Contacts of the helix formed by residues 284 - 296 (chain B) in PDB entry 2C47
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 PRO 284 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139B LEU* 3.9 34.5 - - + -
246B LEU* 5.4 0.4 - - + -
280B CYS* 4.8 2.4 - - - +
283B PHE* 1.3 99.5 - - + +
285B GLU* 1.3 64.7 + - - +
286B GLU* 3.6 14.6 - - - +
287B MET* 3.2 26.4 + - + +
288B ALA 4.0 1.2 + - - -
315B LEU* 3.8 21.1 - - + -
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Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B PHE 3.6 1.7 + - - -
284B PRO* 1.3 72.9 - - - +
286B GLU* 1.3 59.1 + - - +
288B ALA* 3.0 11.9 + - - +
289B THR* 2.7 44.9 + - - +
292B ARG* 3.0 33.9 + - - -
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Residues in contact with GLU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PRO* 3.2 10.1 - - - +
285B GLU* 1.3 86.7 + - - +
287B MET* 1.3 53.8 + - - +
289B THR* 3.6 9.0 - - - +
290B TYR* 2.8 34.7 + - - +
311B LEU* 3.4 40.1 - - + +
312B PHE* 3.9 12.9 - - + -
314B ASP* 5.7 0.3 - - - +
315B LEU* 3.9 25.5 - - + +
318B ARG* 3.1 29.4 + - - -
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Residues in contact with MET 287 (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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139B LEU* 5.0 3.8 - - - -
142B VAL* 5.0 4.3 - - + -
143B LEU* 4.6 13.9 - - + -
146B ALA* 6.1 0.2 - - + -
239B GLY* 5.5 0.7 - - - +
242B PHE* 3.8 29.8 - - + -
243B MET* 3.7 21.0 - - + +
246B LEU* 3.9 29.6 - - + -
280B CYS* 4.3 7.4 - - + -
283B PHE* 4.4 1.8 - - + -
284B PRO* 3.5 23.6 - - + +
285B GLU 3.1 0.4 + - - -
286B GLU* 1.3 77.5 - - - +
288B ALA* 1.3 59.4 + - - +
290B TYR* 3.4 6.2 + - + +
291B LEU* 3.1 30.3 + - - +
312B PHE* 3.8 27.8 - - + -
315B LEU* 5.0 4.5 - - - -
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Residues in contact with ALA 288 (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 ILE* 3.5 27.6 - - + +
277B GLU* 5.8 1.1 - - - -
280B CYS* 3.9 14.0 - - + -
284B PRO 4.0 0.6 + - - -
285B GLU* 3.0 18.8 + - - +
287B MET* 1.3 77.4 - - - +
289B THR* 1.3 60.2 + - - +
291B LEU* 3.2 1.4 + - - +
292B ARG* 2.8 53.6 + - - +
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Residues in contact with THR 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLU* 2.7 38.7 + - - +
286B GLU* 3.6 8.3 - - - -
288B ALA* 1.3 72.6 - - - +
290B TYR* 1.3 62.1 + - - +
292B ARG* 3.5 10.9 + - - +
293B TYR* 3.0 23.8 + - + +
307B TYR* 3.5 24.5 - - + +
311B LEU* 3.6 21.3 - - + +
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Residues in contact with TYR 290 (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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150B ILE* 4.0 19.8 - - + +
235B LEU* 2.6 44.6 + - + +
238B LEU* 3.6 14.7 - - - +
239B GLY* 3.6 21.8 - - - -
242B PHE* 4.1 8.0 - + - -
286B GLU 2.8 20.6 + - - +
287B MET* 3.4 6.7 - - + +
288B ALA 3.2 0.2 - - - -
289B THR* 1.3 73.8 - - - +
291B LEU* 1.3 68.6 + - + +
293B TYR* 3.4 2.3 + - - +
294B VAL* 3.0 36.5 + - + +
308B LEU* 3.7 35.9 - - + -
311B LEU* 3.8 9.3 - - + +
312B PHE* 3.6 29.6 - + + -
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Residues in contact with LEU 291 (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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236B GLU* 4.1 27.6 - - + +
239B GLY* 4.1 15.0 - - - +
240B HIS* 4.4 8.1 - - + +
243B MET* 4.2 10.8 - - + -
276B ILE* 4.1 17.7 - - + -
279B LEU* 3.7 30.1 - - + -
280B CYS* 4.1 15.3 - - - -
287B MET 3.1 11.4 + - - +
288B ALA 3.2 4.0 + - - +
290B TYR* 1.3 81.7 - - + +
292B ARG* 1.3 60.4 + - - +
294B VAL* 3.2 13.6 - - + +
295B ARG* 2.9 44.1 + - + +
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Residues in contact with ARG 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ILE* 3.8 21.6 - - + +
277B GLU* 3.0 41.2 + - - +
285B GLU* 3.0 30.3 + - - -
288B ALA* 2.8 46.0 + - - +
289B THR* 3.8 7.8 + - - +
291B LEU* 1.3 72.6 - - - +
293B TYR* 1.3 63.2 + - - +
295B ARG* 3.8 4.1 - - - +
296B ARG* 3.2 25.5 + - - +
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Residues in contact with TYR 293 (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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289B THR* 3.0 18.6 + - + +
290B TYR 3.6 3.1 - - - +
291B LEU 3.2 0.2 - - - -
292B ARG* 1.3 77.9 - - - +
294B VAL* 1.3 66.1 + - + +
296B ARG* 2.8 69.1 + - - +
297B LEU* 3.4 35.8 + - + +
301B GLU* 5.5 0.3 + - - -
302B LYS 4.6 1.2 + - - -
303B PRO* 3.7 1.6 - - + -
304B ASP* 2.8 37.4 + - + +
307B TYR* 3.9 22.9 - + + +
308B LEU* 3.5 37.9 - - + -
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Residues in contact with VAL 294 (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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232B ARG* 4.2 12.4 - - - +
235B LEU* 3.8 26.0 - - + -
236B GLU* 3.6 35.9 - - + +
290B TYR* 3.0 30.0 + - + +
291B LEU* 3.2 22.2 - - + +
293B TYR* 1.3 83.4 - - + +
295B ARG* 1.3 70.8 + - - +
297B LEU* 3.1 26.7 + - + +
308B LEU* 4.3 6.5 - - + -
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Residues in contact with ARG 295 (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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221B ILE* 3.5 31.1 - - - +
222B ASN* 5.3 6.4 + - - -
232B ARG* 5.4 0.3 + - - -
236B GLU* 2.7 35.7 + - + +
240B HIS* 3.3 27.5 + - - -
252B TRP* 5.4 2.2 - - - -
271B LYS* 4.8 8.7 + - - +
274B THR 4.9 7.3 + - - -
276B ILE* 3.8 30.5 - - + +
279B LEU* 5.4 3.8 - - - +
291B LEU* 2.9 34.4 + - - +
292B ARG* 3.8 6.5 - - - +
294B VAL* 1.3 77.7 - - + +
296B ARG* 1.3 60.0 + - - +
297B LEU 3.5 4.3 + - - +
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Residues in contact with ARG 296 (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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292B ARG 3.2 13.1 + - - +
293B TYR* 2.8 61.2 + - - +
294B VAL 3.1 1.0 - - - -
295B ARG* 1.3 79.1 - - - +
297B LEU* 1.3 66.8 + - + +
298B ASP* 3.6 1.4 + - - +
301B GLU* 4.5 15.8 + - - +
307B TYR* 5.5 3.0 + - - -
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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
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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