Contacts of the helix formed by residues 270 - 279 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236B GLY* 5.5 0.2 - - - -
238B THR* 4.8 6.1 - - - +
265B ALA 3.4 2.2 + - - +
268B ARG* 2.9 12.6 - - + +
269B LYS* 1.3 74.8 - - - +
271B VAL* 1.3 64.1 + - - +
272B TRP* 3.1 14.6 + - - +
273B MET* 3.0 58.1 + - + +
274B ILE* 3.0 26.9 + - - +
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Residues in contact with VAL 271 (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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269B LYS 3.0 8.7 + - - +
270B ASN* 1.3 72.2 + - - +
272B TRP* 1.3 65.2 + - - +
274B ILE* 4.0 5.6 - - - +
275B ASN* 3.2 35.1 + - - +
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Residues in contact with TRP 272 (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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238B THR* 3.3 44.4 - - + -
241B ILE* 3.7 30.3 - - + -
242B SER* 3.2 27.6 - - - -
245B LEU* 5.6 0.2 - - + -
270B ASN* 3.1 9.9 + - - +
271B VAL* 1.3 78.5 - - - +
273B MET* 1.3 83.3 + - + +
275B ASN* 3.3 2.5 + - - +
276B HIS* 2.8 72.9 + + + -
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Residues in contact with MET 273 (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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233B VAL* 3.7 37.9 - - - +
236B GLY* 3.7 32.5 - - - -
237B ASN 4.9 0.2 - - - +
238B THR* 4.4 6.5 - - + +
241B ILE* 4.8 6.1 - - + -
265B ALA* 4.0 12.6 - - + -
268B ARG* 5.3 4.3 - - + -
270B ASN* 3.0 46.0 + - + +
272B TRP* 1.3 97.9 - - + +
274B ILE* 1.3 66.2 + - - +
275B ASN 2.8 2.1 + - - -
276B HIS 2.9 1.9 + - - -
277B LEU* 2.8 38.4 + - + +
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Residues in contact with ILE 274 (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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262B LEU* 6.0 1.3 - - - +
265B ALA* 3.4 35.6 - - + +
266B LYS* 4.1 12.8 - - + +
269B LYS* 3.7 18.4 - - - +
270B ASN 3.0 19.0 + - - +
271B VAL* 4.0 5.8 - - - +
273B MET* 1.3 74.8 - - - +
275B ASN* 1.3 64.4 + - - +
277B LEU* 4.6 2.6 - - - +
278B GLN* 3.0 42.6 + - - +
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Residues in contact with ASN 275 (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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271B VAL* 3.2 24.3 + - - +
272B TRP* 3.6 4.4 - - - +
273B MET 2.8 4.8 + - - -
274B ILE* 1.3 84.9 + - - +
276B HIS* 1.3 66.9 + - + +
278B GLN* 3.4 4.5 + - - +
279B GLU* 2.9 30.4 + - - +
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Residues in contact with HIS 276 (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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242B SER* 5.1 2.0 - - - -
245B LEU* 3.7 23.6 - - + +
272B TRP* 2.8 77.9 + + + +
273B MET 2.9 5.7 + - - +
275B ASN* 1.3 75.9 - - + +
277B LEU* 1.3 66.4 + - + +
278B GLN 3.5 0.2 + - - -
279B GLU* 3.5 19.7 + - - +
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Residues in contact with LEU 277 (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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229B LEU* 5.2 6.1 - - + -
233B VAL* 4.4 15.9 - - + -
241B ILE* 3.6 30.7 - - + -
245B LEU* 4.3 17.4 - - + +
251B VAL* 4.0 22.9 - - + +
261B ALA* 4.6 3.8 - - + -
262B LEU* 3.8 38.8 - - + +
265B ALA* 3.9 15.0 - - + -
273B MET* 2.8 35.7 + - + +
274B ILE* 4.6 2.5 - - - +
276B HIS* 1.3 71.6 - - + +
278B GLN* 1.3 68.7 + - - +
279B GLU 4.1 2.1 - - - -
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Residues in contact with GLN 278 (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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262B LEU* 5.8 8.0 - - - +
274B ILE* 3.0 37.0 + - - +
275B ASN* 3.5 5.6 - - - +
277B LEU* 1.3 81.3 - - - +
279B GLU* 1.3 67.0 + - - +
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Residues in contact with GLU 279 (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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275B ASN 2.9 17.9 + - - +
276B HIS* 3.8 15.9 - - - +
277B LEU 3.4 2.7 - - - -
278B GLN* 1.3 83.3 - - - +
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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