Contacts of the helix formed by residues 267 - 280 (chain O) in PDB entry 3H1I
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 ALA 267 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265O GLY 3.3 5.4 + - - -
266O SER* 1.3 71.3 - - - +
268O GLU* 1.3 54.1 + - - +
269O ALA 2.8 11.8 + - - -
270O ASN* 3.5 25.8 + - - +
271O ALA* 4.2 3.5 + - - +
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Residues in contact with GLU 268 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261O GLY 4.3 0.2 - - - +
262O ALA* 3.5 14.4 - - - +
263O ALA 5.0 0.3 + - - -
266O SER* 2.9 12.1 + - - +
267O ALA* 1.3 77.8 - - - +
269O ALA* 1.3 57.0 + - - +
271O ALA* 3.8 12.7 - - + +
272O PHE* 3.0 27.9 - - + -
416O LYS* 2.7 43.6 + - + +
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Residues in contact with ALA 269 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262O ALA* 3.6 10.9 - - + +
263O ALA 3.9 16.8 - - - +
264O VAL* 5.6 0.2 - - - -
265O GLY* 5.1 3.6 - - - +
266O SER 2.8 21.3 + - - +
267O ALA 2.8 1.8 + - - -
268O GLU* 1.3 68.4 - - - +
270O ASN* 1.3 71.1 + - - +
271O ALA 2.6 4.4 + - - -
272O PHE* 2.6 18.9 + - - +
273O SER* 3.2 12.7 + - - +
315O ASN* 4.3 17.9 - - - +
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Residues in contact with ASN 270 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266O SER 5.1 0.8 + - - -
267O ALA* 4.0 18.8 + - - +
269O ALA* 1.3 79.4 - - - +
271O ALA* 1.3 63.4 + - - +
273O SER* 3.3 11.7 + - - -
274O VAL* 3.1 25.8 + - - +
364O LEU* 4.7 2.7 - - - +
401O LYS* 3.7 41.1 + - - +
402O ILE* 5.2 7.0 + - - +
405O VAL* 4.1 9.9 - - + -
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Residues in contact with ALA 271 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267O ALA 4.2 3.4 + - - +
268O GLU* 3.8 17.3 - - + +
269O ALA 2.6 4.2 + - - -
270O ASN* 1.3 75.2 - - - +
272O PHE* 1.3 63.2 + - - +
274O VAL* 3.1 7.6 + - - +
275O LEU* 2.9 18.2 + - - +
405O VAL* 4.2 13.0 - - + +
409O ASP* 4.0 33.4 - - + +
410O VAL* 4.7 4.0 - - - +
413O ALA* 4.4 7.4 - - + +
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Residues in contact with PHE 272 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260O GLU 5.1 1.1 - - - -
261O GLY* 4.3 4.9 - - - -
262O ALA* 3.5 31.6 - - + -
268O GLU* 3.0 37.0 - - + -
269O ALA* 2.6 11.0 + - - +
271O ALA* 1.3 75.0 - - - +
273O SER* 1.3 50.8 + - - +
275O LEU* 2.4 11.4 + - - +
276O GLN 2.4 35.9 + - - -
313O ASN* 4.1 7.9 - - - +
322O PHE* 3.3 50.4 - + + -
413O ALA* 3.6 36.3 - - + -
416O LYS* 3.7 28.0 - - + -
417O PHE* 5.5 2.0 - - + -
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Residues in contact with SER 273 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269O ALA* 3.2 11.5 + - - +
270O ASN* 3.3 14.2 + - - -
272O PHE* 1.3 76.2 - - - +
274O VAL* 1.3 58.2 + - - +
276O GLN* 2.9 34.7 + - - +
277O HIS* 3.0 19.3 - - - -
313O ASN* 3.9 15.0 + - - +
315O ASN* 4.9 5.7 + - - -
364O LEU* 3.7 21.3 - - - -
62V ARG* 5.5 2.1 + - - -
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Residues in contact with VAL 274 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270O ASN* 3.1 13.1 + - + +
271O ALA 3.1 8.2 + - - +
272O PHE 2.9 0.8 - - - -
273O SER* 1.3 70.6 - - - +
275O LEU* 1.3 54.9 + - - +
