Contacts of the helix formed by residues 263 - 279 (chain A) in PDB entry 3L6B
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A SER* 3.9 18.6 - - - +
213A ASN* 5.8 0.4 - - - -
262A VAL* 1.3 75.6 - - - +
264A GLU* 1.3 65.9 + - - +
265A ASP* 3.7 8.3 + - - +
266A GLU* 2.8 40.2 + - - +
267A ILE* 2.9 23.1 + - - +
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Residues in contact with GLU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A PRO* 4.4 1.9 - - - +
213A ASN* 3.7 27.4 + - - +
234A GLU 4.3 2.5 - - - +
235A THR* 2.7 32.5 + - - -
236A ILE* 2.8 35.7 + - - +
262A VAL 4.0 0.4 + - - +
263A THR* 1.3 72.6 - - - +
265A ASP* 1.3 58.6 + - - +
267A ILE* 3.2 14.2 + - - +
268A LYS* 2.9 44.7 + - - +
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Residues in contact with ASP 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A THR* 3.2 8.5 + - - +
264A GLU* 1.3 78.4 - - - +
266A GLU* 1.3 59.7 + - + +
268A LYS* 3.3 10.2 + - - +
269A CYS* 2.9 50.4 + - - -
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Residues in contact with GLU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A THR 4.6 1.7 - - - +
262A VAL* 3.5 8.8 - - + +
263A THR* 2.8 44.9 + - - +
265A ASP* 1.3 79.7 - - + +
267A ILE* 1.3 57.4 + - - +
269A CYS* 3.9 5.1 - - - +
270A ALA* 3.0 32.2 + - - +
291A ALA* 3.6 15.5 - - + +
295A SER* 3.5 29.8 - - - -
296A GLN 4.8 1.0 + - - -
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Residues in contact with ILE 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A PRO* 4.0 12.3 - - + -
235A THR* 4.4 0.2 - - - +
236A ILE* 3.9 17.9 - - + -
237A ALA* 4.4 4.7 - - + -
262A VAL* 3.7 27.6 - - + +
263A THR 2.9 18.7 + - - +
264A GLU* 3.2 27.8 + - - +
266A GLU* 1.3 76.4 - - - +
268A LYS* 1.3 64.0 + - - +
270A ALA* 4.0 1.3 - - - +
271A THR* 2.8 32.4 + - - +
284A PRO* 3.3 26.7 - - + +
287A GLY 4.7 0.6 - - - +
288A VAL* 3.9 25.4 - - + +
291A ALA* 4.2 5.8 - - - -
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Residues in contact with LYS 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ILE* 3.7 33.6 - - + +
264A GLU* 2.9 32.3 + - - +
265A ASP* 3.7 10.3 - - - +
267A ILE* 1.3 76.7 - - - +
269A CYS* 1.3 63.1 + - - +
271A THR* 4.6 0.9 - - - -
272A GLN* 3.0 23.1 + - - +
284A PRO* 6.3 0.2 - - - -
325A TRP* 3.3 61.1 - - + +
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Residues in contact with CYS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ASP* 2.9 42.8 + - - +
266A GLU* 3.9 5.6 - - - +
268A LYS* 1.3 78.5 - - - +
270A ALA* 1.3 56.8 + - - +
272A GLN* 3.4 6.8 + - - +
273A LEU* 3.0 29.6 + - - +
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Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A GLU 3.0 19.0 + - - +
267A ILE 4.0 0.7 - - - +
269A CYS* 1.3 76.1 - - - +
271A THR* 1.3 63.4 + - - +
273A LEU* 3.3 7.2 + - - +
274A VAL* 3.0 28.8 + - - +
287A GLY* 3.7 9.4 - - - +
290A VAL* 4.0 10.0 - - + +
291A ALA* 3.5 30.3 - - - +
294A LEU* 4.1 11.4 - - + +
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Residues in contact with THR 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ILE* 2.8 22.5 + - - +
