Contacts of the helix formed by residues 241 - 253 (chain B) in PDB entry 1UPX
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 241 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159B HIS* 2.9 32.3 + - + +
162B VAL* 3.6 24.9 - - - +
240B HIS* 1.3 75.2 - - - +
242B LEU* 1.3 61.6 + - - +
243B ARG* 3.1 14.8 + - - +
244B ASP* 2.9 55.2 + - - +
245B LEU 3.4 7.8 + - - -
265B MET* 3.5 11.8 - - - +
305B THR* 3.1 14.6 + - - +
306B THR* 4.7 0.9 - - + -
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Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 5.4 1.3 - - + +
213B ASN* 3.5 28.7 + - - +
217B TYR* 3.7 25.2 + - + -
240B HIS 3.2 9.8 + - - +
241B ASP* 1.3 71.6 + - - +
243B ARG* 1.3 60.8 + - - +
244B ASP 3.3 0.2 - - - -
245B LEU* 3.2 5.9 + - - +
246B GLU 3.0 23.0 + - - -
265B MET* 4.1 11.0 - - + -
268B ALA* 3.7 33.9 - - + +
271B TYR* 3.6 34.1 - - + +
274B PHE* 3.7 12.5 - - + -
451B GLN* 4.3 12.8 - - - +
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Residues in contact with ARG 243 (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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162B VAL* 3.6 27.9 + - + +
163B LEU* 3.8 14.4 - - + +
217B TYR* 3.3 12.6 + - - +
241B ASP* 3.1 10.1 + - - +
242B LEU* 1.3 75.8 - - - +
244B ASP* 1.3 65.9 + - - +
246B GLU* 3.0 30.8 + - - +
247B MET* 3.1 53.6 + - + +
250B LYS* 4.3 6.3 - - - +
339B GLY* 3.0 30.2 + - - +
340B GLU* 4.6 4.9 - - - +
341B HIS* 4.7 3.0 + - - +
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Residues in contact with ASP 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ILE* 4.1 3.8 - - + -
241B ASP* 2.9 28.8 + - - +
242B LEU 3.3 0.2 - - - -
243B ARG* 1.3 77.8 - - - +
245B LEU* 1.3 56.4 + - - +
247B MET* 3.4 8.0 + - - +
248B LEU* 3.0 29.1 + - - +
303B LEU* 5.0 0.2 - - + -
305B THR* 3.3 36.4 - - + +
323B THR* 3.5 7.9 - - - +
324B GLY* 5.8 0.2 - - - -
339B GLY* 6.0 0.5 - - - -
342B LYS* 2.7 42.8 + - - +
344B PHE* 3.6 11.9 - - + -
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Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ILE* 3.7 18.7 - - + +
241B ASP 3.4 2.8 + - - -
242B LEU* 3.2 9.0 + - + +
244B ASP* 1.3 76.5 - - - +
246B GLU* 1.3 60.6 + - - +
248B LEU* 3.1 2.1 + - + -
249B LEU* 2.8 51.3 + - + +
259B VAL* 3.9 21.5 - - + -
261B THR* 5.1 0.2 - - + -
265B MET* 3.8 18.6 - - + -
268B ALA* 3.2 35.4 - - + -
274B PHE* 4.0 19.5 - - + -
280B PHE* 3.8 16.8 - - + -
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Residues in contact with GLU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B THR* 4.9 3.2 - - - +
217B TYR* 2.7 48.4 + - + +
242B LEU 3.0 7.9 + - - +
243B ARG* 3.0 27.9 + - - +
245B LEU* 1.3 76.0 - - - +
247B MET* 1.3 63.7 + - - +
249B LEU* 3.4 4.1 + - - +
250B LYS* 2.7 60.6 + - + +
274B PHE* 3.9 12.1 - - + -
277B TYR* 4.8 4.0 + - - +
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Residues in contact with MET 247 (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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243B ARG* 3.1 58.6 + - + +
244B ASP* 3.8 16.8 - - - +
246B GLU* 1.3 76.9 - - - +
248B LEU* 1.3 57.7 + - - +
250B LYS* 3.4 7.2 + - - +
251B GLN* 3.0 42.6 + - - +
