Contacts of the helix formed by residues 242 - 253 (chain X) in PDB entry 1UL1
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 GLY 242 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240X GLY 3.4 5.1 + - - -
241X ILE* 1.3 75.7 - - - +
243X PRO* 1.3 64.9 - - - -
244X LYS* 3.1 4.0 - - - -
245X ARG* 2.9 13.5 + - - +
246X ALA* 2.7 33.3 + - - +
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Residues in contact with PRO 243 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X GLN 5.6 2.7 - - - +
5X GLY* 5.7 6.7 - - - +
9X LEU* 4.3 16.1 - - + +
230X LEU* 4.1 22.6 - - + +
241X ILE 3.9 4.0 - - - +
242X GLY* 1.3 82.8 - - - +
244X LYS* 1.3 64.4 + - + +
246X ALA* 3.1 10.2 - - + +
247X VAL* 3.0 27.3 + - - +
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Residues in contact with LYS 244 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X LEU* 4.9 13.0 - - + -
12X ASP* 3.6 28.4 + - + -
13X VAL* 5.8 6.1 - - + +
242X GLY 2.9 1.3 + - - -
243X PRO* 1.3 75.6 - - + +
245X ARG* 1.3 69.0 - - - +
247X VAL* 2.7 21.4 + - + +
248X ASP* 3.1 9.2 + - - +
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Residues in contact with ARG 245 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241X ILE* 4.2 6.1 - - + -
242X GLY* 2.9 20.4 + - - +
244X LYS* 1.3 77.1 - - - +
246X ALA* 1.3 64.3 - - - +
248X ASP* 2.9 10.3 + - - +
249X LEU* 2.8 36.0 + - + +
268X TYR* 6.1 1.1 - - - +
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Residues in contact with ALA 246 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226X LEU* 4.2 5.6 - - + -
229X LEU* 4.2 14.3 - - + +
230X LEU* 3.7 22.7 - - + -
241X ILE* 3.6 17.2 - - + +
242X GLY 2.7 15.8 + - - +
243X PRO* 3.1 14.4 - - + +
245X ARG* 1.3 72.2 - - - +
247X VAL* 1.3 65.5 + - - +
249X LEU* 3.4 5.9 + - - +
250X ILE* 3.1 25.5 + - - +
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Residues in contact with VAL 247 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X LEU* 3.7 32.5 - - + -
13X VAL* 5.6 2.0 - - + -
216X LEU* 3.8 25.8 - - + -
218X LEU* 5.2 2.6 - - + +
226X LEU* 4.1 15.9 - - + -
243X PRO 3.2 15.7 - - - +
244X LYS* 2.7 15.8 + - + +
246X ALA* 1.3 70.4 - - - +
248X ASP* 1.3 68.0 + - - +
250X ILE* 2.9 13.6 + - - +
251X GLN* 2.9 36.8 + - + +
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Residues in contact with ASP 248 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244X LYS 3.1 4.7 + - - +
245X ARG* 2.9 12.9 + - - +
247X VAL* 1.3 77.4 - - - +
249X LEU* 1.3 62.9 + - - +
250X ILE 2.8 0.7 + - - -
251X GLN* 2.8 22.7 + - - +
252X LYS* 2.7 42.8 + - - +
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Residues in contact with LEU 249 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229X LEU* 4.9 1.3 - - + -
241X ILE* 3.3 42.2 - - + -
245X ARG* 2.8 27.9 + - + +
246X ALA* 3.6 5.2 - - - +
248X ASP* 1.3 76.7 - - - +
250X ILE* 1.3 56.5 + - - +
252X LYS* 4.4 5.2 - - - -
253X HIS* 3.1 43.6 + - + +
259X ILE* 3.4 29.6 - - + +
263X LEU* 4.0 27.6 - - + -
268X TYR* 5.5 4.0 - - + -
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Residues in contact with ILE 250 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218X LEU* 3.3 27.1 - - + -
222X GLN* 3.9 13.7 - - + +
225X ASP* 3.9 14.4 - - + -
226X LEU* 3.9 29.6 - - + +
229X LEU* 3.7 17.7 - - + -
246X ALA 3.1 13.4 + - - +
247X VAL* 2.9 9.2 + - - +
248X ASP 2.8 4.0 + - - -
249X LEU* 1.3 70.5 - - - +
251X GLN* 1.3 63.6 + - - +
252X LYS 3.1 1.3 - - - -
253X HIS 3.8 1.6 - - - -
254X LYS* 3.1 42.0 + - - +
255X SER 4.7 2.5 - - - -
256X ILE* 4.7 0.4 - - + -
259X ILE* 3.6 19.1 - - + -
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Residues in contact with GLN 251 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216X LEU* 3.2 24.3 - - - +
217X GLY 5.0 2.9 - - - +
218X LEU* 4.3 12.8 - - + +
247X VAL* 2.9 37.0 + - - +
248X ASP* 2.8 30.2 + - - +
250X ILE* 1.3 74.2 - - - +
252X LYS* 1.3 58.2 + - - +
254X LYS* 2.5 31.8 + - - +
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Residues in contact with LYS 252 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248X ASP* 2.7 26.5 + - - +
249X LEU* 3.9 3.1 - - - +
251X GLN* 1.3 81.7 - - - +
253X HIS* 1.3 84.5 + - + +
254X LYS* 3.7 6.6 + - - +
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Residues in contact with HIS 253 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249X LEU* 3.1 35.7 + - + +
250X ILE* 3.1 7.0 - - - +
252X LYS* 1.3 90.8 + - + +
254X LYS* 1.3 52.6 + - - +
255X SER* 2.6 25.4 + - - +
258X GLU* 3.9 30.3 - - + +
259X ILE* 3.6 18.4 - - + +
262X ARG* 4.1 34.1 + - + -
263X LEU* 6.0 0.4 - - - +
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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