Contacts of the helix formed by residues 244 - 259 (chain B) in PDB entry 4LT6
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 244 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B TYR* 4.6 4.9 - - - -
237B SER* 4.7 1.6 - - - -
238B ASN* 4.1 24.3 + - - +
243B LEU* 1.3 73.9 - - - +
245B GLY* 1.3 67.2 + - - -
246B VAL* 3.3 3.6 - - - -
247B SER* 3.0 20.0 + - - -
248B TRP* 3.0 17.5 + - - -
601B 3AT 5.0 3.6 - - - -
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Residues in contact with GLY 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU* 5.4 0.5 - - - +
227B LYS* 4.3 8.8 + - - -
236B TYR* 3.4 28.1 + - - -
244B GLY* 1.3 67.9 - - - -
246B VAL* 1.3 62.0 + - - +
248B TRP* 3.2 5.1 + - - +
249B ALA* 3.0 23.8 + - - +
601B 3AT 3.7 30.5 + - - -
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Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B VAL* 3.9 25.6 - - + -
206B THR* 5.5 1.3 - - - +
209B ILE* 4.5 7.2 - - + -
244B GLY 5.1 1.3 - - - -
245B GLY* 1.3 75.3 - - - +
247B SER* 1.3 65.0 + - - +
249B ALA* 3.4 5.0 + - + +
250B MET* 3.1 35.2 + - + +
324B SER* 5.4 0.9 - - - -
601B 3AT 3.3 79.7 + - + +
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Residues in contact with SER 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ASN* 5.3 1.7 + - - +
243B LEU* 3.6 26.6 - - - -
244B GLY* 3.0 14.1 + - - -
246B VAL* 1.3 76.7 - - - +
248B TRP* 1.3 66.3 + - - +
250B MET* 3.2 13.2 + - - +
251B LEU* 3.0 27.4 + - - +
314B ILE* 4.3 3.6 - - - +
324B SER* 2.9 31.9 + - - -
325B THR* 3.8 5.9 - - - +
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Residues in contact with TRP 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU* 4.1 13.2 - - + -
226B VAL* 3.7 19.5 - - + -
227B LYS* 4.5 7.9 - - + -
229B TRP* 3.9 10.1 - + - -
230B ALA* 3.7 9.2 - - + -
235B ILE* 3.5 42.7 + - + -
236B TYR* 3.4 31.0 - + - -
243B LEU* 3.1 40.0 + - + +
244B GLY 3.0 24.1 + - - -
245B GLY 3.7 5.8 - - - +
247B SER* 1.3 76.8 - - - +
249B ALA* 1.3 62.3 + - - +
251B LEU* 3.2 13.3 + - + +
252B VAL* 2.9 27.0 + - - +
271B PHE* 3.8 10.3 - + - -
336B MET* 3.9 2.5 - - + -
340B PHE* 3.8 29.6 - + - -
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 4.1 26.5 - - + -
209B ILE* 4.5 10.8 - - + -
219B PHE* 3.7 11.0 - - + -
223B LEU* 3.9 22.4 - - + +
245B GLY 3.0 16.1 + - - +
246B VAL* 3.8 6.1 - - - +
248B TRP* 1.3 77.5 - - - +
250B MET* 1.3 58.4 + - - +
252B VAL 3.4 0.2 + - - -
253B ALA* 2.8 30.7 + - - +
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Residues in contact with MET 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B VAL* 5.1 2.5 - - - -
209B ILE* 3.6 20.4 - - + -
246B VAL* 3.1 21.9 + - + +
247B SER* 3.2 3.5 + - - +
249B ALA* 1.3 75.2 - - - +
251B LEU* 1.3 59.7 + - - +
253B ALA* 3.2 7.5 + - - +
254B ARG* 2.8 27.3 + - - +
284B VAL* 4.8 1.3 - - + +
286B LEU* 3.5 20.4 - - + +
314B ILE* 3.4 37.9 - - + +
315B ILE 3.6 22.9 - - - +
316B THR* 3.8 14.8 - - - +
317B PRO* 3.9 9.0 - - - -
324B SER* 3.5 22.4 - - - +
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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
----------------------------------------------------------
243B LEU* 3.8 25.1 - - + -
247B SER 3.0 14.9 + - - +
248B TRP* 3.6 22.7 - - + +
250B MET* 1.3 75.6 - - - +
252B VAL* 1.3 63.7 + - - +
254B ARG* 3.2 1.4 + - - -
255B THR* 3.1 24.3 + - - -
271B PHE* 3.6 15.9 - - + -
275B PHE* 3.3 39.4 - - + -
280B TRP* 4.7 2.5 - - + -
284B VAL* 4.0 11.2 - - + -
312B MET* 5.0 1.8 - - + -
314B ILE* 3.5 25.1 - - + -
340B PHE* 4.0 15.0 - - + -
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B PHE* 4.0 17.0 - - + -
222B THR* 3.6 31.6 - - + -
223B LEU* 3.8 17.9 - - + +
226B VAL* 3.6 34.8 - - + -
248B TRP 2.9 20.5 + - - +
249B ALA 3.9 3.6 - - - +
251B LEU* 1.3 73.6 - - - +
253B ALA* 1.3 67.1 + - - +
