Contacts of the helix formed by residues 269 - 289 (chain A) in PDB entry 3B3S
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 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ALA* 4.0 9.4 - - - +
22A ILE* 4.8 2.9 - - - +
23A THR* 3.5 15.0 - - - -
182A ASN* 3.9 7.9 - - - -
266A ASP* 2.8 16.2 + - - -
267A PRO 3.3 1.2 - - - -
268A THR* 1.3 79.2 + - - +
270A SER* 1.3 58.2 + - - +
271A HIS 3.3 2.9 - - - -
272A ALA* 3.4 6.2 + - - +
273A LYS* 2.9 30.1 + - - +
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Residues in contact with SER 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 5.0 2.0 - - - -
266A ASP* 3.1 6.2 + - - -
268A THR* 3.1 20.5 + - - -
269A GLY* 1.3 77.9 - - - +
271A HIS* 1.3 64.2 + - - +
273A LYS* 3.4 15.9 + - - +
274A LYS* 3.5 22.3 + - - +
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Residues in contact with HIS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A THR 3.4 19.7 - - - -
182A ASN* 3.7 12.3 - - - +
183A TYR 3.5 23.6 - - - -
184A LYS* 3.6 31.2 - - + +
189A ASP 3.0 26.8 + - - -
245A GLU* 3.0 22.2 + - + -
266A ASP* 3.0 14.9 + - + +
270A SER* 1.3 77.2 - - - +
272A ALA* 1.3 63.5 + - - +
274A LYS* 3.0 44.7 + - + +
275A PHE* 3.2 22.4 - + - -
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 4.0 23.3 - - + -
26A ILE* 5.0 0.2 - - + -
120A SER* 4.6 6.3 - - - +
124A ALA* 4.7 1.4 - - + +
181A THR* 3.2 27.1 + - - +
182A ASN* 3.0 27.7 + - + +
269A GLY 3.4 2.8 + - - +
271A HIS* 1.3 75.7 - - - +
273A LYS* 1.3 64.7 + - - +
275A PHE* 3.1 5.4 + - - +
276A THR* 2.9 27.0 + - - +
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Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU 5.2 0.2 - - - -
15A PRO* 5.1 4.2 + - - +
17A VAL* 3.4 30.6 + - + +
19A ALA* 4.2 9.4 - - + +
22A ILE* 3.8 15.7 - - + +
269A GLY 2.9 18.8 + - - +
270A SER* 3.5 10.1 - - - +
271A HIS 3.1 0.2 - - - -
272A ALA* 1.3 77.7 - - - +
274A LYS* 1.3 56.4 + - + +
276A THR* 3.5 1.1 - - - -
277A GLN* 2.9 53.8 + - - +
295A NA 3.0 27.9 - - - -
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Residues in contact with LYS 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LYS* 3.9 10.5 - - - +
189A ASP* 2.8 39.4 + - + +
190A VAL* 4.9 5.3 - - + +
213A LEU* 3.9 4.7 - - - +
216A LEU* 3.8 31.4 - - + -
270A SER* 3.5 21.0 - - - +
271A HIS* 3.0 39.7 + - + +
273A LYS* 1.3 79.1 - - + +
275A PHE* 1.3 63.1 + - + +
277A GLN* 3.2 12.0 + - - +
278A LEU* 2.9 28.1 + - - +
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Residues in contact with PHE 275 (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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124A ALA* 5.2 0.9 - - + -
178A LEU* 4.3 18.5 - - + +
181A THR* 3.3 42.4 - - + -
189A ASP 3.5 17.9 - - - -
190A VAL* 3.9 17.7 - - + -
243A PRO* 3.6 29.4 - - + -
244A PHE 3.3 34.3 - - - -
245A GLU* 3.7 8.1 - - - -
271A HIS* 3.2 31.6 - + - -
272A ALA 3.1 5.3 + - - +
274A LYS* 1.3 75.6 - - + +
276A THR* 1.3 60.9 + - - +
278A LEU* 3.7 7.4 - - + +
279A GLY* 2.9 25.5 + - - -
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Residues in contact with THR 276 (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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17A VAL* 3.7 23.3 - - + -
22A ILE* 3.4 13.6 - - + +
124A ALA* 3.2 42.4 - - - +
