Contacts of the helix formed by residues 275 - 290 (chain A) in PDB entry 6XYY
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 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A HIS* 5.7 1.3 - - + -
274A MET* 1.3 77.4 - - - +
276A SER* 1.3 67.0 + - - +
277A GLU* 3.8 15.7 - - - +
278A LYS* 3.0 38.6 + - - +
279A ALA* 3.1 18.7 + - - +
335A THR* 3.9 0.4 - - - -
336A ILE* 4.4 14.4 - - + -
344A ASP* 5.7 2.5 - - - +
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Residues in contact with SER 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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189A HIS* 2.8 26.9 + - - -
192A PRO* 3.4 17.2 - - - +
274A MET 3.7 1.6 + - - -
275A THR* 1.3 73.1 - - - +
277A GLU* 1.3 67.8 + - - +
279A ALA* 3.2 2.3 + - - +
280A VAL* 2.9 32.1 + - - +
335A THR* 3.9 3.1 - - - +
336A ILE* 3.6 24.3 + - - +
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Residues in contact with GLU 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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275A THR* 3.2 12.8 - - - +
276A SER* 1.3 87.1 + - - +
278A LYS* 1.3 61.8 + - - +
280A VAL* 3.4 7.9 + - - +
281A GLU* 3.1 38.3 + - - +
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Residues in contact with LYS 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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274A MET* 3.6 19.5 - - + +
275A THR* 3.0 27.4 + - - +
277A GLU* 1.3 76.2 - - - +
279A ALA* 1.3 59.4 + - - +
281A GLU* 3.0 20.0 + - + +
282A ILE* 2.8 45.3 + - + +
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Residues in contact with ALA 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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187A PHE 5.2 3.1 - - - +
189A HIS* 3.6 35.6 + - + +
274A MET* 3.7 16.4 - - - -
275A THR 3.1 12.8 + - - +
276A SER 3.6 2.5 - - - +
278A LYS* 1.3 76.7 - - - +
280A VAL* 1.3 51.5 + - - +
282A ILE* 3.8 5.2 - - - +
283A GLY* 2.6 35.9 + - - -
331A PRO 5.8 0.2 - - - -
335A THR* 3.7 14.4 - - + +
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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
----------------------------------------------------------
189A HIS* 3.7 26.2 - - + +
190A LEU* 4.4 5.8 - - + +
192A PRO* 4.0 25.8 - - + -
193A GLU* 3.2 35.7 - - + +
276A SER 2.9 21.8 + - - +
277A GLU* 3.7 7.9 - - - +
278A LYS 3.2 0.2 - - - -
279A ALA* 1.3 74.3 - - - +
281A GLU* 1.3 60.6 + - + +
283A GLY* 3.5 0.2 - - - -
284A LYS* 2.8 37.9 + - - +
297A LEU* 6.3 0.2 - - + -
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Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLU* 3.1 26.3 + - - +
278A LYS* 3.0 23.1 + - + +
280A VAL* 1.3 80.1 - - + +
282A ILE* 1.3 62.7 + - + +
284A LYS* 3.3 11.5 + - + +
285A ALA* 3.1 24.3 + - - +
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Residues in contact with ILE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A MET* 3.7 31.6 - - + -
278A LYS* 2.8 32.4 + - + +
279A ALA* 3.8 4.9 - - - +
281A GLU* 1.3 74.2 - - + +
283A GLY* 1.3 65.8 + - - +
285A ALA* 3.3 5.1 + - - +
286A LEU* 3.1 23.6 + - + +
320A GLN 5.7 0.4 - - - +
323A SER* 3.9 28.7 + - - +
330A PHE 5.2 0.2 - - - +
331A PRO* 3.6 35.4 - - + +
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Residues in contact with GLY 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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188A LEU* 3.7 24.5 - - - +
189A HIS 5.4 0.2 - - - -
190A LEU* 3.9 10.3 - - - -
279A ALA 2.6 21.0 + - - -
280A VAL 3.5 1.1 - - - -