276O GLN 3.0 4.4 + - - -
277O HIS* 3.3 5.6 + - - +
278O VAL* 2.7 49.8 + - + +
357O VAL* 4.2 17.5 - - + +
360O ALA* 3.6 12.4 - - + +
361O LYS* 4.7 11.4 - - + -
364O LEU* 4.0 15.7 - - + -
402O ILE* 4.4 5.6 - - + +
405O VAL* 4.1 23.1 - - + -
410O VAL* 4.0 15.7 - - + -
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Residues in contact with LEU 275 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271O ALA 2.9 11.7 + - - +
272O PHE* 2.4 23.2 + - - +
274O VAL* 1.3 68.2 - - - +
276O GLN* 1.3 62.0 + - - +
278O VAL* 3.7 12.3 - - + -
279O LEU* 2.9 41.9 + - + +
322O PHE* 3.8 17.5 - - + -
344O LEU* 5.1 2.0 - - + -
347O ALA* 5.4 5.8 - - + +
352O VAL* 5.9 1.1 - - + -
410O VAL* 3.8 22.4 - - + +
413O ALA* 3.6 13.0 - - + +
414O ALA* 3.2 44.4 - - + +
417O PHE* 6.1 0.2 - - + -
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Residues in contact with GLN 276 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272O PHE 2.4 19.5 + - - +
273O SER* 2.9 27.1 + - - +
275O LEU* 1.3 70.8 - - - +
277O HIS* 1.3 69.5 + - - +
279O LEU* 2.7 28.9 + - - +
280O GLY 3.1 7.3 + - - -
281O ALA* 4.2 12.3 - - + +
311O ALA* 3.4 37.7 - - + +
313O ASN* 3.4 28.8 + - + +
322O PHE* 4.4 8.9 - - + -
364O LEU* 5.2 1.4 - - - +
61V ARG 4.0 9.7 - - - +
62V ARG* 4.3 14.3 + - - +
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Residues in contact with HIS 277 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273O SER 3.0 22.0 + - - -
274O VAL* 3.8 1.1 - - - +
276O GLN* 1.3 91.9 + - - +
278O VAL* 1.3 61.1 + - - +
280O GLY* 3.1 13.6 + - - +
281O ALA* 4.0 22.9 + - + +
292O THR* 4.1 7.6 - - - +
360O ALA* 3.6 27.1 - - + +
363O GLN* 4.3 28.3 + - + +
364O LEU* 3.1 54.9 - - + +
367O THR* 4.6 14.4 - - + -
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Residues in contact with VAL 278 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274O VAL* 2.7 39.8 + - + +
275O LEU* 3.6 18.6 - - + +
276O GLN 2.9 0.2 + - - -
277O HIS* 1.3 78.2 - - - +
279O LEU* 1.3 60.6 + - + +
280O GLY 3.3 0.2 - - - -
292O THR* 3.9 4.8 - - - +
294O LYS* 3.0 31.0 + - + +
351O GLY 5.8 0.7 - - - +
352O VAL* 4.9 14.6 - - + -
356O ASP* 4.1 28.5 - - + +
357O VAL* 4.8 2.2 - - + -
360O ALA* 3.5 17.3 - - + -
410O VAL* 4.6 7.0 - - + -
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Residues in contact with LEU 279 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275O LEU* 2.9 37.9 - - + +
276O GLN 2.7 7.2 + - - +
278O VAL* 1.3 78.8 - - + +
280O GLY* 1.3 58.8 + - - +
293O SER* 3.1 4.0 + - - -
294O LYS* 3.9 7.2 - - + -
295O LEU* 2.7 58.3 + - + +
311O ALA* 4.1 12.1 - - + -
322O PHE* 4.4 10.3 - - + -
323O GLY 6.0 0.9 - - - +
343O GLN 4.1 15.5 - - - +
344O LEU* 3.3 37.9 - - + -
347O ALA* 4.4 9.0 - - + -
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Residues in contact with GLY 280 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276O GLN 3.1 5.8 + - - -
277O HIS 3.1 10.4 + - - -
278O VAL 3.3 0.2 - - - -
279O LEU* 1.3 80.7 - - - +
281O ALA* 1.3 60.7 + - - -
282O GLY 4.0 1.6 - - - -
292O THR 4.8 0.7 - - - -
293O SER* 3.2 25.7 + - - -
310O SER* 3.7 7.2 - - - -
311O ALA* 3.1 23.6 + - - +
363O GLN* 6.1 0.4 - - - -
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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