127A GLU* 3.7 16.6 - - + -
128A VAL* 3.6 10.8 - - + +
178A LEU* 5.4 0.4 - - - -
272A ALA 2.9 14.2 + - - -
273A LYS 3.5 7.4 - - - -
275A PHE* 1.3 74.1 - - - +
277A GLN* 1.3 59.4 + - - +
279A GLY 3.3 0.5 + - - -
280A LEU* 2.8 28.8 + - - +
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Residues in contact with GLN 277 (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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14A LEU* 3.0 52.4 + - + +
15A PRO* 4.4 3.2 - - - +
17A VAL* 3.9 17.3 - - + -
213A LEU* 3.6 25.7 - - + +
273A LYS* 2.9 48.0 + - - +
274A LYS* 3.7 9.1 - - - +
276A THR* 1.3 76.6 - - - +
278A LEU* 1.3 57.5 + - - +
280A LEU* 3.3 3.5 + - - -
281A ALA* 2.9 26.7 + - - +
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Residues in contact with LEU 278 (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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176A LEU* 5.7 2.0 - - + -
190A VAL* 4.7 5.2 - - + -
192A PHE* 4.1 19.3 - - + -
205A LEU* 4.0 22.4 - - + +
208A LEU* 4.1 18.8 - - + -
209A MET* 3.9 26.0 - - + +
213A LEU* 3.8 11.8 - - + +
243A PRO* 3.9 33.9 - - + -
274A LYS 2.9 17.0 + - - +
275A PHE* 3.7 6.5 - - - +
277A GLN* 1.3 76.8 - - - +
279A GLY* 1.3 57.9 + - - +
281A ALA* 3.3 3.7 + - + +
282A TYR* 2.9 28.1 + - - +
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Residues in contact with GLY 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ILE* 4.0 20.1 - - - +
128A VAL* 4.1 7.4 - - - -
176A LEU* 4.1 13.0 - - - +
178A LEU* 5.6 0.7 - - - -
275A PHE 2.9 16.6 + - - -
276A THR 3.3 3.1 + - - -
278A LEU* 1.3 77.1 - - - +
280A LEU* 1.3 57.6 + - - +
282A TYR* 3.4 5.5 + - - +
283A ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 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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13A TRP* 3.8 17.5 - - + +
14A LEU* 3.7 16.6 - - + -
17A VAL* 3.7 26.5 - - + -
128A VAL* 3.8 22.1 - - + +
131A VAL* 3.8 17.3 - - + -
132A LEU* 3.5 37.2 - - + -
276A THR 2.8 17.2 + - - +
277A GLN 3.7 4.7 - - - +
278A LEU 3.2 0.4 - - - -
279A GLY* 1.3 75.3 - - - +
281A ALA* 1.3 67.2 + - - +
283A ALA* 3.1 1.8 + - - +
284A ILE* 2.9 36.0 + - + +
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Residues in contact with ALA 281 (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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10A VAL* 3.8 31.0 - - + -
14A LEU* 3.9 3.9 - - + +
208A LEU* 4.2 10.8 - - + -
212A TYR* 3.9 19.3 - - + -
213A LEU* 6.3 0.4 - - + -
277A GLN 2.9 16.6 + - - +
278A LEU* 3.3 6.7 + - - +
280A LEU* 1.3 77.2 - - - +
282A TYR* 1.3 57.2 + - - +
284A ILE* 3.8 1.1 - - - +
285A GLU* 2.9 36.0 + - - +
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Residues in contact with TYR 282 (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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92A ILE* 3.3 17.8 - - + +
93A VAL 2.8 28.2 + - - -
94A ILE* 4.1 10.8 - - + -
174A SER* 2.8 37.7 + - - -
176A LEU* 3.7 27.6 + - + -
201A PHE* 3.5 26.2 - + - -
204A TYR* 4.7 1.3 - + - -
205A LEU* 4.0 11.0 - - + -
208A LEU* 3.8 15.2 - - + +
278A LEU 2.9 17.3 + - - +
279A GLY* 3.5 9.9 - - - +
281A ALA* 1.3 77.4 - - - +
283A ALA* 1.3 60.7 + - + +
285A GLU* 4.9 0.2 - - - -
286A MET* 2.8 52.8 + - + +
