Contacts of the helix formed by residues 278 - 295 (chain A) in PDB entry 3ZFW
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 HIS 278 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 3.9 40.8 - - + +
275A GLY 3.4 19.3 + - - +
276A LYS 4.8 0.2 - - - +
277A ASP* 1.3 77.2 - - - +
279A PRO* 1.4 82.4 - - + +
280A ALA* 3.0 39.4 + - + +
281A VAL* 2.9 21.7 + - + +
282A ALA 3.2 8.3 + - - -
311A ILE* 3.9 5.9 - - - +
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Residues in contact with PRO 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ASP 4.6 2.9 - - - +
278A HIS* 1.4 99.5 - - + +
280A ALA* 1.3 54.3 + - - +
282A ALA* 3.3 10.5 + - + +
283A ALA* 2.9 29.0 + - - +
311A ILE* 4.8 1.5 - - + -
312A ARG* 4.6 4.3 + - + +
315A VAL* 4.3 24.9 - - + -
316A LEU* 5.9 8.3 - - + -
210X SER* 5.2 7.1 - - - -
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ARG* 4.0 17.0 - - + +
274A LEU* 4.0 18.2 - - + -
278A HIS* 3.0 23.0 + - + +
279A PRO* 1.3 73.3 - - - +
281A VAL* 1.4 58.9 + - - +
283A ALA* 3.5 7.2 + - - +
284A THR* 3.0 34.5 + - - -
210X SER* 5.8 1.6 - - - +
211X ALA* 4.9 8.9 - - - +
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 3.9 16.7 - - + +
270A ARG* 4.1 25.1 - - + +
271A GLU* 4.3 7.0 - - + +
274A LEU* 5.4 0.2 - - + -
275A GLY 3.4 26.9 - - - +
276A LYS* 4.5 1.1 - - - -
277A ASP 5.0 2.0 - - - +
278A HIS* 2.9 21.1 + - + +
280A ALA* 1.4 73.1 - - - +
282A ALA* 1.3 58.9 + - - +
284A THR* 3.3 3.2 + - - -
285A LEU* 2.9 41.7 + - + +
307A ARG* 3.6 27.6 - - - +
311A ILE* 4.3 5.2 - - + -
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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
----------------------------------------------------------
278A HIS 3.2 2.5 + - - +
279A PRO* 3.4 11.4 - - + +
281A VAL* 1.3 77.8 - - - +
283A ALA* 1.4 56.4 + - - +
285A LEU* 3.2 4.4 + - - -
286A ASN* 3.0 27.5 + - - +
308A ALA* 3.5 25.9 - - - +
311A ILE* 3.9 24.8 - - + +
312A ARG* 3.8 26.0 + - + +
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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
----------------------------------------------------------
279A PRO 2.9 16.8 + - - +
280A ALA* 3.7 6.1 - - - +
282A ALA* 1.4 73.0 - - - +
284A THR* 1.4 56.6 + - - +
286A ASN* 3.5 2.7 + - - +
287A ASN* 3.1 36.0 + - - -
312A ARG* 4.0 10.2 - - - +
208X ASP* 3.3 27.9 - - + +
210X SER* 4.0 3.6 - - - -
211X ALA* 3.8 24.2 - - + +
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Residues in contact with THR 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ASN* 4.2 1.7 + - - +
263A LEU* 3.6 37.2 - - + +
267A LEU* 3.9 25.8 - - + +
270A ARG* 3.2 25.6 + - - +
280A ALA 3.0 18.8 + - - -
281A VAL* 3.8 3.8 - - - -
283A ALA* 1.4 72.9 - - - +
285A LEU* 1.3 59.8 + - - +
287A ASN* 3.4 7.1 + - - +
288A LEU* 2.8 33.0 + - + +
211X ALA* 4.0 5.2 - - - +
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 3.9 23.8 - - + -
281A VAL* 2.9 27.7 + - + +
282A ALA* 3.2 5.1 + - - +
284A THR* 1.3 75.2 - - - +
286A ASN* 1.4 56.6 + - - +
288A LEU* 3.4 5.2 + - - +
289A ALA* 2.9 27.2 + - - +
304A LEU* 3.7 46.6 - - + +
307A ARG* 3.6 38.8 - - - +
308A ALA* 4.0 9.0 - - + +
311A ILE* 3.7 19.5 - - + -
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Residues in contact with ASN 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ALA 3.0 12.6 + - - +
283A ALA 3.6 7.4 - - - +
285A LEU* 1.4 71.8 - - - +
287A ASN* 1.3 70.1 + - - +
289A ALA* 3.0 9.9 + - - +
290A VAL* 2.8 37.1 + - - +
305A CYS* 4.2 3.3 - - - +
308A ALA* 4.3 1.5 - - - +
312A ARG* 4.4 2.7 - - - +
325A LYS* 4.1 0.6 - - - +
326A GLN* 2.8 32.7 + - - +
329A ASN* 2.8 27.3 + - - +
205X LEU* 5.0 0.7 - - - +
206X GLU 3.2 19.8 + - - -
208X ASP* 3.3 16.5 - - + +
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Residues in contact with ASN 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ASN* 5.2 3.4 + - - +
