Contacts of the helix formed by residues 274 - 291 (chain A) in PDB entry 2C3E
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 TRP 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ILE* 3.9 21.8 - - + -
273A ALA* 1.3 70.0 - - - +
275A SER* 1.3 59.4 + - - +
276A ASN 3.1 2.0 - - - -
277A VAL* 2.9 44.6 + - + +
278A LEU* 3.1 37.3 + - + +
281A MET* 6.6 0.2 - - - -
801A CDL 2.6 127.1 + - + +
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Residues in contact with SER 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 3.8 13.2 - - - +
31A VAL* 4.3 0.9 - - - +
32A LYS* 3.5 30.0 - - - +
35A LEU* 3.5 9.0 - - - +
53A ILE* 3.3 33.5 - - - +
272A GLY 3.5 5.2 - - - -
274A TRP* 1.3 75.8 - - - +
276A ASN* 1.3 57.0 + - - +
278A LEU* 3.3 9.2 + - - +
279A ARG* 3.0 27.9 + - - +
801A CDL 3.0 9.3 + - - -
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Residues in contact with ASN 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS* 3.6 29.1 + - + +
224A GLY* 4.5 14.1 + - - -
228A TYR* 3.9 19.2 - - + -
231A ASP* 5.8 0.4 + - - -
272A GLY 2.8 17.7 + - - +
273A ALA 3.5 6.5 + - - +
274A TRP 3.1 0.2 - - - -
275A SER* 1.3 76.4 - - - +
277A VAL* 1.3 62.0 - - - +
279A ARG* 2.8 38.4 + - - +
280A GLY* 3.3 14.7 + - - -
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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
----------------------------------------------------------
221A ALA* 3.9 27.8 - - + +
225A LEU* 4.2 24.5 - - + -
273A ALA 2.9 24.9 - - - +
274A TRP* 2.9 38.7 + - + +
276A ASN* 1.3 76.9 - - - +
278A LEU* 1.3 67.7 + - + +
280A GLY* 3.4 1.6 + - - -
281A MET* 3.1 42.6 + - - +
801A CDL 4.9 1.8 - - + +
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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
----------------------------------------------------------
28A ILE* 4.4 14.6 - - + -
53A ILE* 4.2 17.7 - - + -
274A TRP* 3.1 51.3 + - + +
275A SER* 3.6 7.9 - - - +
277A VAL* 1.3 76.5 - - + +
279A ARG* 1.3 54.7 + - - +
281A MET* 3.2 7.8 + - - +
282A GLY* 2.7 35.0 + - - -
801A CDL 4.3 19.5 - - + -
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Residues in contact with ARG 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 3.8 18.1 - - + +
28A ILE* 3.7 21.5 - - + +
29A GLU* 3.7 43.5 - - + +
32A LYS* 5.6 0.4 - - + -
275A SER 3.0 16.6 + - - +
276A ASN* 2.8 38.7 + - - +
278A LEU* 1.3 75.6 - - - +
280A GLY* 1.3 82.5 + - - +
283A GLY* 2.9 26.8 + - - -
401A CXT 4.5 16.2 + - - -
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Residues in contact with GLY 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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217A GLN* 4.3 2.7 - - - +
220A THR* 5.8 8.9 - - - +
276A ASN 3.3 11.2 + - - -
277A VAL* 3.4 2.7 + - - -
278A LEU 3.2 0.8 - - - -
279A ARG* 1.3 102.5 + - - +
281A MET* 1.3 62.0 + - - +
283A GLY* 3.4 1.7 + - - -
284A ALA* 3.1 22.2 + - - +
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Residues in contact with MET 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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213A TRP* 4.4 12.8 - - + -
214A MET* 5.1 13.0 - - + +
217A GLN* 3.4 46.2 - - + +
218A THR* 4.8 3.4 - - - +
221A ALA* 5.3 7.4 - - + -
277A VAL* 3.1 35.2 + - + +
278A LEU* 4.0 7.6 - - - +
280A GLY* 1.3 72.3 - - - +
282A GLY* 1.3 60.0 + - - +
284A ALA* 3.4 2.4 + - - +
285A PHE* 2.8 31.9 + - - +
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Residues in contact with GLY 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 3.7 14.6 - - - -
278A LEU 2.7 17.2 + - - -
279A ARG 3.9 1.1 - - - -
281A MET* 1.3 78.3 - - - +
