Contacts of the helix formed by residues 252 - 269 (chain B) in PDB entry 3U44
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 PHE 252 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ARG* 4.1 24.2 - - + -
236B THR* 3.2 31.2 - - + -
237B ALA* 3.3 16.2 - - + -
238B ASP* 3.5 31.9 - - + +
246B PRO* 4.1 4.2 - - - +
250B GLU* 3.1 9.3 + - - +
251B LEU* 1.3 87.9 - - + +
253B ARG* 1.3 56.6 + - - +
254B MET 3.2 2.5 - - - -
255B THR* 3.6 9.6 - - - +
256B GLY* 2.7 35.4 + - - -
298B GLU* 4.2 6.3 - - - -
652B PHE* 4.0 12.1 - + - -
655B TYR* 3.9 34.5 - + - -
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Residues in contact with ARG 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLN* 5.4 2.2 + - - -
246B PRO* 3.7 20.2 - - + +
247B HIS 4.2 12.6 - - - +
248B GLU* 4.1 18.9 - - - +
250B GLU 3.0 16.5 + - - +
251B LEU 3.3 3.1 - - - +
252B PHE* 1.3 75.0 - - - +
254B MET* 1.3 78.8 + - - +
257B LYS* 2.9 41.3 + - + +
641B SER* 3.8 6.7 + - - -
645B GLU* 2.7 40.6 + - - +
648B LEU* 4.5 15.3 - - - +
649B ASP* 2.7 44.4 + - - +
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Residues in contact with MET 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B TYR* 3.9 27.1 - - + +
212B GLN* 2.5 49.0 + - + +
251B LEU 4.9 1.2 + - - -
252B PHE 3.2 0.8 - - - -
253B ARG* 1.3 94.8 - - - +
255B THR* 1.3 64.7 + - + +
257B LYS* 2.9 8.5 + - - +
258B THR 3.1 3.8 + - - -
641B SER* 5.9 1.1 - - - +
649B ASP* 3.2 41.5 - - + +
652B PHE* 4.4 21.8 - - + -
653B LEU* 5.5 4.5 - - + -
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Residues in contact with THR 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B PHE 4.5 3.6 - - - +
211B TYR* 3.6 23.3 - - + +
235B LEU* 4.1 8.6 - - + +
236B THR 2.7 43.3 + - - +
237B ALA* 3.4 10.3 - - - +
252B PHE* 3.6 11.5 - - - +
254B MET* 1.3 79.5 - - - +
256B GLY* 1.3 61.9 + - - +
258B THR* 2.7 21.6 + - - +
259B TYR* 2.9 14.4 + - - +
652B PHE* 3.8 21.6 - - + -
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Residues in contact with GLY 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ALA* 4.4 1.8 - - - +
240B PRO* 4.2 23.4 - - - +
241B SER 4.7 1.7 - - - +
246B PRO* 3.8 13.0 - - - +
252B PHE* 2.7 25.0 + - - +
255B THR* 1.3 73.5 + - - +
257B LYS* 1.3 61.7 + - - +
259B TYR* 3.3 5.1 + - - +
260B TYR* 3.1 22.5 + - - +
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Residues in contact with LYS 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLN* 4.3 14.2 + - - +
245B GLU* 3.2 47.3 - - + +
246B PRO* 3.6 9.9 - - + +
253B ARG* 2.9 38.9 + - + +
254B MET* 2.9 5.6 + - - +
256B GLY* 1.3 74.8 - - - +
258B THR* 1.3 63.6 + - + +
260B TYR* 3.2 7.9 + - - +
261B ARG* 3.1 45.0 + - + +
638B GLU* 5.7 1.0 + - - -
645B GLU* 5.8 0.4 + - - -
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Residues in contact with THR 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B TYR 3.2 4.2 + - - +
212B GLN* 3.1 48.5 - - - +
213B PHE* 3.8 23.3 - - + +
218B PHE* 5.1 3.8 - - + -
235B LEU* 4.3 7.8 - - - +
254B MET 3.1 1.2 + - - -
255B THR* 2.7 31.7 + - - -
257B LYS* 1.3 75.4 - - + +
259B TYR* 1.3 63.1 + - - +
261B ARG* 3.8 6.7 - - - +
262B LEU* 2.9 34.2 + - - +
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Residues in contact with TYR 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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5B PHE* 3.6 37.9 - + + -
7B VAL* 4.2 17.3 - - + -
235B LEU* 3.5 23.0 - - + +
240B PRO* 4.2 30.4 + - + -
241B SER 4.2 4.7 - - - -
242B TYR* 3.6 38.2 - + + -
255B THR 2.9 11.4 + - - +
256B GLY 3.5 8.1 - - - +
258B THR* 1.3 75.0 + - - +
260B TYR* 1.3 61.6 + - - +
262B LEU* 3.1 4.7 + - - +
263B HIS* 2.7 57.6 + + + +
275B TYR* 4.1 11.1 - - - -
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Residues in contact with TYR 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B SER 3.8 10.1 - - - +
242B TYR* 3.0 38.0 - - - +
243B GLU* 4.0 13.9 + - - -
244B ARG 4.4 6.5 - - - +
245B GLU* 3.4 42.6 - - + -
256B GLY 3.1 10.3 + - - +
257B LYS* 3.2 10.5 + - - +
