Contacts of the helix formed by residues 241 - 260 (chain B) in PDB entry 3L6D
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 ARG 241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B GLY* 3.5 26.9 + - - +
239B GLN 4.0 1.0 + - - -
240B ALA* 1.3 71.8 - - - +
242B LEU* 1.3 65.3 + - - +
243B ASP* 2.5 46.8 + - - +
244B VAL* 3.5 20.3 + - + +
245B HIS* 2.8 27.8 + - - -
282B GLY 4.0 1.6 - - - +
283B ASP* 3.5 34.9 + - - +
284B GLN 3.5 5.6 - - - -
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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
----------------------------------------------------------
240B ALA 3.5 1.0 + - - -
241B ARG* 1.3 71.8 - - - +
243B ASP* 1.3 59.2 + - - +
245B HIS* 3.1 3.1 + - - +
246B ALA* 2.8 25.5 + - - +
273B VAL* 3.7 19.2 - - + +
276B ALA* 3.9 11.4 - - + -
277B ALA* 3.5 38.8 - - + +
281B TYR* 3.4 24.7 - - + +
282B GLY* 3.3 5.5 + - - -
284B GLN 2.7 13.6 + - - +
285B ASP 4.3 5.4 - - - +
286B ILE* 4.1 14.1 - - + +
289B THR* 3.3 39.3 - - - +
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Residues in contact with ASP 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ARG* 2.5 45.1 + - - +
242B LEU* 1.3 73.6 - - - +
244B VAL* 1.3 81.2 + - - +
246B ALA* 3.2 10.2 + - - +
247B ASP* 3.1 28.9 + - - +
277B ALA* 5.1 5.2 - - + -
282B GLY* 2.8 32.8 + - - +
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ARG* 3.7 28.9 - - + +
242B LEU 3.3 0.4 - - - -
243B ASP* 1.3 88.9 + - - +
245B HIS* 1.3 70.3 + - + +
247B ASP* 3.2 13.2 + - + +
248B ALA* 3.0 22.6 + - + +
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Residues in contact with HIS 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TYR* 2.7 31.4 + + - -
184A PHE* 3.8 22.4 - + - -
187A MSE 4.9 0.2 - - + -
240B ALA* 3.4 36.1 + - + -
241B ARG 2.8 24.2 + - - -
242B LEU 3.1 8.6 + - - +
244B VAL* 1.3 76.2 - - + +
246B ALA* 1.3 56.8 - - - +
248B ALA* 3.3 4.7 + - + -
249B PHE* 2.7 58.4 + + + -
273B VAL* 4.9 0.4 - - + -
286B ILE* 3.7 28.8 - - + +
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Residues in contact with ALA 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU 2.8 13.6 + - - +
243B ASP* 3.2 13.4 + - - +
245B HIS* 1.3 73.8 - - - +
247B ASP* 1.3 58.9 + - - +
249B PHE* 3.4 4.6 + - - +
250B ALA* 3.0 24.6 + - - +
273B VAL* 4.1 24.1 - - + +
274B GLN* 3.2 33.8 + - - +
277B ALA* 4.6 8.1 - - + -
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Residues in contact with ASP 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ASP* 3.1 18.6 + - - +
244B VAL* 3.3 13.9 - - + +
245B HIS 3.1 0.2 - - - -
246B ALA* 1.3 75.3 - - - +
248B ALA* 1.3 66.1 + - - +
250B ALA* 3.4 7.8 + - - +
251B HIS* 3.1 35.4 + - + +
274B GLN* 5.3 0.2 - - - +
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Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A PHE* 4.8 13.2 - - + -
244B VAL* 3.0 11.6 + - + +
245B HIS* 3.6 10.5 - - + +
247B ASP* 1.3 78.3 - - - +
249B PHE* 1.3 70.1 + - + +
251B HIS* 3.2 12.1 + - - +
252B ILE* 3.0 29.0 + - + +
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Residues in contact with PHE 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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184A PHE* 3.2 54.1 - + + -
187A MSE 5.9 1.1 - - + -
188A VAL* 4.2 6.5 - - + -
245B HIS* 2.7 51.5 + + + +
246B ALA* 3.7 5.2 - - - +
248B ALA* 1.3 74.9 - - + +
250B ALA* 1.3 57.6 + - - +
252B ILE* 3.2 2.2 + - - -
253B ALA* 2.9 26.3 + - - +
266B PHE* 3.5 18.9 - + + -
269B VAL* 4.1 24.0 - - + -
270B CYS* 3.8 17.7 - - + -
273B VAL* 3.6 38.4 - - + -
274B GLN* 5.5 1.1 - - + +
286B ILE* 4.7 4.7 - - + -
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Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ALA 3.0 16.7 + - - +
247B ASP* 3.4 6.5 + - - +
249B PHE* 1.3 75.7 - - - +
251B HIS* 1.3 57.8 + - - +
253B ALA* 3.4 7.5 + - - +
254B GLN* 3.0 29.5 + - - +
270B CYS* 4.5 3.5 - - - -
274B GLN* 3.7 15.7 - - - +
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Residues in contact with HIS 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A THR* 6.3 3.6 - - + -