283A GLY* 1.3 55.8 + - - +
285A PHE* 3.2 10.3 + - - +
286A VAL* 2.9 32.1 + - - +
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Residues in contact with GLY 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER* 3.8 13.8 - - - -
25A VAL* 3.7 14.7 - - - +
279A ARG* 2.9 18.9 + - - -
280A GLY 3.8 1.1 - - - -
281A MET 3.2 0.4 - - - -
282A GLY* 1.3 76.7 - - - +
284A ALA* 1.3 61.4 + - - +
286A VAL* 2.9 15.0 + - - +
287A LEU* 3.1 17.5 + - - +
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Residues in contact with ALA 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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213A TRP* 4.1 6.4 + - + +
217A GLN* 3.1 39.7 - - - +
280A GLY 3.1 13.0 + - - +
281A MET 3.8 2.5 - - - +
283A GLY* 1.3 75.4 - - - +
285A PHE* 1.3 61.2 + - - +
287A LEU* 3.6 16.6 + - + +
288A VAL* 3.3 22.3 + - - +
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Residues in contact with PHE 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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213A TRP* 3.9 22.4 - + + -
281A MET 2.8 19.1 + - - +
282A GLY* 3.5 9.4 - - - +
283A GLY 3.0 0.2 - - - -
284A ALA* 1.3 77.1 - - - +
286A VAL* 1.3 66.2 + - + +
288A VAL* 3.0 22.1 + - + +
289A LEU* 2.9 54.8 - - + +
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 4.3 15.5 - - + +
21A SER* 3.6 28.9 - - - +
24A ALA* 3.8 23.3 - - + -
25A VAL* 5.1 2.5 - - + -
282A GLY 2.9 19.1 + - - +
283A GLY* 2.9 8.5 + - - +
285A PHE* 1.3 74.6 - - + +
287A LEU* 1.3 67.1 + - + +
288A VAL 2.9 2.4 + - - -
289A LEU* 3.1 17.9 + - + +
290A TYR* 2.9 24.4 + - + +
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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
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17A ALA* 4.2 24.0 - - + +
18A ALA* 5.1 1.6 - - - +
21A SER* 3.6 25.1 - - - +
283A GLY 3.1 16.7 + - - +
284A ALA* 3.7 15.5 - - - +
286A VAL* 1.3 77.7 - - + +
288A VAL* 1.3 57.6 + - + +
290A TYR* 3.6 8.4 - - + +
291A ASP* 2.5 33.7 + - - +
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Residues in contact with VAL 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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213A TRP* 3.7 26.0 - - + +
284A ALA 3.3 16.2 - - - +
285A PHE* 3.0 25.3 + - + +
286A VAL 2.9 1.4 - - - -
287A LEU* 1.3 75.6 - - - +
289A LEU* 1.3 71.2 + - + +
290A TYR 3.2 0.5 + - - -
291A ASP* 3.3 18.3 + - - +
292A GLU* 4.3 2.9 - - - +
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Residues in contact with LEU 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 PHE* 2.9 57.4 - - + +
286A VAL* 3.1 16.1 + - + +
288A VAL* 1.3 78.0 - - + +
290A TYR* 1.3 57.2 + - - +
292A GLU* 2.8 34.9 - - - +
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Residues in contact with TYR 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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13A ALA* 4.6 7.6 + - + +
16A VAL* 3.9 18.5 - - - +
17A ALA* 3.4 37.6 + - + -
20A ILE* 3.5 33.7 - - + -
286A VAL* 2.9 22.4 + - + +
287A LEU* 3.6 12.1 - - + +
288A VAL 3.1 0.2 - - - -
289A LEU* 1.3 78.9 - - - +
291A ASP* 1.3 61.7 + - - +
292A GLU* 2.4 26.9 + - - +
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Residues in contact with ASP 291 (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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287A LEU* 2.5 27.9 - - - +
288A VAL* 3.3 9.7 + - - +
289A LEU 3.2 1.8 - - - -
290A TYR* 1.3 77.6 - - - +
292A GLU* 1.3 71.1 + - - +
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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