Contacts of the helix formed by residues 274 - 292 (chain A) in PDB entry 1Z15
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 GLY 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLN* 3.5 28.3 - - - -
271A ASP* 4.3 6.3 + - - -
272A PRO 3.5 1.6 - - - -
273A SER* 1.3 81.2 + - - +
275A ALA* 1.3 67.1 + - - -
276A PHE 3.2 2.7 - - - -
277A VAL* 3.2 23.4 + - - +
278A TRP* 3.3 6.4 - - - -
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Residues in contact with ALA 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLN* 3.4 3.5 + - - +
249A PRO* 5.5 12.1 - - + -
252A TYR* 5.7 2.8 - - - -
273A SER 3.4 3.5 + - - -
274A GLY* 1.3 72.7 - - - -
276A PHE* 1.3 72.7 + - + +
278A TRP* 3.3 18.9 + - - +
279A THR* 3.4 17.8 + - + +
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Residues in contact with PHE 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 4.0 38.4 - + + +
21A GLN* 3.0 31.9 + - + +
22A GLU* 4.2 7.6 - - + +
77A LEU* 4.0 13.7 - - + -
99A PRO* 3.8 5.6 - - + -
100A ALA* 3.5 30.3 - - + -
118A THR* 5.2 5.4 - - - -
275A ALA* 1.3 83.3 - - + +
277A VAL* 1.3 63.7 + - - +
278A TRP 3.2 0.2 - - - -
279A THR* 3.4 18.2 - - + +
280A THR* 2.7 33.8 + - - +
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLN* 3.5 30.5 + - + +
24A THR* 4.6 5.2 - - + -
25A GLY* 3.6 13.6 - - - +
261A ILE* 5.7 0.4 - - + -
265A ILE* 3.8 28.7 - - + -
271A ASP 3.8 21.3 - - - +
272A PRO 4.4 2.7 - - - +
274A GLY* 3.3 20.0 - - - +
276A PHE* 1.3 78.3 - - - +
278A TRP* 1.3 75.8 + - + +
281A TYR* 2.9 31.6 + - + +
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Residues in contact with TRP 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A TYR* 3.7 36.1 - + + -
253A ASP* 3.6 25.3 - - + +
258A ASN* 3.9 28.0 - - + -
261A ILE* 3.8 34.8 - - + -
262A VAL* 3.7 22.0 - - + -
265A ILE* 5.2 0.2 - - + -
272A PRO* 2.8 32.0 + - + -
273A SER 4.5 3.0 + - - -
274A GLY 3.3 16.7 + - - -
275A ALA* 3.3 8.5 + - - +
276A PHE 3.2 0.2 - - - -
277A VAL* 1.3 85.6 - - + +
279A THR* 1.3 60.2 + - + +
280A THR 3.2 1.8 - - - -
281A TYR* 4.3 3.6 - + + -
282A ALA* 3.0 29.5 + - - +
312A VAL* 3.7 23.9 - - + +
313A MET* 3.9 5.6 - - + +
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Residues in contact with THR 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PRO* 2.8 29.9 + - - +
117A THR* 2.8 40.5 + - - +
118A THR* 4.4 10.1 - - - +
252A TYR* 5.8 2.7 - - + -
275A ALA* 3.4 13.4 + - + +
276A PHE* 3.4 20.5 + - + -
278A TRP* 1.3 76.9 - - + +
280A THR* 1.3 59.7 + - - +
282A ALA* 3.5 0.5 + - - +
283A ALA 3.1 13.5 + - - -
313A MET* 3.8 21.3 - - + -
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Residues in contact with THR 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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22A GLU* 3.2 41.2 - - + +
26A ALA* 3.6 22.2 - - + +
74A ILE* 4.2 10.3 - - + -
99A PRO* 3.4 22.8 - - - +
276A PHE* 2.7 23.0 + - - +
277A VAL 3.9 2.5 - - - -
279A THR* 1.3 76.7 + - - +
281A TYR* 1.3 66.5 + - - +
283A ALA* 3.0 11.8 + - - +
284A LEU* 3.2 17.6 + - + +
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Residues in contact with TYR 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLY* 3.8 17.0 + - - +
28A GLN* 4.0 4.5 - - + -
29A ALA* 3.5 33.9 - - + -
32A ASP* 2.6 36.0 + - - +
33A ILE* 6.0 2.1 - - + +
261A ILE* 3.8 35.1 - - + +
277A VAL* 2.9 22.0 + - + +
278A TRP* 3.9 7.2 - + + +
280A THR* 1.3 75.4 - - - +
282A ALA* 1.3 62.8 + - - +
284A LEU* 3.2 4.3 + - - +
285A GLN* 3.1 52.2 + - + -
312A VAL* 3.8 17.3 - - + -
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A THR* 4.5 2.7 - - - -
278A TRP 3.0 19.3 + - - +
279A THR 3.7 4.5 - - - +
280A THR 3.2 0.2 - - - -
281A TYR* 1.3 77.9 - - - +
283A ALA* 1.3 58.0 + - - +
285A GLN* 3.3 13.2 + - - +
286A SER* 3.0 32.0 + - - -
311A THR* 3.8 22.4 - - + +
312A VAL* 4.2 2.0 - - + +
313A MET* 3.8 20.0 - - + -
316A LEU* 4.4 6.5 - - + -
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 4.2 22.2 - - + +
97A ILE* 3.9 21.3 - - + +
99A PRO* 4.6 3.1 - - + -
