Contacts of the helix formed by residues 263 - 279 (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 THR 263 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B GLU* 3.2 28.9 - - + +
196B ALA* 4.5 9.0 - - + -
253B ALA* 5.9 0.2 - - - -
256B LEU* 3.8 22.8 - - + +
257B HIS* 4.7 4.4 + - - -
261B VAL* 3.4 28.0 + - + -
262B TRP* 1.3 81.0 - - - +
264B PRO* 1.3 67.9 - - - +
265B VAL 3.3 0.2 + - - -
266B PHE* 3.4 7.8 + - + +
267B ASP* 3.0 34.6 + - - -
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Residues in contact with PRO 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ALA* 3.6 8.6 - - + +
271A GLN* 3.8 20.0 - - - +
272A VAL* 3.5 26.5 - - + -
293A PHE* 4.4 1.3 - - + -
192B GLU* 3.3 5.2 - - - +
262B TRP* 3.4 41.9 - - + +
263B THR* 1.3 88.4 - - - +
265B VAL* 1.3 62.3 + - - +
267B ASP* 3.4 11.8 + - + +
268B ALA* 3.0 23.0 + - - +
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Residues in contact with VAL 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ALA* 5.1 0.4 - - + -
265A VAL* 3.6 25.8 - - + +
268A ALA* 3.8 6.3 - - - -
269A VAL* 4.0 28.5 - - + +
272A VAL* 3.9 21.3 - - + -
188B VAL* 4.1 9.6 - - + +
189B THR* 3.7 26.2 - - + -
192B GLU* 2.8 27.6 + - + +
264B PRO* 1.3 69.3 - - - +
266B PHE* 1.3 62.7 + - - +
268B ALA* 3.0 6.4 + - - +
269B VAL* 3.0 26.0 + - + +
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Residues in contact with PHE 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ALA* 3.6 37.2 - - + -
184A PHE* 4.6 5.8 - - + -
185A ALA* 4.0 14.1 - - + +
192B GLU* 2.8 22.2 + - - +
249B PHE* 3.5 29.4 - + + -
252B ILE* 3.7 24.7 - - + -
253B ALA* 3.9 11.2 - - + -
256B LEU* 4.2 14.1 - - + -
263B THR* 3.4 12.7 + - - +
265B VAL* 1.3 75.3 - - - +
267B ASP* 1.3 61.6 + - - +
269B VAL* 3.2 16.0 + - + +
270B CYS* 2.9 44.4 + - - -
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Residues in contact with ASP 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ALA* 4.8 7.1 - - - +
257B HIS* 3.2 31.9 + - - -
262B TRP* 5.7 1.9 - - - -
263B THR* 3.0 30.4 + - - +
264B PRO* 3.5 12.5 - - + +
265B VAL 3.3 0.2 - - - -
266B PHE* 1.3 76.7 - - - +
268B ALA* 1.3 57.8 + - - +
270B CYS* 3.3 9.2 + - - +
271B GLN* 2.9 26.7 + - - +
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Residues in contact with ALA 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A PRO* 3.5 34.9 - - + +
265A VAL* 3.9 8.3 - - - -
268A ALA* 4.0 4.3 - - + -
264B PRO 3.0 12.5 + - - +
265B VAL 3.0 9.4 + - - +
267B ASP* 1.3 74.0 - - - +
269B VAL* 1.3 61.8 + - - +
271B GLN* 3.1 14.3 + - - +
272B VAL* 2.9 31.7 + - - +
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ALA* 3.8 33.9 - - + +
188A VAL* 3.9 30.1 - - + -
265A VAL* 3.8 28.5 - - + -
249B PHE* 4.1 17.3 - - + -
265B VAL 3.0 16.7 + - - +
266B PHE* 3.4 16.8 - - + +
268B ALA* 1.3 77.3 - - - +
270B CYS* 1.3 61.7 + - - +
272B VAL* 3.4 3.5 + - - +
273B VAL* 3.2 23.2 + - - +
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Residues in contact with CYS 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B PHE* 3.8 31.0 - - - -
250B ALA* 4.5 2.0 - - - -
253B ALA* 4.0 11.9 - - + -
266B PHE* 2.9 44.6 + - - -
267B ASP* 3.5 11.4 - - - +
269B VAL* 1.3 77.0 - - - +
271B GLN* 1.3 52.5 + - - +
273B VAL* 3.3 1.0 + - - +
274B GLN* 2.8 49.1 + - + +