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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
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92A ILE* 4.9 4.0 - - + -
94A ILE* 5.7 3.1 - - + -
128A VAL* 4.4 8.5 - - + -
132A LEU* 4.2 24.2 - - + -
137A PHE* 4.1 3.0 - - - -
143A ILE* 4.0 17.7 - - + +
145A PHE* 5.2 4.5 - - + -
279A GLY 2.9 17.9 + - - +
280A LEU 3.7 4.0 - - - +
282A TYR* 1.3 83.9 - - + +
284A ILE* 1.3 60.0 + - - +
287A GLY* 2.9 29.0 + - - +
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Residues in contact with ILE 284 (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 GLN* 3.9 11.2 - - + +
9A THR* 3.8 17.5 - - + -
10A VAL* 3.7 37.5 - - + -
13A TRP* 3.7 28.5 - - + -
14A LEU* 5.0 0.2 - - + -
132A LEU* 4.0 17.3 - - + -
137A PHE* 3.9 11.0 - - + -
280A LEU* 2.9 36.9 + - + +
281A ALA* 3.9 2.5 - - - +
283A ALA* 1.3 78.3 - - - +
285A GLU* 1.3 63.6 + - - +
288A SER* 2.7 35.7 + - - +
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Residues in contact with GLU 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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2A PRO* 4.9 2.5 - - + +
3A PRO 3.7 4.9 - - - +
4A ILE* 3.4 12.5 - - - +
5A THR* 3.0 22.3 + - - -
6A GLN* 2.8 30.0 + - - +
10A VAL* 4.2 4.3 - - + -
204A TYR* 3.2 20.0 + - - +
208A LEU* 4.1 15.0 - - + -
212A TYR* 2.6 31.5 + - + -
281A ALA 2.9 19.1 + - - +
282A TYR 4.3 0.4 - - - +
284A ILE* 1.3 79.5 - - - +
286A MET* 1.3 61.8 + - - +
288A SER* 3.2 2.6 + - - -
289A ALA* 3.1 24.0 + - - +
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Residues in contact with MET 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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1A MET* 4.0 14.4 - - + -
2A PRO* 3.4 33.2 - - + -
92A ILE* 3.7 20.0 - - + -
141A ARG* 3.0 40.2 + - - +
173A VAL* 3.5 32.1 - - + -
174A SER* 3.6 12.6 - - - +
204A TYR* 3.7 19.7 - - + +
282A TYR* 2.8 40.8 + - + +
285A GLU* 1.3 73.4 - - - +
287A GLY* 1.3 61.6 + - - +
288A SER 3.3 0.5 + - - -
289A ALA* 3.5 2.7 + - - +
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Residues in contact with GLY 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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92A ILE* 4.1 12.2 - - - +
137A PHE* 4.7 0.2 - - - -
139A PRO* 3.6 15.0 - - - +
140A LYS 2.9 25.3 + - - -
141A ARG* 3.0 14.3 + - - -
143A ILE* 4.4 4.0 - - - -
283A ALA 2.9 21.3 + - - -
286A MET* 1.3 77.7 - - - +
288A SER* 1.3 59.7 + - - +
289A ALA 4.2 0.7 - - - -
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Residues in contact with SER 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 GLN* 3.7 36.3 + - - +
137A PHE* 3.9 16.3 - - - -
139A PRO* 5.4 0.3 - - - +
140A LYS* 3.3 33.5 + - - +
284A ILE* 2.7 23.9 + - - +
285A GLU 3.9 1.1 - - - -
286A MET 3.1 0.2 - - - -
287A GLY* 1.3 77.7 - - - +
289A ALA* 1.3 61.9 + - - +
290A THR 4.1 0.2 + - - -
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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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2A PRO* 3.7 37.5 - - + -
141A ARG* 3.1 42.0 + - - +
285A GLU 3.1 11.6 + - - +
286A MET 3.5 0.4 + - - -
288A SER* 1.3 79.8 - - - +
290A THR* 1.3 62.0 + - - +
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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