Contacts of the helix formed by residues 270 - 283 (chain A) in PDB entry 5LSW
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 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A LEU 4.7 0.2 - - - -
269A ASP* 1.3 72.6 + - - +
271A THR* 1.3 65.3 + - - +
273A LYS* 3.3 11.9 + - + +
274A ARG* 3.2 38.8 + - + +
268C ASP* 2.6 49.0 + - - +
269C ASP* 4.0 11.1 + - - +
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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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230A LYS* 4.5 4.7 - - - +
269A ASP* 3.3 11.1 + - - -
270A THR* 1.3 80.4 - - - +
272A THR* 1.3 62.7 + - - +
274A ARG* 3.3 7.0 + - - +
275A TRP* 3.3 52.8 + - + +
230C LYS* 3.1 27.6 + - - +
269C ASP* 3.0 8.0 + - - -
271C THR* 3.0 29.6 + - + -
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Residues in contact with THR 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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226A ALA 5.2 1.0 + - - +
229A LEU* 4.5 1.6 - - + +
230A LYS* 3.7 38.9 - - + +
233A VAL* 4.4 20.2 - - + -
266A LEU* 3.7 28.5 - - + -
269A ASP* 2.3 30.5 + - - -
270A THR 3.3 0.4 - - - -
271A THR* 1.3 76.9 - - - +
273A LYS* 1.3 57.8 + - - +
275A TRP* 3.2 10.0 + - + +
276A LEU* 3.0 27.5 + - - +
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Residues in contact with LYS 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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263A ALA* 4.3 12.6 + - - +
266A LEU* 3.2 54.1 - - + +
267A LYS* 3.9 29.3 - - - +
269A ASP 3.3 6.5 - - - +
270A THR* 3.3 14.7 + - + +
272A THR* 1.3 74.5 - - - +
274A ARG* 1.3 64.8 + - + +
276A LEU* 4.5 1.3 - - - +
277A ALA* 3.0 30.0 + - - +
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Residues in contact with ARG 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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270A THR* 3.2 27.8 + - + +
271A THR* 3.3 10.7 + - - +
273A LYS* 1.3 77.3 - - + +
275A TRP* 1.3 63.2 + - + +
277A ALA* 4.6 2.4 - - - +
278A GLN* 3.1 30.4 + - - +
226C ALA* 6.2 1.8 - - - +
227C ARG* 4.2 31.3 - - - +
806D VAL* 4.1 15.5 - - - +
810D ASP* 2.4 46.5 + - + -
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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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187A GLN* 5.5 4.3 - - - -
230A LYS* 3.6 52.9 - - + -
231A HIS* 6.2 0.7 - + - -
233A VAL* 4.0 11.4 - - + +
234A ARG* 3.5 42.3 - - + +
237A LEU* 4.1 24.2 - - + +
271A THR* 3.3 27.3 + - + +
272A THR* 3.2 12.9 + - + +
273A LYS 3.1 0.6 - - - -
274A ARG* 1.3 83.5 - - + +
276A LEU* 1.3 60.3 + - - +
278A GLN* 3.3 7.9 + - - +
279A LEU* 3.0 28.4 + - - +
230C LYS* 5.5 1.3 - - - -
810D ASP* 3.2 34.9 + - + +
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Residues in contact with LEU 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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229A LEU* 6.3 0.4 - - + -
233A VAL* 3.7 22.8 - - + +
257A LEU* 3.7 53.8 - - + +
259A ASP 6.1 0.9 - - - +
262A PHE* 5.5 3.8 - - + -
266A LEU* 3.9 24.2 - - + -
272A THR* 3.0 15.6 + - + +
273A LYS* 4.2 4.3 - - - +
275A TRP* 1.3 75.9 - - - +
277A ALA* 1.3 62.8 + - - +
279A LEU* 3.1 26.6 + - + +
280A VAL* 3.2 18.7 + - + +
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Residues in contact with ALA 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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273A LYS 3.0 17.8 + - - +
274A ARG* 4.6 2.7 - - - +
276A LEU* 1.3 76.7 - - - +
278A GLN* 1.3 62.5 + - - +
280A VAL* 3.2 16.4 - - + +
281A LYS* 3.2 38.4 - - - +
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Residues in contact with GLN 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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237A LEU* 4.3 20.9 - - + +
274A ARG 3.1 22.6 + - - +
275A TRP* 3.6 7.0 - - - +
276A LEU 3.3 0.4 - - - -
277A ALA* 1.3 78.3 - - - +
279A LEU* 1.3 60.4 + - - +
281A LYS* 3.7 11.3 + - + +
282A ASN* 2.8 40.1 + - - +
807D ASP* 3.1 49.9 + - - +
810D ASP* 4.6 8.0 - - - +
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Residues in contact with LEU 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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233A VAL* 4.8 4.5 - - + +
236A TYR* 3.6 47.8 - - + +
237A LEU* 3.9 13.7 - - + +
240A SER* 3.7 19.3 - - - +
249A LEU* 4.8 3.8 - - + -
253A LEU* 4.1 20.9 - - + -
257A LEU* 5.3 0.7 - - + -
275A TRP 3.0 13.3 + - - +
276A LEU* 3.1 24.8 + - + +
278A GLN* 1.3 75.7 - - - +
280A VAL* 1.3 67.1 + - + +
282A ASN* 3.1 15.2 + - - +
283A LEU* 3.2 26.1 + - + +
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Residues in contact with VAL 280 (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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253A LEU* 4.0 24.7 - - + -
257A LEU 4.2 14.6 - - - +
258A LYS* 4.9 8.5 - - + -
276A LEU* 3.2 16.1 + - + +
277A ALA* 3.2 22.9 - - + +
279A LEU* 1.3 77.2 - - + +
281A LYS* 1.3 64.3 + - + +
283A LEU* 3.0 10.2 + - - +
284A GLN* 3.0 37.8 + - - +
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Residues in contact with LYS 281 (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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277A ALA* 3.2 31.6 + - - +
278A GLN* 3.9 9.8 - - + +
279A LEU 3.2 0.6 - - - -
280A VAL* 1.3 82.0 - - + +
282A ASN* 1.3 62.5 + - - +
284A GLN* 3.3 24.0 + - - +
285A GLU* 3.7 10.7 + - - +
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Residues in contact with ASN 282 (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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237A LEU* 4.1 8.1 - - - +
240A SER* 3.9 22.8 + - - +
241A ASP* 5.5 1.6 + - - -
246A ARG* 2.9 46.4 + - - +
250A ARG* 3.4 9.4 + - - -
278A GLN* 2.8 31.6 + - - +
279A LEU* 3.1 9.3 + - - +
281A LYS* 1.3 79.9 - - - +
283A LEU* 1.3 61.3 + - + +
284A GLN 3.7 0.3 + - - -
285A GLU* 3.7 3.9 + - - +
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Residues in contact with LEU 283 (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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240A SER* 5.0 2.5 - - - -
246A ARG* 3.4 39.7 - - + +
249A LEU* 3.6 34.1 - - + +
250A ARG* 2.9 35.2 + - + +
253A LEU* 3.7 27.6 - - + -
258A LYS* 5.6 1.8 - - - -
279A LEU* 3.2 26.9 + - + +
280A VAL* 3.0 11.0 + - - +
282A ASN* 1.3 77.0 - - - +
284A GLN* 1.3 59.1 + - + +
285A GLU 3.3 0.9 - - - -
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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