Contacts of the helix formed by residues 260 - 268 (chain A) 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 SER 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A HIS* 3.5 4.5 - - - -
251A VAL 3.6 11.2 + - - -
252A ASP* 3.8 15.6 + - - -
253A ALA 3.1 15.9 - - - -
254A GLN* 4.5 4.3 - - - -
258A GLY 3.7 0.2 + - - -
259A GLU* 1.3 74.7 - - - +
261A ALA* 1.3 64.9 + - - +
262A LEU* 3.3 11.6 + - - +
263A ASP* 2.8 40.2 + - - +
264A LEU* 3.2 13.9 + - - +
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Residues in contact with ALA 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A LEU* 3.9 42.2 - - + -
230A HIS* 3.4 21.7 + - + +
233A VAL* 3.8 15.2 - - + +
250A ASN 5.1 0.7 - - - +
251A VAL* 3.7 11.4 + - + +
253A ALA 3.8 1.2 + - - -
260A SER* 1.3 73.6 - - - +
262A LEU* 1.3 62.1 + - - +
264A LEU* 3.2 8.8 + - - +
265A ALA* 3.1 19.8 + - - +
277A LEU* 5.7 3.1 - - + -
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A VAL* 3.9 19.3 + - + +
252A ASP* 5.1 7.2 - - - +
260A SER* 3.1 9.4 + - - +
261A ALA* 1.3 77.0 - - - +
263A ASP* 1.3 66.2 + - - +
265A ALA* 2.9 17.3 + - + +
266A LYS* 3.0 47.7 + - - +
274A ILE* 3.7 31.2 - - + +
277A LEU* 3.9 17.9 - - + +
278A GLN* 4.2 13.0 - - + +
281A ARG* 6.0 2.5 - - + -
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Residues in contact with ASP 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A GLN* 4.8 2.3 + - - -
258A GLY 3.7 6.6 - - - +
259A GLU* 3.5 14.8 - - + -
260A SER* 2.8 37.1 + - - +
262A LEU* 1.3 77.9 - - - +
264A LEU* 1.3 56.7 + - - +
266A LYS* 3.5 19.2 + - - +
267A GLN* 3.0 42.0 + - - +
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ASN* 4.7 0.2 - - - +
230A HIS* 3.5 43.5 - - + +
233A VAL* 3.7 13.4 - - + +
234A LEU* 4.0 32.5 - - + -
255A ASN* 4.5 3.6 - - - +
259A GLU* 3.5 36.8 - - + +
260A SER 3.2 9.4 + - - +
261A ALA* 3.5 7.0 - - - +
262A LEU 3.1 0.6 - - - -
263A ASP* 1.3 74.7 - - - +
265A ALA* 1.3 64.7 + - - +
267A GLN* 3.8 10.8 - - - +
268A ARG* 3.1 24.1 + - - +
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Residues in contact with ALA 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A VAL* 3.8 11.8 - - + +
261A ALA 3.1 11.7 + - - +
262A LEU* 2.9 14.5 + - + +
264A LEU* 1.3 74.9 - - - +
266A LYS* 1.3 61.1 + - - +
268A ARG* 3.3 4.4 + - - +
269A LYS 3.0 20.8 + - - -
270A ASN 3.2 12.0 + - - -
273A MET* 4.0 16.2 - - + +
274A ILE* 3.4 30.2 - - + +
277A LEU* 5.5 1.8 - - + -
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Residues in contact with LYS 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A LEU* 3.0 50.5 + - + +
263A ASP* 3.8 17.9 + - - +
265A ALA* 1.3 72.6 - - - +
267A GLN* 1.3 59.8 + - + +
268A ARG 3.0 1.6 - - - -
269A LYS* 2.6 25.8 + - - +
274A ILE* 3.8 26.4 - - + +
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Residues in contact with GLN 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A GLU* 2.7 37.1 + - - +
263A ASP* 3.0 31.5 + - - +
264A LEU* 3.8 13.6 - - - +
265A ALA 3.4 0.2 - - - -
266A LYS* 1.3 76.9 - - + +
268A ARG* 1.3 59.5 + - - +
269A LYS* 3.5 2.1 + - - +
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Residues in contact with ARG 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A VAL* 5.5 2.0 - - + +
264A LEU 3.1 17.9 + - - +
265A ALA* 3.6 6.1 - - - +
266A LYS 3.0 1.0 - - - -
267A GLN* 1.3 75.0 - - - +
269A LYS* 1.3 69.8 + - - +
270A ASN* 3.2 12.2 + - + +
273A MET* 4.9 8.1 - - + -
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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