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Residues in contact with GLN 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A TRP* 3.7 29.8 - - + +
264A PRO* 4.2 11.9 - - - +
267B ASP 2.9 13.7 + - - +
268B ALA* 3.3 13.9 - - - +
270B CYS* 1.3 75.0 - - - +
272B VAL* 1.3 58.1 + - - +
274B GLN* 4.0 4.3 - - - +
275B ARG* 2.9 34.6 + - + +
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A VAL* 4.2 10.1 - - + -
262A TRP* 4.1 11.2 - - + -
264A PRO* 3.4 33.7 - - + -
265A VAL* 4.1 10.8 - - + -
268B ALA 2.9 13.2 + - - +
269B VAL 3.6 7.2 - - - +
270B CYS 3.3 0.2 - - - -
271B GLN* 1.3 76.2 - - - +
273B VAL* 1.3 58.2 + - - +
275B ARG* 3.5 2.9 + - - +
276B ALA* 2.9 27.0 + - - +
289B THR* 3.6 21.8 - - + -
292B SER* 4.5 4.5 + - - +
293B PHE* 3.5 31.0 - - + -
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A VAL* 4.0 15.3 - - + -
242B LEU* 3.7 26.9 - - + +
246B ALA* 4.1 23.1 - - + +
249B PHE* 3.6 27.8 - - + -
269B VAL 3.2 16.7 + - - +
270B CYS* 4.1 1.8 - - - +
272B VAL* 1.3 74.8 - - + +
274B GLN* 1.3 67.8 + - - +
276B ALA* 3.3 5.2 + - - +
277B ALA* 2.9 22.7 + - - +
286B ILE* 4.4 7.4 - - + -
289B THR* 4.3 13.7 - - + +
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Residues in contact with GLN 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ALA* 3.2 38.4 + - + +
247B ASP* 5.8 0.2 + - - -
249B PHE* 5.5 0.6 - - - +
250B ALA* 3.7 19.0 - - - +
270B CYS* 2.8 38.4 + - + +
271B GLN* 4.0 4.7 - - - +
273B VAL* 1.3 72.0 - - - +
275B ARG* 1.3 57.4 + - - +
277B ALA* 3.0 11.1 + - - +
278B ALA* 2.9 27.5 + - - +
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Residues in contact with ARG 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A TRP* 3.3 44.2 - - + -
271B GLN* 2.9 21.6 + - + +
272B VAL 3.7 3.3 + - - +
274B GLN* 1.3 76.8 - - - +
276B ALA* 1.3 61.2 + - - +
278B ALA* 3.1 9.4 + - + +
279B MSE 3.0 47.2 + - + +
292B SER* 2.7 37.8 + - - -
293B PHE* 4.7 1.0 - - - +
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Residues in contact with ALA 276 (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 LEU* 3.9 25.1 - - + -
272B VAL 2.9 20.1 + - - +
273B VAL* 3.7 6.7 - - - +
275B ARG* 1.3 73.2 - - - +
277B ALA* 1.3 61.8 + - - +
279B MSE 3.1 10.1 + - - -
281B TYR* 3.1 27.9 + - + +
289B THR* 4.5 5.8 - - + -
292B SER* 3.9 29.1 - - - +
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 3.5 16.9 - - + +
243B ASP* 5.1 5.2 - - + -
246B ALA* 4.6 10.3 - - + -
273B VAL 2.9 13.3 + - - +
274B GLN* 3.1 17.0 - - - +
276B ALA* 1.3 76.7 - - - +
278B ALA* 1.3 59.9 + - - +
279B MSE 3.1 1.4 + - - -
280B GLY* 3.2 12.8 + - - -
281B TYR 4.1 0.9 + - - -
282B GLY* 4.2 12.8 + - - +
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B GLN 2.9 12.3 + - - +
275B ARG* 3.1 14.1 + - + +
277B ALA* 1.3 74.7 - - - +
279B MSE 1.3 60.1 + - + +
280B GLY 3.3 1.2 + - - -
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Residues in contact with MSE 279 (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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275B ARG* 3.0 52.7 + - + +
276B ALA 3.5 9.6 - - - +
277B ALA 3.0 1.2 - - - -
278B ALA* 1.3 80.9 - - + +
280B GLY* 1.3 58.9 + - - +
281B TYR* 3.5 28.2 - - + +
291B LYS 5.3 1.1 - - - +
292B SER* 4.0 21.5 - - - +
294B ALA 5.7 3.1 - - - +
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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