268A LYS 3.7 4.5 - - - -
270A ALA* 1.3 76.6 - - - +
272A GLN* 1.3 62.6 + - - +
274A VAL* 3.2 4.3 + - - +
275A TRP* 3.0 55.9 + - + +
282A ILE* 3.9 19.7 - - + +
284A PRO* 3.5 27.0 + - + +
287A GLY* 3.5 10.4 - - - -
325A TRP* 3.7 12.3 - - + -
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Residues in contact with GLN 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A LYS 3.0 17.0 + - - +
269A CYS* 3.9 6.1 - - - +
271A THR* 1.3 77.5 - - - +
273A LEU* 1.3 57.1 + - - +
275A TRP* 3.3 16.0 + - + +
276A GLU* 2.9 60.3 + - + +
325A TRP* 4.5 9.7 - - + +
326A VAL* 3.5 26.6 - - + +
327A LYS* 2.8 42.6 + - - +
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 5.5 1.8 - - + -
34A LEU* 4.1 19.7 - - + -
37A LEU* 3.9 31.4 - - + -
269A CYS 3.0 18.3 + - - +
270A ALA 3.5 4.9 - - - +
272A GLN* 1.3 77.4 - - - +
274A VAL* 1.3 57.1 + - + +
276A GLU* 4.8 4.7 - - - +
277A ARG* 2.8 58.5 + - + +
290A VAL* 5.4 0.4 - - + -
294A LEU* 3.9 25.6 - - + -
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Residues in contact with VAL 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.4 11.9 - - + -
270A ALA 3.0 14.5 + - - +
271A THR 3.2 6.9 + - - +
273A LEU* 1.3 72.4 - - - +
275A TRP* 1.3 65.6 + - - +
278A MET* 2.9 38.9 + - + +
279A LYS 3.1 6.2 + - - -
280A LEU* 3.7 29.5 + - + +
282A ILE* 3.7 28.5 - - + -
290A VAL* 3.9 27.4 - - + -
312A LEU* 4.7 3.1 - - + -
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Residues in contact with TRP 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A THR* 3.0 33.8 + - + +
272A GLN* 3.5 19.1 - - + +
274A VAL* 1.3 75.7 - - - +
276A GLU* 1.3 62.9 + - + +
279A LYS* 3.1 29.9 + - - +
280A LEU 3.2 23.8 - - - +
281A LEU* 3.7 24.6 - - + +
282A ILE* 2.8 30.8 + - + +
317A VAL* 4.3 10.8 - - + -
319A LEU* 6.0 2.2 - - + -
322A SER* 4.1 17.3 - - - -
325A TRP* 3.5 33.4 - + - -
326A VAL* 4.9 16.2 - - + -
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Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A GLN* 2.9 51.8 + - + +
273A LEU* 4.2 5.2 + - + +
275A TRP* 1.3 81.6 - - + +
277A ARG* 1.3 71.1 + - + +
279A LYS* 2.8 32.0 + - - +
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Residues in contact with ARG 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A SER* 5.1 2.1 + - - -
33A ILE* 3.7 57.4 - - + +
34A LEU* 4.3 5.8 - - + -
273A LEU* 2.8 44.0 + - + +
276A GLU* 1.3 85.9 - - + +
278A MET* 1.3 58.6 + - + +
279A LYS* 3.6 5.6 - - - +
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Residues in contact with MET 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 4.2 12.8 - - + +
30A THR 3.9 17.9 - - - +
31A SER* 3.9 16.4 - - - +
34A LEU* 4.0 13.7 - - + -
44A PHE* 3.6 48.5 - - + -
274A VAL* 2.9 24.7 + - + +
277A ARG* 1.3 79.3 - - + +
279A LYS* 1.3 74.9 + - - +
280A LEU* 3.3 36.5 + - + +
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A VAL 3.1 0.6 + - - -
275A TRP* 3.1 18.1 + - - +
276A GLU* 2.8 28.3 + - - +
277A ARG 4.7 4.7 - - - +
278A MET* 1.3 81.2 - - - +
280A LEU* 1.3 61.6 + - - +
281A LEU 4.0 1.6 + - - -
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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