255B THR* 3.2 8.4 + - - -
256B CYS* 2.9 24.2 + - - -
271B PHE* 3.9 8.1 - - + -
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Residues in contact with ALA 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ILE* 3.9 18.4 - - + +
212B LEU* 5.6 2.5 - - + +
213B VAL* 3.9 24.5 - - + +
219B PHE* 4.1 3.6 - - + -
249B ALA 2.8 19.1 + - - +
250B MET* 3.4 5.8 - - - +
252B VAL* 1.3 76.1 - - - +
254B ARG* 1.3 62.6 + - - +
256B CYS* 3.1 11.4 + - - +
257B GLN* 3.1 17.8 + - - +
286B LEU* 3.9 14.8 - - + -
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Residues in contact with ARG 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLY* 4.9 1.8 - - - -
21B ILE* 3.9 18.8 - - - +
22B THR* 3.0 39.0 + - - +
250B MET 2.8 13.1 + - - +
251B LEU 3.5 7.9 - - - +
252B VAL 3.2 0.4 - - - -
253B ALA* 1.3 76.8 - - - +
255B THR* 1.3 63.0 + - - +
257B GLN* 3.0 32.5 + - - +
258B LEU* 3.3 42.6 + - + +
275B PHE* 3.9 20.6 - - + -
278B TRP* 4.5 19.7 - - + -
284B VAL* 4.0 11.9 - - + -
285B LEU 3.3 30.6 + - - +
286B LEU* 3.7 8.7 - - + +
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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
----------------------------------------------------------
222B THR* 5.8 0.9 - - + -
251B LEU 3.1 13.5 + - - -
252B VAL* 3.4 10.1 - - - -
254B ARG* 1.3 76.0 - - - +
256B CYS* 1.3 63.5 + - - +
258B LEU* 3.2 10.0 + - - -
259B TYR* 3.2 25.5 + - + +
267B LEU* 3.7 17.8 - - + +
270B LYS* 3.9 12.1 - - + +
271B PHE* 3.3 48.0 - - + +
274B VAL* 5.0 3.7 - - + +
275B PHE* 3.5 9.1 - - - -
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Residues in contact with CYS 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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213B VAL* 4.1 14.8 - - + -
214B PRO* 3.2 21.2 - - + +
215B ASN 5.6 1.3 - - - +
218B THR* 4.7 2.0 - - - +
219B PHE* 3.9 29.4 - - + -
222B THR* 4.9 1.1 - - - -
252B VAL* 2.9 26.2 + - - +
253B ALA 3.1 9.6 + - - +
255B THR* 1.3 76.9 - - - +
257B GLN* 1.3 63.8 + - - +
259B TYR 3.4 1.8 - - - -
260B PRO* 3.3 14.7 - - - +
267B LEU* 3.9 30.5 - - + -
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Residues in contact with GLN 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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19B TYR* 4.1 5.9 + - + +
20B GLY* 3.3 35.6 - - - +
22B THR 5.7 0.2 - - - +
23B SER 5.2 0.2 - - - -
24B PRO* 3.8 20.6 - - - +
212B LEU* 2.8 36.7 + - - +
214B PRO* 4.1 9.6 - - + +
253B ALA* 3.1 15.2 + - - +
254B ARG* 3.0 29.8 + - - +
256B CYS* 1.3 78.6 - - - +
258B LEU* 1.3 62.3 + - + +
259B TYR 3.5 0.2 + - - -
260B PRO* 3.8 4.5 - - - +
286B LEU* 3.2 33.4 + - - +
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Residues in contact with LEU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 3.7 11.9 - - - +
23B SER 4.0 6.5 - - - +
24B PRO* 3.5 5.3 - - - +
25B ILE* 2.8 48.5 + - + -
26B SER 3.6 3.8 + - - -
254B ARG* 3.3 53.2 - - + +
255B THR* 3.2 4.6 + - - +
257B GLN* 1.3 78.9 - - - +
259B TYR* 1.3 77.7 + - + +
260B PRO* 3.7 2.0 - - - -
274B VAL* 3.7 36.1 - - + -
278B TRP* 5.5 2.7 - - + -
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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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25B ILE* 3.5 24.8 - - + +
26B SER* 3.9 33.0 - - - +
255B THR* 3.2 10.7 + - + -
256B CYS* 3.4 4.3 - - - +
258B LEU* 1.3 96.7 - - + +
260B PRO* 1.3 64.4 - - - +
261B ASN 3.3 3.8 + - - -
262B ALA* 3.5 14.6 + - + -
267B LEU* 3.3 32.6 - - + +
270B LYS* 3.4 60.2 + - + +
273B LEU* 4.1 10.4 - - - +
274B VAL* 4.1 15.5 - - + +
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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
------------------------------------------------------------
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