Contacts of the strand formed by residues 275 - 282 (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 ASP 275 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ALA 3.9 0.5 - - - +
219A LEU* 3.4 6.2 - - - -
220A GLY* 2.9 32.2 + - - +
221A TYR 3.2 21.1 + - - +
222A ASP* 3.8 22.7 + - - +
266A ILE* 4.0 15.8 - - + +
267A LYS 3.5 5.4 - - - +
268A THR* 3.2 32.1 - - - +
270A GLY 5.4 0.3 + - - -
273A TRP 3.7 0.6 + - - -
274A GLY* 1.3 73.5 - - - -
276A TYR* 1.3 59.4 + - - +
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Residues in contact with TYR 276 (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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196A TYR* 3.3 30.4 - + - -
197A ALA* 3.8 36.3 - - + -
200A TYR* 3.6 59.8 - + + -
205A THR 5.2 0.2 - - - -
206A LEU* 3.8 24.0 - - + -
207A THR 4.6 1.7 + - - -
217A LEU* 3.7 19.6 - - + +
218A ALA 3.6 6.7 - - - -
219A LEU* 3.9 5.8 - - + -
266A ILE* 3.3 8.3 - - - +
267A LYS* 2.9 39.6 + - + +
269A CYS* 4.6 1.1 - - - -
274A GLY 3.8 1.0 + - - -
275A ASP* 1.3 72.7 - - - +
277A VAL* 1.3 62.1 + - - +
278A ILE* 4.1 12.3 - - + -
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Residues in contact with VAL 277 (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* 5.3 2.0 - - + -
166A VAL* 6.4 0.2 - - + -
216A ASN 4.1 0.2 - - - +
217A LEU* 3.5 4.9 - - - +
218A ALA* 3.0 35.5 + - + +
221A TYR 3.4 25.6 - - - +
222A ASP 4.1 9.0 - - - +
223A GLY* 4.2 10.5 - - - +
226A ALA* 4.2 13.5 - - + -
230A TRP* 4.2 18.8 - - + -
264A CYS* 5.2 2.2 - - + -
265A GLY 3.5 8.7 - - - +
266A ILE* 3.9 20.6 - - + -
276A TYR* 1.3 81.9 - - - +
278A ILE* 1.3 68.2 + - - +
279A CYS* 4.6 7.0 - - - -
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Residues in contact with ILE 278 (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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192A TYR* 4.9 2.7 - - + -
193A ALA* 3.4 27.4 - - + +
196A TYR* 3.8 28.0 - - + -
197A ALA* 4.1 4.5 - - + +
215A GLU* 3.7 26.2 - - + +
216A ASN 3.4 4.0 - - - -
217A LEU* 3.6 17.3 - - + -
264A CYS* 3.2 4.3 - - - +
265A GLY 2.9 37.3 + - - +
276A TYR* 4.1 17.0 - - + -
277A VAL* 1.3 73.7 - - - +
279A CYS* 1.3 74.6 + - - +
280A SER* 4.1 12.1 - - - +
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Residues in contact with CYS 279 (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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166A VAL* 4.2 5.2 - - - -
170A HIS* 3.9 10.8 - - - -
215A GLU* 3.4 4.7 - - - -
216A ASN 2.9 31.2 + - - +
227A VAL* 5.0 1.1 - - - -
230A TRP* 3.7 25.3 - - + -
262A VAL* 4.2 0.9 - - + -
263A GLY 3.7 0.2 - - - -
264A CYS* 2.1 44.9 - - - -
277A VAL* 4.6 5.6 - - - -
278A ILE* 1.3 76.4 - - - +
280A SER* 1.3 60.6 + - - +
281A TYR* 3.4 26.2 - - + +
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Residues in contact with SER 280 (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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189A LEU* 3.6 25.8 - - - +
192A TYR* 3.7 19.9 - - - -
193A ALA* 3.7 10.6 - - - +
213A TYR* 4.3 9.9 - - - -
214A GLY 3.4 9.8 + - - -
215A GLU* 4.8 1.6 + - - -
262A VAL* 3.3 6.8 - - - +
263A GLY 2.8 37.2 + - - -
278A ILE* 4.1 7.6 - - - +
279A CYS* 1.3 74.5 - - - +
281A TYR* 1.4 60.4 + - - +
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Residues in contact with TYR 281 (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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170A HIS* 2.9 37.6 + + - -
183A LEU* 4.7 4.0 - - + -
189A LEU* 4.3 1.8 - - - -
213A TYR* 3.3 9.1 - - - +
214A GLY* 2.8 29.1 + - - -
215A GLU 3.9 7.9 - - - -
216A ASN* 3.1 34.2 + - - -
230A TRP* 3.6 4.7 - - - -
253A GLN* 3.6 48.0 - - + +
254A VAL* 4.3 2.0 - - + +
259A THR* 3.8 13.5 - - + -
261A GLN 3.5 3.6 - - - -
262A VAL* 3.6 17.7 - - + -
279A CYS* 3.4 34.9 - - + +
280A SER* 1.4 74.5 - - - +
282A ASP* 1.3 60.6 + - - +
283A PRO 4.0 2.2 - - - +
284A ALA 4.1 2.1 + - - -
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Residues in contact with ASP 282 (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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189A LEU* 4.0 20.4 - - + +
212A PRO 4.7 4.3 - - - +
213A TYR* 4.1 12.7 - - + -
259A THR* 4.0 0.4 - - - +
260A THR* 3.1 6.0 + - - -
261A GLN* 3.0 34.9 + - + +
281A TYR* 1.3 76.7 - - - +
283A PRO* 1.3 82.6 + - - +
284A ALA 4.6 1.0 + - - -
302A DIO 3.6 34.2 - - - +
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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