Contacts of the helix formed by residues 279 - 299 (chain A) in PDB entry 2ADS
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 GLU 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A ARG* 4.7 18.3 + - - +
278A MSE 1.3 77.6 - - - +
280A PRO* 1.3 86.8 - - + +
281A GLY 2.6 6.7 + - - +
282A LYS* 2.8 28.8 + - + +
283A ARG* 4.4 6.7 - - - -
635A GLU* 4.3 23.6 - - + +
637A THR* 4.9 3.8 - - + -
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Residues in contact with PRO 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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279A GLU* 1.3 90.3 - - + +
281A GLY* 1.3 62.8 + - - +
283A ARG* 3.7 4.9 + - + +
284A LEU* 3.1 29.5 + - - +
607A PHE* 4.7 19.3 - - + -
609A ASN* 5.7 5.4 - - - +
635A GLU 3.0 28.9 - - - +
636A GLY* 3.5 21.1 - - - +
637A THR* 3.8 10.2 - - + -
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Residues in contact with GLY 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLU* 2.6 7.1 + - - +
280A PRO* 1.3 77.0 - - - +
282A LYS* 1.3 54.3 + - - -
284A LEU* 3.8 6.5 - - - +
285A ASN* 2.9 44.7 + - - -
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Residues in contact with LYS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ARG* 4.8 11.6 - - - +
278A MSE 3.3 46.1 - - + +
279A GLU* 2.8 22.0 + - + +
281A GLY* 1.3 75.2 - - - +
283A ARG* 1.3 59.2 + - - +
285A ASN* 4.3 3.3 - - - +
286A LEU* 3.1 27.0 + - - +
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Residues in contact with ARG 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ARG* 5.0 0.2 - - - +
278A MSE 3.1 45.5 + - + +
279A GLU* 3.6 4.9 + - - +
280A PRO* 4.0 8.1 - - + +
282A LYS* 1.3 76.1 - - - +
284A LEU* 1.3 55.1 + - - +
286A LEU* 3.2 4.8 + - - +
287A ILE* 2.8 51.7 + - + +
605A ARG* 3.5 27.6 - - - +
607A PHE* 5.3 7.9 - - + -
637A THR* 4.6 6.7 - - - +
6G C 3.0 39.9 + - - +
7G C 3.2 28.4 + - - -
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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
----------------------------------------------------------
6A LEU* 4.9 7.0 - - + -
8A ASN* 6.5 0.2 - - - -
10A TYR* 4.6 3.8 - - - +
280A PRO* 3.1 18.5 + - + +
281A GLY* 3.8 7.4 - - - +
283A ARG* 1.3 77.7 - - - +
285A ASN* 1.3 64.1 + - - +
287A ILE* 3.7 9.6 + - + +
288A ARG* 3.0 54.7 + - - +
309A GLU* 3.8 26.9 - - + +
607A PHE* 3.9 42.6 - - + -
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Residues in contact with ASN 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 GLY* 2.9 25.4 + - - +
282A LYS* 4.6 3.4 - - - +
284A LEU* 1.3 83.7 - - - +
286A LEU* 1.3 59.4 + - - +
288A ARG* 3.4 27.6 - - - +
289A TYR* 2.9 24.8 + - - +
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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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159A LEU* 4.2 20.9 - - + -
278A MSE 4.0 31.4 - - + -
282A LYS 3.1 16.7 + - - +
283A ARG* 3.2 6.7 + - - +
285A ASN* 1.3 74.0 - - - +
287A ILE* 1.3 59.3 + - + +
288A ARG 3.0 0.9 - - - -
289A TYR* 2.7 34.0 + - + +
290A ILE* 2.9 28.6 + - + +
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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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8A ASN* 3.8 24.2 - - + +
10A TYR* 3.6 34.1 - - + +
157A LEU* 3.9 28.0 - - + +
159A LEU* 6.5 0.2 - - + -
283A ARG* 2.8 38.3 + - + +
284A LEU* 3.8 9.0 - - + +
286A LEU* 1.3 74.4 - - + +
288A ARG* 1.3 57.2 + - - +
290A ILE* 3.0 30.3 + - + +
291A LEU* 3.0 16.0 + - + +
605A ARG* 6.0 1.3 - - - +
607A PHE* 5.1 3.4 - - + -
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Residues in contact with ARG 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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6A LEU* 4.0 11.7 - - - +
10A TYR* 4.5 2.7 - - + +
284A LEU* 3.0 49.3 + - - +
285A ASN* 3.4 23.2 - - - +
286A LEU 3.0 0.4 - - - -
287A ILE* 1.3 77.4 - - - +
289A TYR* 1.3 55.6 + - - +
291A LEU* 3.8 11.2 + - + +
292A ARG* 3.3 39.5 + - - +
307A PRO 5.2 8.3 + - - +
309A GLU* 3.3 39.8 + - - +
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Residues in contact with TYR 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 ASN 2.9 11.6 + - - +
286A LEU* 2.7 25.9 + - + +
288A ARG* 1.3 70.8 - - - +
290A ILE* 1.3 66.3 + - + +
291A LEU 3.5 0.2 + - - -
292A ARG* 3.6 27.3 + - + +
293A ARG* 3.0 55.8 + - + +
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Residues in contact with ILE 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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114A PHE* 6.1 3.1 - - + -
