Contacts of the helix formed by residues 266 - 281 (chain O) in PDB entry 5G04
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 ASP 266 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A HIS* 3.5 8.2 - - - -
32A PRO* 3.4 14.2 - - - +
116A ALA* 2.9 20.9 - - - +
118A THR* 2.2 30.5 + - - -
261O ASN* 2.7 21.8 + - + +
264O VAL* 3.3 18.3 - - - +
265O GLN* 1.3 69.8 - - - +
267O VAL* 1.3 55.2 + - - +
269O SER* 3.3 28.3 + - - +
270O SER* 2.6 28.8 + - - +
314O PHE* 3.1 8.3 - - - -
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Residues in contact with VAL 267 (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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115A LYS* 3.4 34.1 - - + -
116A ALA 3.0 8.0 + - - +
117A PHE* 3.5 25.4 - - + -
162A HIS* 3.9 10.3 - - + +
265O GLN 3.4 3.4 + - - -
266O ASP* 1.3 73.2 - - - +
268O PHE* 1.3 84.2 + - + +
270O SER* 3.1 14.1 + - - -
271O THR* 3.4 13.5 - - - +
310O LEU* 4.9 1.0 - - - +
314O PHE* 3.8 27.8 - - + -
316O HIS* 3.9 13.9 - - + -
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Residues in contact with PHE 268 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ALA 3.7 1.2 + - - +
117A PHE* 3.9 23.3 - + + -
118A THR 3.3 42.4 - - - +
119A VAL* 3.5 23.1 - - + -
153A ILE* 5.0 3.1 - - + -
160A ASN* 3.8 31.2 - - + -
161A MET 4.3 9.0 - - - -
162A HIS* 4.2 15.3 - + + -
168A ASP* 4.8 9.0 - - + -
267O VAL* 1.3 99.4 - - + +
269O SER* 1.3 67.7 + - - +
271O THR* 2.9 14.2 - - + +
272O HIS* 2.9 33.6 + + + +
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Residues in contact with SER 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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35A LEU* 3.3 26.1 - - - +
118A THR* 3.8 6.7 - - - -
237O GLN* 4.5 0.3 + - - -
261O ASN* 3.2 24.6 + - - -
266O ASP* 3.3 31.1 - - - +
268O PHE* 1.3 79.2 - - - +
270O SER* 1.3 53.4 + - - +
272O HIS* 3.2 8.1 + - - +
273O SER* 2.6 43.0 + - - -
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Residues in contact with SER 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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258O TYR* 3.3 20.7 - - - -
261O ASN* 3.7 8.0 - - - +
262O LEU* 3.0 35.2 - - - -
266O ASP 2.6 22.9 + - - -
267O VAL 3.1 7.8 + - - -
269O SER* 1.3 79.2 - - - +
271O THR* 1.3 63.2 + - - -
273O SER* 3.7 1.5 - - - -
274O LEU* 2.8 26.5 + - - +
310O LEU* 3.9 4.6 - - - +
314O PHE* 3.3 10.0 - - - -
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Residues in contact with THR 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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168A ASP* 5.4 7.6 - - - +
420C TYR* 5.0 10.9 + - + -
267O VAL 3.4 11.7 - - - +
268O PHE* 2.9 28.5 - - + +
270O SER* 1.3 78.1 + - - +
272O HIS* 1.3 70.4 + - + +
275O LEU* 3.1 45.1 + - - +
307O LEU* 4.0 8.1 - - - +
310O LEU* 3.7 21.1 - - - +
311O HIS* 6.1 2.9 - - - -
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Residues in contact with HIS 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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35A LEU* 5.2 14.1 - - + -
37A LEU* 3.4 33.1 - - + +
118A THR 5.3 2.9 - - - -
120A ASP* 5.6 4.1 + - - -
389C ARG* 4.8 1.2 + - - -
420C TYR* 3.2 32.6 + + - -
424C ARG* 4.0 24.1 + - - -
268O PHE* 2.9 33.9 + + + +
269O SER* 3.5 11.7 - - - +
271O THR* 1.3 81.5 - - + +
273O SER* 1.3 62.3 + - - +
276O HIS* 3.5 22.3 + - - +
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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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254O HIS* 3.9 11.1 - - - +
257O SER* 3.8 8.5 - - - -
258O TYR* 3.7 30.7 - - - -
261O ASN* 3.0 17.7 + - - -
269O SER* 2.6 21.9 + - - -
272O HIS* 1.3 75.4 - - - +
274O LEU* 1.3 56.0 + - - +
276O HIS* 3.3 7.9 - - - +
277O TYR* 3.0 28.2 + - - +
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Residues in contact with LEU 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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417C TYR* 5.8 0.2 - - - +
255O TYR* 4.6 1.6 - - + -