263A LEU* 3.9 10.5 - - + +
283A ALA 3.1 21.2 + - - +
284A THR* 3.8 5.5 - - - +
286A ASN* 1.3 74.6 + - - +
288A LEU* 1.3 65.1 + - - +
290A VAL* 3.2 5.6 + - - +
291A LEU* 3.1 26.9 + - - +
207X TRP* 3.2 41.6 - - + +
208X ASP 2.8 46.2 + - - -
211X ALA* 4.4 11.1 - - - +
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ALA* 3.5 36.3 - - + +
263A LEU* 3.8 14.6 - - + +
264A ASN* 3.5 29.6 - - - +
267A LEU* 3.9 24.2 - - + -
284A THR* 2.8 31.1 + - + +
285A LEU* 3.5 6.3 - - - +
287A ASN* 1.3 75.2 - - - +
289A ALA* 1.4 54.8 + - - +
291A LEU* 3.3 7.8 + - - +
292A TYR* 2.9 42.8 + - + -
304A LEU* 3.8 16.4 - - + -
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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
----------------------------------------------------------
285A LEU 2.9 14.4 + - - +
286A ASN 3.3 10.1 - - - +
288A LEU* 1.4 70.7 - - - +
290A VAL* 1.4 59.9 + - - +
292A TYR* 3.3 2.1 + - - -
293A GLY* 3.0 26.0 + - - -
301A ALA* 3.5 36.4 - - + +
304A LEU* 4.0 8.2 - - + +
305A CYS* 4.1 19.3 - - - +
333A LEU* 4.8 0.2 - - + -
205X LEU* 4.5 9.1 - - + +
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ARG* 6.0 0.4 - - - -
286A ASN* 2.8 29.1 + - - +
287A ASN* 3.2 9.8 + - - +
289A ALA* 1.4 72.3 - - - +
291A LEU* 1.3 59.2 + - + +
293A GLY* 3.4 2.3 + - - -
294A LYS* 3.1 38.8 + - + +
205X LEU* 3.6 41.0 + - + +
206X GLU 3.5 26.9 - - - +
207X TRP* 3.6 23.8 - - + +
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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
----------------------------------------------------------
251A ARG* 4.1 13.7 - - + -
256A TYR* 3.8 35.7 - - + +
259A ALA* 3.8 16.6 - - + -
260A ALA* 3.6 37.0 - - + +
263A LEU* 3.9 22.4 - - + -
287A ASN 3.1 12.7 + - - +
288A LEU* 3.3 7.2 + - - +
290A VAL* 1.3 74.3 - - + +
292A TYR* 1.4 63.9 + - - +
294A LYS* 3.2 20.9 + - + +
295A ARG* 3.3 13.8 + - - +
207X TRP* 3.7 17.9 - - + -
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Residues in contact with TYR 292 (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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260A ALA* 5.0 10.5 - - + +
264A ASN* 4.6 11.6 + - - -
288A LEU* 2.9 46.4 + - + +
289A ALA 3.3 0.4 + - - +
291A LEU* 1.4 74.6 - - - +
293A GLY* 1.3 59.3 + - - +
295A ARG* 3.3 19.6 + - - +
297A LYS* 3.0 59.5 + - + +
300A GLU* 3.8 28.7 - - + -
301A ALA* 3.7 20.4 - - + -
304A LEU* 4.0 19.5 - - + -
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Residues in contact with GLY 293 (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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289A ALA 3.0 13.7 + - - -
290A VAL 3.7 5.2 - - - -
291A LEU 3.2 0.4 - - - -
292A TYR* 1.3 74.9 - - - +
294A LYS* 1.3 57.9 + - - +
295A ARG 3.2 0.7 - - - -
296A GLY* 3.1 14.7 + - - -
298A TYR* 3.3 37.9 + - - -
301A ALA* 4.2 1.3 - - - +
333A LEU* 4.6 6.7 - - - -
203X THR 5.4 3.0 - - - +
204X ASN* 5.4 1.5 - - - +
205X LEU* 5.5 5.2 - - - -
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Residues in contact with LYS 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ARG* 6.1 3.6 - - - -
254A ASN* 5.3 1.4 + - - -
256A TYR* 3.6 58.3 + - + +
290A VAL* 3.1 30.4 + - + +
291A LEU* 3.2 12.8 + - + +
293A GLY* 1.3 74.3 - - - +
295A ARG* 1.3 58.7 + - - +
296A GLY 3.3 1.0 + - - -
204X ASN* 3.4 47.4 - - + +
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Residues in contact with ARG 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A TYR* 3.9 19.7 - - + -
257A LYS* 3.9 52.7 - - - +
291A LEU 3.3 9.7 + - - +
292A TYR* 3.3 24.3 + - - +
293A GLY 3.2 0.6 - - - -
294A LYS* 1.3 75.2 - - - +
296A GLY* 1.3 60.7 + - - +
297A LYS* 3.2 49.5 + - + +
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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