Contacts of the helix formed by residues 273 - 285 (chain B) in PDB entry 3R2A
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 ASP 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269B CYS 5.3 1.4 + - - -
270B GLN 4.5 9.1 + - - +
271B ALA 3.2 1.0 + - - -
272B ALA* 1.3 74.6 - - - +
274B LYS* 1.3 60.6 + - - +
276B LEU* 2.9 28.0 - - - +
277B PHE* 3.8 1.7 + - - +
305B TRP* 5.9 0.2 - - - -
453C GLU* 3.2 37.1 - - + +
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Residues in contact with LYS 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B ALA* 3.2 14.7 + - - +
272B ALA 3.0 0.2 - - - -
273B ASP* 1.3 83.4 - - - +
275B GLN* 1.3 76.2 + - + +
276B LEU 3.1 0.2 - - - -
277B PHE* 2.9 25.3 - - + +
327B ALA* 4.2 19.2 + - + +
328B THR* 4.7 17.2 + - + +
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Residues in contact with GLN 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B VAL 5.3 0.2 + - - -
271B ALA 4.1 0.6 + - - +
272B ALA* 2.9 16.0 + - - +
274B LYS* 1.3 110.2 - - + +
276B LEU* 1.3 64.4 + - - +
277B PHE* 2.9 3.0 - - - +
278B THR* 1.0 97.1 + - + +
279B LEU* 2.9 23.9 + - - +
305B TRP* 4.7 3.2 - - - -
309B LEU* 4.6 18.7 - - + +
316B ARG* 6.0 1.1 - - - +
327B ALA* 4.2 25.8 - - + -
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B ALA 3.0 3.8 + - - +
273B ASP* 2.9 23.3 + - - +
275B GLN* 1.3 79.6 - - - +
277B PHE* 1.3 61.5 + - - +
279B LEU* 3.7 1.0 - - - +
280B VAL* 3.0 36.7 + - + +
305B TRP* 3.8 32.8 - - + -
453C GLU* 4.1 23.6 - - - +
2340E GLY 5.5 7.9 - - - +
2341E LEU* 5.2 11.9 - - + +
2343E ALA 5.8 1.8 - - - +
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Residues in contact with PHE 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B ASP 3.8 1.7 + - - +
274B LYS* 2.9 19.6 + - + +
275B GLN* 4.9 2.7 - - - -
276B LEU* 1.3 79.7 - - - +
278B THR* 1.3 70.3 + - - +
280B VAL* 3.2 4.4 + - + +
281B GLU* 3.1 39.8 + - + +
284B LYS* 5.9 3.1 - - - -
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Residues in contact with THR 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B VAL* 3.9 39.6 + - + +
275B GLN* 1.0 123.7 + - + +
276B LEU 3.4 0.2 - - - -
277B PHE* 1.3 84.7 - - - +
279B LEU* 1.3 66.7 + - + +
281B GLU* 3.5 1.7 + - - -
282B TRP* 3.1 22.6 + - + +
371B ARG* 5.4 8.5 - - - +
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B GLN 2.9 19.9 + - - +
276B LEU* 3.7 4.9 - - - +
278B THR* 1.3 82.2 - - + +
280B VAL* 1.3 64.0 + - + +
282B TRP* 3.3 8.8 + - + +
283B ALA* 3.1 21.0 + - - +
301B LEU* 4.6 15.5 - - + +
305B TRP* 3.5 51.8 - - + +
308B LEU* 4.0 32.8 - - + -
309B LEU* 5.0 9.4 - - + -
371B ARG* 4.0 16.6 - - - +
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B LEU* 3.0 35.6 + - + +
277B PHE* 3.2 4.5 + - + +
279B LEU* 1.3 74.4 - - + +
281B GLU* 1.3 66.4 + - - +
283B ALA* 3.3 5.1 + - + +
284B LYS* 3.1 39.5 + - + +
301B LEU* 4.7 12.6 - - + -
305B TRP* 6.2 0.4 - - + -
2341E LEU* 5.4 6.5 - - + +
2343E ALA 4.8 6.7 - - - +
2344E ILE* 3.5 38.4 - - + -
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Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B ALA* 4.4 11.3 - - + +
242B VAL* 4.5 12.6 - - + -
277B PHE* 3.1 35.9 + - + +
278B THR* 4.1 2.9 - - - +
280B VAL* 1.3 76.2 - - - +
282B TRP* 1.3 64.3 + - - +
284B LYS* 3.1 36.6 + - + +
285B ARG* 2.9 52.6 + - - +
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Residues in contact with TRP 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ILE* 5.3 0.2 - - - +
238B ALA* 3.9 25.2 - - + +
239B GLU* 1.9 36.9 + - - +
242B VAL* 4.8 9.4 - - + +
278B THR* 3.1 18.3 + - + +
279B LEU* 3.5 12.1 - - + +
280B VAL 3.1 0.4 - - - -
281B GLU* 1.3 80.7 - - - +
283B ALA* 1.3 83.6 + - + +
284B LYS 3.3 0.2 + - - -
285B ARG* 3.5 8.1 + - - +
286B ILE* 3.4 35.6 + - + +
308B LEU* 4.2 11.4 - - + -
368B GLY 4.4 2.0 + - - -
371B ARG* 3.5 58.6 - - + +
372B ALA* 3.9 1.8 - - - -
375B LEU* 3.6 41.1 - - + -
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Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B LEU 3.1 10.8 + - - +
280B VAL* 4.0 4.9 - - + +
282B TRP* 1.3 99.6 - - + +
284B LYS* 1.3 58.6 + - + +
286B ILE* 3.6 6.4 + - - +
289B PHE* 2.3 59.2 - - + +
301B LEU* 4.3 15.0 - - + -
375B LEU* 4.4 2.5 - - + -
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Residues in contact with LYS 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B PHE* 5.9 3.2 - - - -
280B VAL* 3.1 31.4 + - + +
281B GLU* 3.1 28.4 + - + +
283B ALA* 1.3 78.0 - - - +
285B ARG* 1.3 62.9 + - + +
286B ILE 3.3 5.7 + - - +
289B PHE* 4.4 3.8 - - + -
290B SER* 3.1 23.0 + - - -
2344E ILE* 3.2 47.2 + - + -
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Residues in contact with ARG 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B ARG* 3.7 35.9 + - - +
237B GLU* 5.2 5.7 - - - +
238B ALA* 3.8 34.4 - - + +
241B ALA* 4.6 12.4 - - - +
281B GLU* 2.9 42.9 + - - +
282B TRP 3.5 2.2 + - - +
283B ALA 3.3 0.6 - - - -
284B LYS* 1.3 80.7 - - + +
286B ILE* 1.3 62.5 + - - +
287B PRO* 3.4 6.9 - - - +
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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
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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