117A THR* 3.6 26.2 + - - +
279A THR 3.1 7.2 + - - +
280A THR* 3.0 11.9 + - - +
282A ALA* 1.3 76.1 - - - +
284A LEU* 1.3 58.2 + - - +
286A SER* 3.2 4.4 + - - -
287A LEU* 3.0 27.0 + - - +
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 4.5 7.4 - - + -
7A VAL* 5.2 2.2 - - + -
26A ALA* 3.9 26.9 - - + -
29A ALA* 3.7 19.5 - - + -
30A VAL* 4.1 22.7 - - + -
33A ILE* 4.1 9.1 - - + +
44A LEU* 4.7 9.6 - - + +
46A ILE* 6.0 0.2 - - + -
74A ILE* 4.1 34.1 - - + -
280A THR 3.2 16.7 + - - +
281A TYR 3.2 7.2 + - - +
283A ALA* 1.3 76.5 - - - +
285A GLN* 1.3 59.3 + - - +
287A LEU* 3.3 16.2 + - + +
288A GLN* 2.8 30.1 + - - +
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Residues in contact with GLN 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA* 5.8 0.2 - - + -
33A ILE* 4.9 4.0 - - + -
281A TYR* 3.1 37.7 + - + +
282A ALA* 3.3 7.8 + - - +
284A LEU* 1.3 76.1 - - - +
286A SER* 1.3 61.6 + - - +
288A GLN* 3.6 18.5 + - - +
289A ALA* 3.2 21.5 + - - +
309A VAL* 4.0 4.9 - - - +
310A ASP 4.2 7.5 + - - +
311A THR* 3.2 24.5 - - + +
312A VAL* 2.8 37.6 + - - +
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Residues in contact with SER 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 4.5 5.8 - - - -
117A THR* 4.1 3.8 - - - +
282A ALA 3.0 14.9 + - - -
283A ALA* 3.4 10.5 - - - -
284A LEU 3.1 0.4 - - - -
285A GLN* 1.3 76.5 - - - +
287A LEU* 1.3 66.0 + - - +
289A ALA* 3.3 4.2 + - - +
290A GLY* 3.0 17.3 + - - -
304A LEU* 3.7 19.4 - - - +
309A VAL* 4.2 8.7 - - - +
311A THR* 4.3 8.5 - - - +
316A LEU* 4.4 0.2 - - - +
318A TRP* 3.4 35.3 - - - -
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 3.8 39.7 - - + -
44A LEU* 5.3 2.7 - - + -
72A TYR* 4.0 24.9 - - + -
74A ILE* 4.3 8.7 - - + -
95A LEU* 3.9 27.1 - - + -
97A ILE* 4.4 10.9 - - + +
283A ALA 3.0 15.6 + - - +
284A LEU* 3.3 12.5 + - + +
286A SER* 1.3 76.5 - - - +
288A GLN* 1.3 57.2 + - - +
290A GLY* 3.1 3.1 + - - +
291A LEU* 2.8 47.8 + - + +
300A ILE* 4.6 7.0 - - + -
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Residues in contact with GLN 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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33A ILE* 3.6 42.6 + - + +
38A GLY 4.7 6.9 + - - -
39A ILE* 3.8 20.1 - - + +
44A LEU* 5.6 1.5 - - + +
284A LEU 2.8 18.2 + - - +
285A GLN* 3.6 16.6 + - - +
286A SER 3.1 0.2 - - - -
287A LEU* 1.3 76.1 - - - +
289A ALA* 1.3 62.9 + - - +
291A LEU* 3.3 2.6 + - - +
292A ASN* 3.1 40.9 + - - +
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Residues in contact with ALA 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 GLN 3.2 11.0 + - - +
286A SER 3.3 7.8 + - - +
288A GLN* 1.3 82.3 - - - +
290A GLY* 1.3 63.4 + - - +
292A ASN* 3.5 12.9 + - - +
293A GLN* 3.6 16.3 - - - +
303A TYR* 3.9 12.5 + - + +
304A LEU* 4.7 0.2 - - + -
309A VAL* 4.0 29.2 - - + -
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Residues in contact with GLY 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 SER 3.0 12.2 + - - -
287A LEU 3.5 3.1 - - - -
289A ALA* 1.3 78.3 - - - +
291A LEU* 1.3 56.1 + - - +
293A GLN* 2.9 21.1 + - - +
294A SER 3.0 13.2 + - - +
300A ILE* 3.7 30.2 - - - +
303A TYR* 4.2 14.7 - - - -
304A LEU* 4.5 0.9 - - - +
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 4.3 14.1 - - + -
39A ILE* 3.5 40.7 - - + +
40A LYS* 5.0 3.5 + - - +
44A LEU* 4.0 18.4 - - + -
72A TYR* 3.7 35.7 - - + +
287A LEU* 2.8 40.7 + - + +
288A GLN* 4.8 0.2 - - - -
290A GLY* 1.3 66.3 - - - +
292A ASN* 1.3 60.7 + - - +
293A GLN 3.0 5.9 + - - -
294A SER 3.3 13.7 + - - +
295A ASP* 3.7 18.2 - - - +
300A ILE* 3.9 11.2 - - + +
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Residues in contact with ASN 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 4.0 21.4 - - - +
40A LYS* 3.1 47.1 + - - +
288A GLN* 3.1 33.3 + - - +
289A ALA* 3.8 12.6 - - - +
290A GLY 3.2 0.6 - - - -
291A LEU* 1.3 77.1 - - - +
293A GLN* 1.3 67.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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