Contacts of the helix formed by residues 250 - 262 (chain B) in PDB entry 5LUA
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 THR 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248B LYS 3.7 2.9 + - - +
249B GLU* 1.3 83.9 - - - +
251B LEU* 1.3 64.2 + - - +
252B HIS* 3.7 6.3 + - - +
253B LYS* 3.2 25.5 + - - +
254B GLN 3.1 17.2 + - - -
276B SER 3.5 11.4 - - - -
277B THR* 3.4 24.2 - - - +
278B MET 3.5 4.5 - - - +
279B LYS* 4.1 17.3 - - - +
280B VAL* 3.9 4.6 - - - +
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B PHE* 6.2 0.4 - - + -
183B VAL* 3.9 18.4 - - + -
185B TYR* 3.3 32.7 + - + +
205B TYR* 4.5 12.8 + - + -
250B THR* 1.3 69.2 - - - +
252B HIS* 1.3 60.9 + - - +
254B GLN* 3.3 4.5 + - - +
255B TYR* 2.9 31.4 + - - +
275B ILE* 4.0 14.4 - - + +
276B SER* 3.7 14.1 - - - +
278B MET 3.0 14.4 + - - +
280B VAL* 4.1 24.6 - - + +
283B PHE* 3.7 36.3 - - + -
284B GLN* 4.9 3.6 - - - +
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Residues in contact with HIS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TYR* 4.9 0.2 - - - -
250B THR* 3.9 7.0 - - - +
251B LEU* 1.3 77.0 - - - +
253B LYS* 1.3 61.4 + - + +
255B TYR* 3.4 16.8 + + - +
256B HIS* 2.9 47.9 + + + +
269B GLN* 4.9 8.6 + - - -
276B SER* 2.8 39.1 + - - +
277B THR* 5.1 2.9 - - + -
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Residues in contact with LYS 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLU* 3.6 33.6 + - - -
249B GLU* 3.8 19.5 - - + +
250B THR* 3.2 19.8 + - - +
252B HIS* 1.3 80.8 - - + +
254B GLN* 1.3 61.4 + - - +
256B HIS* 3.1 7.0 + - + +
257B LEU* 2.8 43.4 + - + +
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Residues in contact with GLN 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B TYR* 2.7 31.6 + - + +
237B TRP* 3.3 14.1 + - + -
240B ASP* 3.0 23.2 + - - +
241B SER* 2.9 25.8 + - - +
249B GLU* 3.2 21.2 + - - +
250B THR 3.1 11.2 + - - +
251B LEU* 3.7 9.0 - - - +
253B LYS* 1.3 75.6 - - - +
255B TYR* 1.3 58.0 + - - +
257B LEU* 3.8 1.3 - - - +
258B VAL* 2.9 46.8 + - + +
280B VAL* 4.7 8.3 - - + +
284B GLN* 3.3 17.1 + - - +
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Residues in contact with TYR 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B TYR* 5.3 1.4 + - - -
205B TYR* 3.8 12.8 - - + +
207B THR* 3.9 27.1 - - + +
251B LEU 2.9 17.0 + - - +
252B HIS* 3.5 15.3 - + - +
254B GLN* 1.3 77.9 - - - +
256B HIS* 1.3 63.2 + + + +
258B VAL* 3.4 4.6 + - - +
259B LYS* 2.8 63.2 + - + +
267B VAL* 3.4 31.0 + - + -
268B MET* 3.7 17.4 - - - +
269B GLN* 3.4 43.2 + - + +
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Residues in contact with HIS 256 (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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252B HIS* 2.9 37.8 + + + +
253B LYS* 3.6 8.1 - - + +
255B TYR* 1.3 87.9 - + + +
257B LEU* 1.3 59.8 + - + +
259B LYS* 3.5 15.2 + - + +
260B SER* 2.9 44.3 + - - -
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Residues in contact with LEU 257 (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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240B ASP* 3.5 16.2 - - + +
244B GLU* 3.3 26.2 - - - +
249B GLU* 4.0 2.2 - - - +
253B LYS* 2.8 38.3 + - + +
254B GLN* 3.9 3.6 - - - +
256B HIS* 1.3 74.3 - - + +
258B VAL* 1.3 61.7 + - + +
260B SER* 3.3 4.3 + - - -
261B HIS* 3.0 61.0 + - + +
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Residues in contact with VAL 258 (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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207B THR* 5.7 0.9 - - + -
233B TYR* 3.6 41.1 - - + +
236B ASN* 3.8 12.9 + - + +
237B TRP* 3.4 39.3 - - + +
240B ASP* 5.2 1.3 - - + -
254B GLN* 2.9 26.4 + - + +
255B TYR* 3.8 4.7 - - - +
257B LEU* 1.3 75.5 - - + +
259B LYS* 1.3 56.8 + - - +
261B HIS* 3.5 0.6 + - - -
262B THR* 2.7 43.9 + - - +
267B VAL* 4.1 5.8 - - + -
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Residues in contact with LYS 259 (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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255B TYR* 2.8 52.9 + - + +
256B HIS* 3.6 17.5 + - + +
258B VAL* 1.3 75.3 - - - +
260B SER* 1.3 63.4 + - - +
262B THR 3.4 17.0 - - - +
263B GLN* 5.4 0.2 + - - -
265B SER 5.3 0.3 - - - +
266B HIS* 6.0 4.5 - - - +
267B VAL* 3.8 32.3 + - + +
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Residues in contact with SER 260 (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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41A TYR* 4.8 1.4 - - - -
42A ASN* 5.4 1.2 + - - -
256B HIS* 2.9 34.0 + - - -
257B LEU* 3.3 8.8 + - - +
259B LYS* 1.3 76.8 - - - +
261B HIS* 1.3 72.3 + - - +
263B GLN* 3.4 24.4 + - - +
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Residues in contact with HIS 261 (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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41A TYR* 3.0 73.4 + + + +
232B TRP* 5.2 1.4 - - - -
236B ASN* 3.5 28.7 + - + +
240B ASP* 6.5 0.7 - - + -
257B LEU* 3.0 44.5 + - + +
258B VAL* 5.3 0.7 - - - -
260B SER* 1.3 82.6 - - - +
262B THR* 1.3 59.9 + - - +
263B GLN* 3.3 2.2 + - - -
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Residues in contact with THR 262 (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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209B ALA 4.6 0.7 - - - +
232B TRP* 4.5 11.2 - - + -
233B TYR* 3.9 9.4 - - + +
236B ASN* 2.8 17.8 + - - +
258B VAL* 2.7 26.8 + - - +
259B LYS 3.4 10.7 + - - +
260B SER 3.3 0.9 - - - +
261B HIS* 1.3 74.4 - - - +
263B GLN* 1.3 61.0 + - - +
264B THR* 4.0 11.4 - - - +
265B SER* 3.2 40.9 - - - +
267B VAL* 3.6 21.6 - - + +
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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