104A ALA* 5.9 7.4 - - + +
247B ASP* 3.1 34.3 + - + +
248B ALA* 3.5 11.2 - - - +
249B PHE 3.2 0.2 - - - -
250B ALA* 1.3 72.7 - - + +
252B ILE* 1.3 67.2 + - + +
254B GLN* 3.2 17.2 + - - +
255B SER* 3.1 26.3 + - - -
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Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A THR* 3.8 34.7 - - + +
180A HIS* 3.7 28.0 - - + -
181A ALA* 4.0 10.8 - - + -
184A PHE* 3.9 21.1 - - + -
248B ALA* 3.0 22.6 + - + +
249B PHE* 3.2 6.3 + - - +
251B HIS* 1.3 77.3 - - + +
253B ALA* 1.3 61.6 + - - +
254B GLN 3.2 0.3 + - - -
255B SER* 3.3 6.5 + - - -
256B LEU* 3.0 30.7 + - + +
266B PHE* 3.7 22.9 - - + -
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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
----------------------------------------------------------
249B PHE 2.9 17.0 + - - +
250B ALA* 3.7 6.7 - - - +
251B HIS 3.3 0.2 - - - -
252B ILE* 1.3 76.2 - - - +
254B GLN* 1.3 57.3 + - - +
256B LEU* 3.6 5.5 + - - +
257B HIS* 2.8 44.7 + - + +
263B THR* 5.9 0.2 - - - -
266B PHE* 3.9 10.7 - - + -
267B ASP* 4.8 6.5 - - - +
270B CYS* 4.0 19.3 - - + -
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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
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250B ALA 3.0 16.6 + - - +
251B HIS* 3.6 17.3 + - - +
252B ILE 3.1 0.4 - - - -
253B ALA* 1.3 75.8 - - - +
255B SER* 1.3 56.8 + - - +
257B HIS* 3.3 6.3 + - + +
258B ALA* 2.8 44.4 + - - +
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Residues in contact with SER 255 (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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177A THR* 4.1 21.1 + - - -
200B PHE* 3.8 11.3 - - - -
251B HIS 3.1 14.9 + - - -
252B ILE* 3.3 7.3 + - - -
254B GLN* 1.3 77.2 - - - +
256B LEU* 1.3 62.2 + - - +
258B ALA* 3.6 6.4 + - - +
259B GLN* 3.2 23.0 + - - +
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Residues in contact with LEU 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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177A THR* 3.8 15.7 - - + -
178A VAL* 4.4 4.7 - - + -
181A ALA* 4.4 11.0 - - + -
196B ALA* 4.3 11.2 - - + -
200B PHE* 3.8 25.1 - - + -
252B ILE* 3.0 32.6 + - + +
253B ALA* 3.7 5.2 - - - +
255B SER* 1.3 77.1 - - - +
257B HIS* 1.3 64.7 + - + +
259B GLN* 3.2 7.6 + - - +
261B VAL* 3.2 42.9 + - + +
263B THR* 3.8 27.6 - - + +
266B PHE* 4.2 15.7 - - + -
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Residues in contact with HIS 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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253B ALA* 2.8 35.2 + - + +
254B GLN* 3.3 8.5 + - + +
256B LEU* 1.3 80.6 - - + +
258B ALA* 1.3 57.6 + - - +
260B GLY* 2.8 21.7 + - - -
261B VAL 4.7 9.6 - - - -
263B THR* 4.7 4.9 + - - -
267B ASP* 3.2 32.9 + - - -
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Residues in contact with ALA 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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254B GLN* 2.8 28.3 + - - +
255B SER* 4.0 8.1 - - - +
257B HIS* 1.3 72.2 - - - +
259B GLN* 1.3 60.8 + - - +
260B GLY 3.3 0.5 + - - -
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Residues in contact with GLN 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ARG* 2.6 40.1 + - - +
200B PHE* 3.7 42.0 - - + +
255B SER 3.2 17.9 + - - +
256B LEU 3.7 4.0 - - - +
257B HIS 3.2 1.0 - - - -
258B ALA* 1.3 77.2 - - - +
260B GLY* 1.3 61.6 + - - +
261B VAL* 3.4 8.3 - - + +
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Residues in contact with GLY 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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199B ARG* 3.8 17.3 + - - -
257B HIS* 2.8 15.8 + - - -
258B ALA 3.1 1.8 - - - -
259B GLN* 1.3 78.7 - - - +
261B VAL* 1.3 64.7 + - - +
262B TRP* 3.8 1.2 + - - +
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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