Contacts of the helix formed by residues 272 - 287 (chain A) in PDB entry 5L9Y
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 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A ASN* 6.2 0.4 - - - +
270A GLN* 2.8 48.2 + - + +
271A PRO* 1.3 73.4 - - - +
273A ARG* 1.3 57.8 + - - +
274A LYS* 3.3 4.5 - - + +
275A THR* 2.9 13.3 + - - +
276A ALA* 2.8 30.3 + - - +
608A 6S6 3.2 63.1 + - - +
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Residues in contact with ARG 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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272A ARG* 1.3 73.3 - - - +
274A LYS* 1.3 65.5 + - + +
276A ALA* 3.4 6.6 + - - +
277A LYS* 3.1 24.4 + - + +
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Residues in contact with LYS 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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227A ASN* 5.9 0.9 - - - -
272A ARG* 3.3 3.0 - - + +
273A ARG* 1.3 82.2 - - + +
275A THR* 1.3 62.6 + - - +
277A LYS* 3.6 11.3 + - + +
278A MET* 3.2 23.6 + - - +
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Residues in contact with THR 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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227A ASN* 3.6 25.8 + - + +
268A VAL* 3.7 21.7 - - + +
269A GLY 3.3 30.0 - - - +
270A GLN 3.6 13.6 + - - +
271A PRO* 4.6 1.6 - - + -
272A ARG* 2.9 19.1 + - - +
274A LYS* 1.3 75.9 - - - +
276A ALA* 1.3 60.5 + - - +
278A MET* 3.2 6.1 + - - +
279A LEU* 2.8 28.2 + - - +
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Residues in contact with ALA 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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271A PRO* 4.3 18.3 - - + +
272A ARG 2.8 19.2 + - - +
273A ARG* 3.7 7.6 - - - +
275A THR* 1.3 72.5 - - - +
277A LYS* 1.3 57.6 + - - +
279A LEU* 3.3 8.1 + - - +
280A LYS* 2.8 31.4 + - - +
325A LYS* 6.4 0.7 - - + -
329A VAL* 4.1 21.8 - - + +
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Residues in contact with LYS 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 ARG* 3.1 18.2 + - + +
274A LYS* 3.6 11.2 - - + +
276A ALA* 1.3 74.9 - - - +
278A MET* 1.3 63.3 + - - +
280A LYS* 3.4 6.3 + - - +
281A SER* 2.9 30.1 + - - +
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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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226A PRO* 3.8 19.5 - - + +
227A ASN* 3.5 40.4 - - + +
236A PHE* 4.2 19.3 - - + -
237A ILE 3.4 24.5 - - - +
238A ASN* 4.5 4.0 - - - -
239A GLY* 3.6 14.2 - - - +
242A LEU* 5.2 4.3 - - + -
268A VAL* 4.6 8.7 - - + -
274A LYS 3.2 11.8 + - - +
275A THR* 3.2 9.8 + - - +
277A LYS* 1.3 77.5 - - - +
279A LEU* 1.3 59.5 + - - +
281A SER* 3.2 8.6 + - - -
282A PHE* 2.9 33.0 + - + +
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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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266A PRO* 3.8 32.8 - - + -
268A VAL* 4.1 21.0 - - + +
271A PRO* 6.1 2.9 - - + -
275A THR 2.8 17.3 + - - +
276A ALA* 3.7 6.5 - - - +
278A MET* 1.3 79.1 - - - +
280A LYS* 1.3 56.9 + - - +
282A PHE* 3.3 3.8 + - + +
283A LEU* 2.9 40.6 + - + +
293A VAL* 3.9 17.0 - - + -
295A TRP* 5.8 1.1 - - + -
326A VAL* 4.7 22.9 - - + +
329A VAL* 3.7 26.7 - - + -
330A VAL* 4.8 0.7 - - + -
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Residues in contact with LYS 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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276A ALA 2.8 22.3 + - - +
277A LYS* 3.8 7.0 - - - +