141A VAL* 4.5 10.3 - - + -
157A LEU* 3.5 30.7 - - + -
159A LEU* 4.0 26.7 - - + -
286A LEU* 2.9 33.0 + - + +
287A ILE* 3.0 11.4 + - + +
289A TYR* 1.3 81.2 - - + +
291A LEU* 1.3 62.6 + - - +
293A ARG* 3.3 19.5 + - + +
294A TYR* 3.3 40.0 + - + +
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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
----------------------------------------------------------
10A TYR* 4.0 35.7 - - + +
155A LEU* 4.7 6.3 - - + -
157A LEU* 5.3 8.5 - - + -
287A ILE* 3.0 16.8 + - + +
288A ARG* 3.8 11.9 - - + +
290A ILE* 1.3 75.8 - - - +
292A ARG* 1.3 61.9 + - + +
294A TYR* 3.1 12.8 + - + +
295A VAL* 2.9 31.6 + - + +
305A ILE* 3.5 34.8 - - + +
306A SER 3.7 22.2 - - - +
307A PRO* 4.4 10.8 - - + +
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Residues in contact with ARG 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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288A ARG* 3.3 28.2 + - - +
289A TYR* 3.8 23.2 - - + +
290A ILE 3.3 0.2 - - - -
291A LEU* 1.3 78.7 - - + +
293A ARG* 1.3 62.4 + - + +
295A VAL* 3.2 19.2 + - - +
296A LYS* 3.2 17.9 + - - +
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Residues in contact with ARG 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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114A PHE* 3.5 39.1 - - + -
118A PHE* 6.1 0.2 - - - -
121A LYS* 5.9 2.4 - - - +
289A TYR* 3.0 56.6 + - + +
290A ILE* 3.3 10.7 + - + +
291A LEU 3.2 0.8 - - - -
292A ARG* 1.3 74.7 - - + +
294A TYR* 1.3 68.7 + - + +
296A LYS* 3.4 11.0 + - + +
297A ALA* 3.2 24.1 + - - +
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Residues in contact with TYR 294 (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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111A LYS* 6.1 2.5 - - + -
114A PHE* 5.5 11.4 - + + -
141A VAL* 3.6 24.9 + - + +
142A ASN 4.4 0.5 + - - -
143A GLU* 3.1 36.4 + - + -
155A LEU* 4.8 3.8 - - + -
157A LEU* 3.5 28.0 - - + +
290A ILE* 3.3 24.2 + - + -
291A LEU* 3.1 13.1 + - + +
293A ARG* 1.3 81.1 - - + +
295A VAL* 1.3 58.3 + - - +
297A ALA* 3.3 5.3 + - + -
298A LEU* 2.9 47.7 + - + +
305A ILE* 4.0 26.5 - - + -
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Residues in contact with VAL 295 (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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291A LEU* 2.9 24.0 + - + +
292A ARG* 3.2 8.7 + - - +
294A TYR* 1.3 75.4 - - + +
296A LYS* 1.3 59.4 + - + +
299A ARG* 3.0 61.8 + - + +
303A TRP 4.6 10.8 - - - +
304A TYR* 4.9 10.8 - - + -
305A ILE* 4.4 35.7 - - + +
307A PRO* 6.2 2.0 - - + -
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Residues in contact with LYS 296 (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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292A ARG 3.2 15.5 + - - +
293A ARG* 3.7 13.7 - - + +
294A TYR 3.3 0.4 - - - -
295A VAL* 1.3 77.2 - - - +
297A ALA* 1.3 64.1 + - + +
298A LEU 3.3 1.4 + - - -
299A ARG* 4.6 14.7 + - - +
300A ASP* 3.9 16.5 - - - +
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Residues in contact with ALA 297 (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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110A VAL* 4.9 11.5 - - + +
293A ARG 3.2 15.7 + - - +
294A TYR* 3.3 8.3 + - + +
296A LYS* 1.3 81.3 - - + +
298A LEU* 1.3 71.3 + - + +
301A TYR* 4.5 5.7 - - - +
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Residues in contact with LEU 298 (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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110A VAL* 4.5 25.4 - - + -
294A TYR* 2.9 34.4 + - + +
296A LYS 3.2 0.4 - - - -
297A ALA* 1.3 90.4 - - + +
299A ARG* 1.3 53.5 + - - +
300A ASP 3.2 3.1 - - - -
301A TYR* 3.1 17.5 + - + +
302A GLY 2.8 14.9 + - - -
303A TRP* 2.8 68.2 + - + +
305A ILE* 5.6 3.8 - - + -
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Residues in contact with ARG 299 (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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15A ARG 5.4 0.2 - - - +
295A VAL* 3.0 41.1 + - + +
296A LYS* 4.2 14.1 + - - +
298A LEU* 1.3 75.3 - - - +
300A ASP* 1.3 78.5 + - - +
302A GLY* 3.3 14.2 + - - +
303A TRP 3.3 12.5 + - - -
304A TYR* 5.5 5.6 - - + +
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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
------------------------------------------------------------
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