282A ILE* 1.3 75.9 - - - +
284A LYS* 1.3 56.5 + - - +
286A LEU* 3.2 8.4 + - - +
287A ILE* 3.1 27.9 + - - +
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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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190A LEU* 4.0 1.7 - - + +
193A GLU* 2.7 40.1 + - - -
280A VAL* 2.8 23.6 + - + +
281A GLU* 3.5 15.3 - - + +
283A GLY* 1.3 70.9 - - - +
285A ALA* 1.3 62.2 + - + +
287A ILE* 3.2 12.6 - - + +
288A ASN* 2.9 29.5 + - - +
294A ALA* 3.4 29.4 - - + +
297A LEU* 4.8 8.3 - - + -
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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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281A GLU 3.1 17.3 + - - +
282A ILE* 3.6 6.3 - - - +
284A LYS* 1.3 77.2 - - + +
286A LEU* 1.3 53.8 + - - +
288A ASN* 3.1 9.5 + - - +
289A ASP* 2.6 47.8 + - - +
323A SER* 4.4 11.7 - - - +
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Residues in contact with LEU 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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44A PHE* 5.5 0.4 - - + -
184A ALA* 3.4 32.1 - - + -
188A LEU* 4.5 17.5 - - + -
282A ILE* 3.1 14.7 + - + +
283A GLY* 3.4 7.9 - - - +
285A ALA* 1.3 73.7 - - - +
287A ILE* 1.3 63.6 + - - +
289A ASP* 3.1 6.8 + - - -
290A CYS* 2.9 47.5 + - - -
308A MET* 4.2 13.5 - - + -
316A ILE* 4.2 14.8 - - + +
319A GLN* 4.1 6.7 - - + -
320A GLN* 3.9 30.7 - - + +
323A SER* 5.1 2.5 + - - +
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Residues in contact with ILE 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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188A LEU* 4.8 3.8 - - + -
190A LEU* 3.7 27.1 - - + -
283A GLY 3.1 18.2 + - - +
284A LYS* 3.2 15.3 - - + +
285A ALA 3.2 0.2 - - - -
286A LEU* 1.3 74.4 - - - +
288A ASN* 1.3 61.9 + - - +
290A CYS* 3.1 12.0 + - - +
291A ASN 3.3 0.2 + - - -
292A CYS* 3.2 40.6 + - + +
294A ALA* 3.6 17.3 - - + -
297A LEU* 5.0 2.0 - - + -
304A VAL* 3.8 21.3 - - + -
305A MET* 5.2 0.2 - - - -
308A MET* 3.5 34.3 - - + -
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Residues in contact with ASN 288 (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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284A LYS* 2.9 21.2 + - - +
285A ALA* 3.6 8.9 - - - +
287A ILE* 1.3 72.8 - - - +
289A ASP* 1.3 61.2 + - - +
291A ASN* 2.9 25.3 + - - +
292A CYS 3.8 4.5 - - - +
293A ASN* 4.2 3.5 - - - -
294A ALA* 3.2 35.9 + - - +
295A SER 4.5 2.0 + - - +
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Residues in contact with ASP 289 (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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285A ALA* 2.6 35.0 + - - +
286A LEU* 3.1 9.7 + - - +
288A ASN* 1.3 75.1 - - - +
290A CYS* 1.3 58.9 + - - +
291A ASN* 3.4 6.9 + - - +
315A THR* 5.4 0.7 - - - +
319A GLN* 3.9 29.3 + - + +
322A ASN* 3.0 40.2 + - - +
323A SER* 5.0 1.6 + - - -
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Residues in contact with CYS 290 (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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286A LEU* 2.9 40.3 + - - +
287A ILE 3.1 3.7 + - - +
289A ASP* 1.3 78.1 - - - +
291A ASN* 1.3 73.6 + - - +
292A CYS* 3.3 7.5 + - - -
307A CYS* 4.7 0.5 - - - -
308A MET* 4.1 22.2 - - - -
311A VAL* 4.1 18.1 - - + +
315A THR* 4.3 20.4 - - - -
316A ILE* 4.4 10.5 - - - -
319A GLN* 4.5 3.6 - - - -
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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