279A LEU* 1.3 72.5 - - - +
281A SER* 1.3 59.5 + - - +
283A LEU* 3.3 0.7 + - - -
284A LYS* 3.0 56.5 + - - +
329A VAL* 3.6 19.8 - - + +
332A SER* 3.2 29.9 + - - +
333A THR* 3.8 15.2 - - + +
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Residues in contact with SER 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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238A ASN* 5.6 0.2 - - - +
239A GLY* 3.4 16.3 + - - +
240A SER* 4.1 19.0 + - - -
277A LYS* 2.9 21.8 + - - +
278A MET* 3.2 9.5 + - - -
280A LYS* 1.3 74.2 - - - +
282A PHE* 1.3 63.4 + - - +
284A LYS* 3.5 14.0 + - - +
285A ALA* 3.0 26.0 + - - +
602A NAG 6.4 0.7 - - - -
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Residues in contact with PHE 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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239A GLY* 3.2 15.8 + - - +
242A LEU* 3.9 14.1 - - + -
243A GLY* 3.6 25.4 - - - -
246A PHE* 3.4 49.4 - + + -
266A PRO* 3.6 39.3 - - + -
278A MET* 2.9 20.2 + - + +
279A LEU* 3.6 5.2 - - - +
280A LYS 3.2 0.2 - - - -
281A SER* 1.3 77.4 + - - +
283A LEU* 1.3 65.0 + - + +
286A GLY* 2.7 37.8 + - - -
290A ILE* 4.0 26.9 - - + -
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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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279A LEU* 2.9 35.5 + - + +
280A LYS 3.3 1.7 + - - +
282A PHE* 1.3 85.4 - - + +
284A LYS* 1.3 62.8 + - - +
287A GLY* 3.1 15.0 + - - +
290A ILE* 3.8 28.7 - - + -
293A VAL* 3.9 13.5 - - + -
329A VAL* 4.4 3.4 - - + -
330A VAL* 3.9 30.1 - - + -
333A THR* 3.3 29.6 - - - +
334A ARG* 2.9 34.4 + - + -
337A LYS* 5.7 0.2 - - + -
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Residues in contact with LYS 284 (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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280A LYS* 3.0 51.6 + - - +
281A SER* 3.6 15.0 - - - +
282A PHE 3.4 0.2 - - - -
283A LEU* 1.3 75.2 - - - +
285A ALA* 1.3 58.9 + - - +
332A SER 5.4 1.6 + - - -
333A THR* 4.3 14.1 - - + +
334A ARG* 3.0 22.1 + - - +
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Residues in contact with ALA 285 (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* 3.5 31.2 - - - +
243A GLY* 3.9 7.0 - - - -
244A GLU* 4.5 10.2 - - - +
247A ILE* 3.6 18.1 - - - +
281A SER 3.0 13.9 + - - +
282A PHE 3.9 1.6 - - - +
284A LYS* 1.3 83.7 - - - +
286A GLY* 1.3 60.5 + - - +
287A GLY 3.9 0.5 + - - -
288A GLU* 5.1 1.9 + - - +
334A ARG* 4.4 2.6 + - - -
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Residues in contact with GLY 286 (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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243A GLY* 3.6 25.1 - - - -
246A PHE* 5.1 0.4 - - - -
247A ILE* 4.4 5.8 - - - -
282A PHE* 2.7 24.3 + - - -
285A ALA* 1.3 74.7 - - - +
287A GLY* 1.3 61.9 + - - +
288A GLU* 3.1 4.9 + - - -
289A VAL* 3.2 22.5 + - - +
290A ILE* 4.0 6.8 + - - +
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Residues in contact with GLY 287 (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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282A PHE* 3.6 1.6 + - - -
283A LEU* 3.1 31.9 + - - -
285A ALA 3.6 1.4 + - - -
286A GLY* 1.3 77.0 - - - +
288A GLU* 1.3 59.0 + - - +
289A VAL 3.3 0.8 + - - -
290A ILE* 3.6 13.7 - - - +
334A ARG* 3.6 13.1 - - - +
337A LYS* 3.0 30.1 + - - -
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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
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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