259B TYR* 1.3 86.5 - - - +
261B ARG* 1.3 79.8 + - + +
263B HIS* 3.4 2.1 + - - +
264B GLN* 3.0 52.8 + - + +
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Residues in contact with ARG 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B PHE* 3.9 25.1 - - + -
245B GLU* 3.1 25.8 + - - -
257B LYS* 3.1 33.0 + - + +
258B THR* 3.8 8.3 - - - +
260B TYR* 1.3 89.3 - - + +
262B LEU* 1.3 65.1 + - - +
264B GLN* 3.0 12.5 + - - +
265B LYS* 2.8 22.0 + - - +
638B GLU* 2.9 37.3 + - - -
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 3.8 12.6 - - + -
213B PHE* 4.6 14.1 - - + -
218B PHE* 3.9 23.8 - - + -
221B LEU* 4.3 14.6 - - + -
225B MET* 4.9 6.7 - - - +
233B PHE* 3.8 45.1 - - + -
235B LEU* 4.2 16.8 - - + -
258B THR* 2.9 31.3 + - - +
259B TYR 3.5 2.5 - - - +
261B ARG* 1.3 74.3 - - - +
263B HIS* 1.3 54.3 + - - +
265B LYS* 2.9 10.1 + - + +
266B ALA* 2.8 34.0 + - - +
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Residues in contact with HIS 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 3.5 27.5 - + + -
242B TYR* 3.5 39.7 + + + +
259B TYR* 2.7 50.6 + + + +
260B TYR 3.8 3.4 - - - +
262B LEU* 1.3 72.7 - - - +
264B GLN* 1.3 58.7 + - - +
266B ALA* 3.4 3.3 + - - +
267B LYS* 2.9 39.6 + - + +
273B ILE* 4.1 12.2 - - + +
275B TYR* 3.0 29.6 + + - -
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Residues in contact with GLN 264 (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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242B TYR 5.3 2.8 + - - +
260B TYR* 3.0 47.9 + - + +
261B ARG* 3.0 14.6 + - - +
263B HIS* 1.3 76.3 + - - +
265B LYS* 1.3 61.9 + - - +
267B LYS* 3.1 7.8 + - + +
268B GLU* 2.9 33.8 + - + +
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Residues in contact with LYS 265 (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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218B PHE* 4.5 17.3 - - + -
222B GLU* 3.4 34.4 - - + +
225B MET* 3.4 17.7 - - + -
261B ARG 2.8 11.4 + - - +
262B LEU* 3.3 12.3 - - + +
264B GLN* 1.3 76.2 - - - +
266B ALA* 1.3 58.2 + - - +
268B GLU* 2.8 36.2 + - - +
269B LEU* 3.0 45.9 + - - +
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Residues in contact with ALA 266 (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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3B ALA* 4.5 18.8 - - + -
5B PHE* 4.6 4.7 - - + -
225B MET* 4.1 12.7 - - - +
262B LEU 2.8 15.5 + - - +
263B HIS* 3.7 7.0 - - - +
265B LYS* 1.3 76.2 - - - +
267B LYS* 1.3 61.1 + - - +
269B LEU 3.8 0.2 - - - -
270B ASN 3.4 2.4 + - - -
271B LEU* 3.1 41.9 + - + +
273B ILE* 4.1 17.0 - - + -
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Residues in contact with LYS 267 (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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242B TYR* 6.0 3.2 - - - -
263B HIS* 2.9 31.4 + - + +
264B GLN* 3.1 11.2 + - + +
266B ALA* 1.3 73.8 - - - +
268B GLU* 1.3 60.7 - - - +
269B LEU 3.1 1.3 - - - -
270B ASN* 3.0 20.0 + - - +
271B LEU 5.9 0.2 - - - -
273B ILE* 4.7 11.0 - - + -
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Residues in contact with GLU 268 (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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264B GLN* 2.9 18.7 + - + +
265B LYS* 2.8 51.2 + - + +
267B LYS* 1.3 76.7 - - - +
269B LEU* 1.3 61.1 + - + +
270B ASN* 3.1 9.8 + - - +
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Residues in contact with LEU 269 (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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222B GLU* 3.8 4.3 - - + +
225B MET* 3.7 26.9 - - + -
226B VAL* 3.4 40.6 - - + -
265B LYS* 3.0 32.3 + - - +
266B ALA 3.7 0.2 - - - -
267B LYS 3.1 0.6 - - - -
268B GLU* 1.3 75.9 - - + +
270B ASN* 1.3 79.1 + - - +
271B LEU* 2.9 26.6 - - + +
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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
------------------------------------------------------------
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