Contacts of the helix formed by residues 264 - 274 (chain B) in PDB entry 3UXO
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 264 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B SER* 3.3 25.1 - - - +
260B GLN* 3.9 8.8 - - - +
261B PRO* 3.1 28.8 + - + +
263B ASP* 1.3 91.9 + - - +
265B TYR* 1.3 61.7 + - - +
266B TYR 3.6 1.3 - - - -
267B CYS* 3.8 4.0 + - - -
268B GLY 3.5 13.3 + - - -
295B GLU 4.3 0.5 - - - +
296B TYR* 3.0 58.3 - - + +
297B THR* 4.2 15.1 - - + +
313B VAL* 5.1 3.1 - - - -
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Residues in contact with TYR 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 3.7 21.5 - - + -
175B ALA 3.6 2.4 - - - -
176B THR* 2.6 29.5 + - - -
194B LEU* 2.8 42.6 + - + -
195B LEU 4.2 1.1 - - - -
196B THR* 3.5 30.3 - - + +
260B GLN* 4.5 11.9 - - + -
261B PRO 3.2 6.0 + - - +
262B LYS* 3.5 18.6 + - + +
263B ASP 3.6 2.4 - - - -
264B GLN* 1.3 78.3 - - - +
266B TYR* 1.3 92.9 + + + +
268B GLY* 2.9 5.4 + - - -
269B VAL* 2.9 39.5 + - + +
313B VAL 5.7 0.8 + - - -
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Residues in contact with TYR 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 4.5 12.5 - - - +
262B LYS* 4.2 22.2 + - - -
265B TYR* 1.3 103.0 - + + +
267B CYS* 1.3 65.4 + - - +
268B GLY 3.1 1.1 - - - -
269B VAL* 3.2 19.7 - - + +
270B LEU* 3.1 24.9 + - - +
313B VAL* 3.9 11.3 + - + +
314B ASP* 3.1 33.0 - - - -
315B SER* 3.8 28.5 - - - +
316B GLU* 3.8 5.3 - - + +
319B ILE* 4.1 5.4 - - + +
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Residues in contact with CYS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B GLN 3.8 4.4 + - - +
265B TYR 3.3 0.4 - - - -
266B TYR* 1.3 76.6 - - - +
268B GLY* 1.3 56.6 + - - +
270B LEU* 3.7 3.9 - - - +
271B TYR* 3.2 26.3 + - - +
293B ILE* 5.8 2.6 - - - +
294B ASN 4.1 6.0 - - - +
295B GLU* 3.5 6.2 - - - +
296B TYR 3.3 24.2 - - - +
297B THR* 3.5 33.4 - - - +
298B ILE* 3.8 7.6 - - - -
313B VAL* 4.2 21.3 - - + +
319B ILE* 3.8 24.8 - - - +
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Residues in contact with GLY 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 3.3 14.5 - - - +
260B GLN* 3.6 15.5 - - - -
264B GLN 3.5 2.8 + - - -
265B TYR 2.9 8.8 + - - -
267B CYS* 1.3 78.2 - - - +
269B VAL* 1.3 59.3 + - - -
271B TYR* 3.3 1.5 + - - -
272B PHE* 2.8 32.2 + - - -
295B GLU 3.4 14.8 + - - -
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B THR* 4.1 15.0 - - + +
178B CYS* 4.2 4.9 - - - -
182B ARG* 4.7 5.6 - - - +
194B LEU* 3.4 15.3 - - + -
265B TYR* 2.9 52.0 + - + +
266B TYR* 3.2 33.2 - - + +
268B GLY* 1.3 70.7 - - - +
270B LEU* 1.3 54.3 + - - +
272B PHE 3.5 0.3 - - - -
273B THR* 2.6 45.0 + - - +
316B GLU* 3.8 16.8 - - + +
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Residues in contact with LEU 270 (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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266B TYR 3.1 19.1 + - - +
267B CYS* 3.7 5.4 - - - +
269B VAL* 1.3 76.2 - - - +
271B TYR* 1.3 65.6 + - + +
273B THR 3.0 9.9 + - - -
274B GLY* 3.1 14.6 + - - -
278B PHE* 4.3 5.2 - - + -
279B ASN* 3.6 8.1 - - - +
282B MET* 3.7 26.0 - - - -
283B ARG* 5.8 2.0 - - - +
293B ILE* 4.7 14.6 - - + -
316B GLU* 3.3 18.6 - - + +
319B ILE* 3.7 28.9 - - + -
320B PHE* 3.8 24.2 - - + -
333B ARG* 3.6 21.3 - - - +
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Residues in contact with TYR 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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267B CYS 3.2 15.5 + - - +
268B GLY 3.3 2.9 + - - +
270B LEU* 1.3 80.4 - - + +
272B PHE* 1.3 86.0 + + + +
273B THR 3.4 0.5 + - - -
274B GLY 4.1 1.4 - - - +
279B ASN* 2.5 42.6 + - + +
280B LYS* 6.0 2.3 - - - -
283B ARG* 3.0 46.2 - - - +
293B ILE* 6.4 0.4 - - + -
294B ASN 5.2 0.4 - - - +
295B GLU* 3.8 48.2 + - + -
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Residues in contact with PHE 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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178B CYS* 3.7 6.5 - - + -
179B GLY* 2.8 24.6 + - - -
192B ASP* 4.0 18.1 - - - +
194B LEU* 3.8 30.7 - - + -
258B ARG* 3.2 44.4 - - - -
260B GLN* 4.1 20.6 - - - -
268B GLY* 2.8 30.5 + - - +
269B VAL 3.5 0.9 - - - -
271B TYR* 1.3 96.6 - + - +
273B THR* 1.3 57.5 + - - +
274B GLY 4.8 0.8 - - - +
295B GLU* 3.9 22.9 - - + -
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Residues in contact with THR 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B CYS* 3.8 4.7 - - - +
179B GLY* 3.6 12.0 - - - +
182B ARG* 2.7 59.6 + - + +
183B ARG* 3.1 28.7 + - + -
269B VAL 2.6 23.9 + - - -
270B LEU 3.0 4.1 + - - -
272B PHE* 1.3 76.0 - - - +
274B GLY* 1.3 72.2 + - - +
330B PRO* 4.3 6.3 - - + -
333B ARG* 3.8 12.6 - - - +
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Residues in contact with GLY 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ARG* 4.1 3.4 + - - -
270B LEU 3.1 11.8 + - - -
271B TYR 4.1 0.9 - - - +
272B PHE 4.8 0.3 - - - -
273B THR* 1.3 88.6 - - - +
275B SER* 1.3 71.3 + - - +
278B PHE* 4.1 12.1 - - - -
279B ASN* 3.6 11.0 + - - -
333B ARG* 4.1 21.9 - - - +
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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