Contacts of the strand formed by residues 261 - 268 (chain A) in PDB entry 5ETE
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 GLN 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A LEU* 4.1 2.4 - - - +
184A SER* 3.2 23.4 + - - +
185A TRP 4.4 2.6 + - - -
186A SER* 3.7 24.1 - - - +
189A LEU* 3.6 13.5 - - + -
259A THR* 3.8 6.2 - - - +
260A THR* 1.3 86.8 + - - +
262A VAL* 1.3 61.9 + - - +
281A TYR* 3.5 3.6 - - - -
282A ASP* 3.0 32.9 + - + +
302A DIO 3.3 24.1 - - - +
303A DIO 3.7 31.7 - - - +
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Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 3.8 27.8 - - + -
170A HIS* 4.1 12.1 - - - +
183A LEU* 4.0 20.9 - - + -
184A SER 3.1 3.3 + - - +
185A TRP* 3.3 12.5 - - + -
186A SER 3.0 21.7 + - - -
189A LEU* 3.7 5.8 - - - -
261A GLN* 1.3 75.4 - - - +
263A GLY* 1.3 61.8 + - - +
264A CYS* 3.9 20.6 - - - -
279A CYS* 4.2 0.4 - - + -
280A SER 3.3 14.1 - - - +
281A TYR* 3.6 24.9 - - + -
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Residues in contact with GLY 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A TRP* 4.1 7.6 - - - -
186A SER 4.1 3.4 - - - -
189A LEU* 3.6 14.3 - - - +
190A ALA* 3.7 17.0 - - - -
193A ALA* 3.7 1.9 - - - +
262A VAL* 1.3 76.1 - - - +
264A CYS* 1.3 61.8 + - - -
280A SER* 2.8 36.7 + - - +
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Residues in contact with CYS 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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162A PHE* 3.7 21.8 - - + -
166A VAL* 3.7 17.7 - - + -
185A TRP* 3.3 19.1 - - + -
190A ALA* 3.8 17.4 - - - +
193A ALA* 3.6 6.7 - - - -
194A GLN* 4.7 1.6 - - - +
262A VAL* 3.9 10.5 - - - -
263A GLY* 1.3 75.8 - - - -
265A GLY* 1.3 59.5 + - - +
277A VAL* 5.2 1.1 - - + -
278A ILE 3.2 7.6 - - - +
279A CYS* 2.1 49.4 - - - -
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Residues in contact with GLY 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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162A PHE* 4.0 5.7 - - - -
193A ALA* 3.5 3.8 - - - +
194A GLN* 3.3 26.9 - - - -
197A ALA* 4.3 5.8 - - - -
264A CYS* 1.3 75.4 - - - +
266A ILE* 1.3 63.2 + - - +
277A VAL* 3.5 6.9 - - - +
278A ILE 2.9 31.0 + - - +
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Residues in contact with ILE 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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162A PHE* 3.8 33.9 - - + -
194A GLN* 3.0 31.0 + - - +
197A ALA* 4.1 3.3 - - - +
222A ASP* 4.5 2.9 - - + -
223A GLY 4.4 8.3 - - - +
265A GLY* 1.3 75.4 - - - +
267A LYS* 1.3 69.3 + - - +
268A THR* 5.0 5.4 - - + +
275A ASP* 4.0 22.9 - - + +
276A TYR 3.3 13.7 - - - +
277A VAL* 3.9 17.3 - - + -
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Residues in contact with LYS 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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194A GLN* 5.3 0.7 - - - +
197A ALA* 3.2 29.4 - - + +
198A ASP* 3.3 22.2 + - - +
199A ASN 4.6 0.2 - - - -
200A TYR* 2.9 30.9 + - + +
202A CYS* 4.2 14.5 - - - -
266A ILE* 1.3 77.8 - - - +
268A THR* 1.3 72.7 + - - +
269A CYS* 3.4 5.4 + - - +
275A ASP* 3.5 1.0 - - - -
276A TYR* 2.9 41.1 + - + +
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Residues in contact with THR 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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202A CYS* 5.1 0.3 - - - -
266A ILE* 5.2 5.6 - - + -
267A LYS* 1.3 80.7 - - - +
269A CYS* 1.3 63.7 + - - +
270A GLY* 3.4 2.2 - - - -
275A ASP* 3.2 25.8 - - - +
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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