339B GLY* 4.5 1.3 - - - +
340B GLU 3.6 12.1 - - - +
341B HIS* 4.0 6.5 - - - +
342B LYS* 3.6 48.0 - - + +
344B PHE* 3.8 12.6 - - + -
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Residues in contact with LEU 248 (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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235B ILE* 3.9 44.9 - - + -
237B ILE* 4.2 20.0 - - + -
244B ASP 3.0 18.1 + - - +
245B LEU* 3.6 4.9 - - + +
247B MET* 1.3 78.0 - - - +
249B LEU* 1.3 51.8 + - - +
251B GLN* 3.4 1.0 + - - -
252B THR* 2.7 41.5 + - + +
259B VAL* 4.0 27.8 - - + -
303B LEU* 4.4 4.7 - - + -
344B PHE* 3.7 37.9 - - + -
347B ILE* 4.6 2.2 - - + -
348B ILE* 4.6 0.9 - - + -
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Residues in contact with LEU 249 (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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245B LEU* 2.8 37.1 + - + +
246B GLU 3.8 3.6 - - - +
248B LEU* 1.3 73.5 - - - +
250B LYS* 1.3 61.5 + - - +
252B THR* 3.2 4.4 + - - -
253B GLU* 3.2 5.0 + - - +
259B VAL* 3.8 24.5 - - + -
274B PHE* 3.7 30.1 - - + -
277B TYR* 3.8 28.4 - - + -
279B HIS* 2.9 35.3 + - - +
280B PHE* 3.8 35.4 - - + -
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Residues in contact with LYS 250 (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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243B ARG* 4.3 7.5 - - - +
246B GLU* 2.7 54.4 + - - +
247B MET* 3.8 6.9 - - - +
249B LEU* 1.3 75.1 - - - +
251B GLN* 1.3 64.0 + - + +
253B GLU* 3.3 20.1 - - - +
276B LYS* 6.2 0.2 - - - +
277B TYR* 3.5 28.5 - - + +
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Residues in contact with GLN 251 (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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247B MET* 3.0 29.3 + - - +
248B LEU* 4.0 3.1 - - - +
250B LYS* 1.3 79.7 - - + +
252B THR* 1.3 59.5 + - - +
253B GLU 3.3 2.6 + - - +
255B THR* 3.4 14.0 - - - +
341B HIS* 3.5 20.0 - - + -
342B LYS 2.8 23.6 + - - -
343B ASP* 3.9 4.0 - - - +
344B PHE* 2.9 37.6 + - + +
345B SER* 4.0 2.1 + - - -
348B ILE* 3.5 19.0 - - + +
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Residues in contact with THR 252 (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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235B ILE* 4.3 0.9 - - + -
248B LEU* 2.7 30.2 + - + +
249B LEU* 3.2 2.9 + - - -
251B GLN* 1.3 75.8 - - - +
253B GLU* 1.3 64.1 + - - +
254B GLY 3.2 0.5 + - - -
255B THR* 2.7 29.7 + - - +
256B GLY 4.5 0.5 + - - -
257B VAL* 3.7 20.7 - - + +
259B VAL* 3.5 16.4 - - + +
279B HIS* 2.9 35.1 + - - -
348B ILE* 3.7 25.4 - - + -
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Residues in contact with GLU 253 (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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249B LEU 3.2 7.9 + - - +
250B LYS* 3.3 18.2 - - - +
251B GLN 3.3 3.0 - - - +
252B THR* 1.3 76.2 - - - +
254B GLY* 1.3 67.6 + - - +
255B THR* 3.4 5.9 + - - +
277B TYR* 3.7 17.5 - - - +
278B ALA 5.6 0.7 + - - -
279B HIS* 3.5 26.0 + - - -
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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