - + + -
69B ILE* 4.2 8.9 - - + +
238C THR* 3.6 27.1 - - + -
241C ILE* 4.1 18.4 - - + -
242C SER* 3.4 26.7 - - - -
270C ASN* 3.0 10.0 + - - +
271C VAL* 1.3 77.5 - - - +
273C MET* 1.3 83.2 + - + +
275C ASN* 3.9 2.7 - - - +
276C HIS* 2.7 69.1 + + - -
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Residues in contact with MET 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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233C VAL* 4.0 23.8 - - - +
236C GLY* 3.8 16.2 - - - -
238C THR* 3.9 8.3 - - + -
241C ILE* 3.7 34.5 - - + -
265C ALA* 3.9 11.7 - - + -
268C ARG* 3.8 12.6 - - - -
270C ASN* 3.0 30.2 + - + +
272C TRP* 1.3 88.8 - - + +
274C ILE* 1.3 65.7 - - - +
276C HIS* 3.3 0.9 + - - -
277C LEU* 2.9 35.0 + - + +
452C SO4 3.2 26.5 - - - +
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Residues in contact with ILE 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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262C LEU* 4.0 11.4 - - + +
265C ALA* 3.9 4.7 - - + +
266C LYS* 3.7 46.0 - - + +
269C LYS* 4.5 4.0 - - - -
270C ASN 2.9 29.6 + - - +
271C VAL* 3.3 13.0 + - + +
273C MET* 1.3 76.0 - - - +
275C ASN* 1.3 65.0 + - - +
277C LEU* 3.9 1.0 - - - +
278C GLN* 3.0 58.7 + - - +
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Residues in contact with ASN 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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67B TYR 2.9 26.6 - - - +
68B GLY* 3.0 19.9 + - - +
102B ARG* 4.3 15.5 - - - +
271C VAL* 2.9 29.9 + - - +
272C TRP 3.9 3.1 - - - +
274C ILE* 1.3 84.2 - - - +
276C HIS* 1.3 60.1 + - + +
278C GLN* 3.4 11.3 + - - +
279C GLU* 2.9 39.9 + - - +
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Residues in contact with HIS 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MET* 5.4 5.8 - - + -
51A THR* 3.9 3.5 + - - -
323A SO4 2.6 33.0 + - - -
67B TYR* 3.9 13.7 - + - -
102B ARG* 6.1 1.1 - - - -
242C SER* 4.8 3.6 - - - -
245C LEU* 3.8 20.8 - - + +
272C TRP* 2.7 79.2 + + + +
273C MET* 3.8 3.4 - - - +
275C ASN* 1.3 79.5 - - + +
277C LEU* 1.3 60.7 + - + +
279C GLU* 3.3 15.5 + - - +
280C ALA* 2.9 28.9 + - - +
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Residues in contact with LEU 277 (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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229C LEU* 4.7 3.6 - - + -
233C VAL* 4.3 8.1 - - + -
241C ILE* 3.8 28.0 - - + -
245C LEU* 3.9 9.6 - - + -
251C VAL* 3.4 35.6 - - + +
261C ALA* 3.5 43.1 - - + +
262C LEU* 3.6 14.4 - - + +
265C ALA* 4.0 11.4 - - + -
273C MET* 2.9 25.1 + - + +
276C HIS* 1.3 76.3 - - + +
278C GLN* 1.3 62.7 + - - +
280C ALA* 3.2 2.3 + - - -
281C ARG* 3.1 18.0 + - - +
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Residues in contact with GLN 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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262C LEU* 4.2 17.7 - - + -
266C LYS* 4.2 16.0 - - - +
274C ILE* 3.0 43.8 + - - +
275C ASN* 3.7 10.7 + - - +
277C LEU* 1.3 76.2 - - - +
279C GLU* 1.3 63.0 + - + +
281C ARG* 3.2 18.7 + - - +
282C GLN* 3.1 39.2 + - - +
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Residues in contact with GLU 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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50A MET* 5.6 8.4 - - - +
51A THR* 4.7 6.2 + - - -
100B ASN* 4.4 5.5 - - - +
101B ASN* 6.0 0.2 - - - +
102B ARG* 3.3 38.2 + - - +
275C ASN* 2.9 26.9 + - - +
276C HIS* 3.6 25.5 + - - +
278C GLN* 1.3 73.4 - - + +
280C ALA* 1.3 66.3 + - - +
282C GLN* 3.2 18.2 + - - +
283C ALA* 3.0 22.2 + - - +
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Residues in contact with ALA 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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245C LEU* 3.7 35.4 - - + +
249C ALA 5.3 2.5 - - - +
251C VAL* 3.9 6.5 - - + -
276C HIS 2.9 13.6 + - - +
277C LEU 3.5 8.7 - - - +
278C GLN 3.2 0.2 - - - -
279C GLU* 1.3 76.6 - - - +
281C ARG* 1.3 58.7 + - - +
283C ALA* 3.0 8.6 + - - +
284C LYS* 2.8 30.0 + - - +
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Residues in contact with ARG 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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251C VAL* 4.4 10.6 - - + +
252C ASP* 2.6 43.2 + - - +
260C SER* 5.5 0.4 + - - -
262C LEU* 3.1 33.7 - - - +
266C LYS* 5.9 0.4 - - - +
277C LEU 3.1 12.7 + - - +
278C GLN* 3.2 19.4 + - - +
280C ALA* 1.3 76.5 - - - +
282C GLN* 1.3 67.5 + - + +
284C LYS* 3.1 25.1 + - - +
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Residues in contact with GLN 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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101B ASN* 4.1 15.2 - - - +
278C GLN* 3.1 36.1 + - - +
279C GLU* 3.2 17.5 + - - +
281C ARG* 1.3 82.5 - - + +
283C ALA* 1.3 59.3 + - - +
284C LYS 3.7 5.1 - - - +
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Residues in contact with ALA 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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279C GLU 3.0 12.3 + - - +
280C ALA* 3.0 11.4 + - - +
282C GLN* 1.3 74.2 - - - +
284C LYS* 1.3 68.4 + - - +
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Residues in contact with LYS 284 (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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280C ALA 2.8 13.5 + - - +
281C ARG* 3.1 21.0 + - - +
282C GLN 3.7 4.9 - - - +
283C ALA* 1.3 83.8 - - - +
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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