258O TYR* 3.5 38.5 - - + +
270O SER 2.8 19.8 + - - +
273O SER* 1.3 70.1 - - - +
275O LEU* 1.3 79.9 + - + +
277O TYR* 3.3 5.9 + - - +
278O PHE* 3.1 64.6 + - + -
303O ALA 4.9 0.7 - - - +
306O ASN* 3.6 14.8 - - + +
307O LEU* 3.9 27.4 - - + +
310O LEU* 4.1 16.6 - - + -
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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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389C ARG* 3.9 3.4 - - - -
417C TYR* 3.3 37.8 + - + +
420C TYR* 3.3 46.0 - - + -
421C TYR* 4.2 3.1 - - - +
271O THR* 3.1 33.5 + - - +
272O HIS 4.7 0.2 - - - +
274O LEU* 1.3 93.4 - - + +
276O HIS* 1.3 65.3 + - - +
279O ASP* 3.1 29.9 + - - +
307O LEU* 3.7 23.1 - - + -
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Residues in contact with HIS 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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36A ASN 4.6 0.4 - - - -
37A LEU* 3.5 34.1 + - + -
39A LEU* 4.3 1.0 - - - +
389C ARG* 3.3 44.6 + - + +
393C GLU* 3.7 26.5 - - + +
254O HIS* 3.4 40.5 + + - +
272O HIS 3.5 13.0 + - - +
273O SER* 3.3 13.2 - - - +
275O LEU* 1.3 75.8 - - - +
277O TYR* 1.3 62.7 + - - +
279O ASP* 3.2 16.3 - - - +
280O ARG* 3.3 9.1 + - + +
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Residues in contact with TYR 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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17D TRP* 3.7 2.1 - + - -
18D PHE* 3.5 28.5 + + - +
251O ALA* 3.3 24.6 - - - +
252O GLU* 4.1 11.0 - - + -
254O HIS* 3.7 17.2 - - + +
255O TYR* 3.5 47.8 - + + +
273O SER 3.0 14.2 + - - +
274O LEU* 3.7 5.6 - - - +
275O LEU 3.3 0.6 - - - -
276O HIS* 1.3 79.6 - - - +
278O PHE* 1.3 95.6 + + - +
280O ARG* 3.4 1.7 + - - +
281O LEU* 2.9 62.8 + - + +
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Residues in contact with PHE 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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409C TYR* 4.4 6.2 + - - -
417C TYR* 3.9 7.2 - - - +
17D TRP* 4.0 22.7 - + + -
255O TYR* 4.7 0.4 - + - -
274O LEU* 3.1 55.3 + - + +
277O TYR* 1.3 99.1 - + - +
279O ASP* 1.3 66.4 + - - +
281O LEU* 4.0 17.3 + - + +
299O SER* 3.6 33.1 - - - +
300O LEU* 4.7 4.3 - - - +
302O TYR* 4.1 17.0 - + + -
303O ALA* 3.5 28.0 - - + -
306O ASN* 3.7 24.2 - - + -
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Residues in contact with ASP 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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382C SER* 5.0 0.7 + - - +
385C ILE* 3.6 22.5 - - + +
386C GLN* 3.4 19.7 + - - +
389C ARG* 2.5 44.6 + - + -
405C LEU* 3.4 8.6 - - - +
409C TYR* 3.2 13.0 + - - -
421C TYR* 2.6 26.1 + - - -
275O LEU 3.1 14.1 + - - +
276O HIS 3.2 10.1 - - - +
277O TYR 3.2 0.2 - - - -
278O PHE* 1.3 79.5 - - - +
280O ARG* 1.3 64.5 + - - +
281O LEU 3.5 1.9 + - - +
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Residues in contact with ARG 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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40A ARG* 3.3 15.2 - - - +
386C GLN* 2.6 39.1 + - - +
389C ARG* 3.9 19.3 - - + -
390C HIS* 3.3 17.9 + - - -
393C GLU* 2.7 44.9 + - - +
248O PRO 4.6 3.4 - - - +
249O ASP* 3.6 38.0 + - - +
251O ALA* 4.2 17.1 - - + +
254O HIS* 5.0 7.6 - - + +
276O HIS* 3.3 16.4 + - + +
277O TYR 3.4 2.0 + - - +
279O ASP* 1.3 79.4 - - - +
281O LEU* 1.3 58.9 + - - +
282O ILE 3.3 1.6 + - - -
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Residues in contact with LEU 281 (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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382C SER* 5.1 0.9 + - - -
386C GLN* 3.9 4.6 + - - -
17D TRP* 4.5 0.4 - - + -
18D PHE* 5.0 5.2 - - - +
251O ALA* 3.8 8.0 - - + +
252O GLU* 4.1 17.7 - - + +
277O TYR* 2.9 63.2 + - + +
278O PHE* 4.0 18.4 - - + -
279O ASP 3.4 4.2 - - - +
280O ARG* 1.3 74.6 - - - +
282O ILE* 1.3 70.8 + - - +
283O LEU* 3.9 33.4 - - + +
299O SER* 3.0 28.7 + - - -
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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