Contacts of the helix formed by residues 284 - 296 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A LEU* 4.0 35.9 - - + -
246A LEU* 5.4 0.2 - - + -
280A CYS* 4.8 2.4 - - - +
283A PHE* 1.4 100.0 - - + +
285A GLU* 1.3 65.5 + - - +
286A GLU* 3.6 14.8 - - - +
287A MET* 3.2 23.3 + - + +
288A ALA* 4.0 1.6 + - - +
315A LEU* 3.7 22.0 - - + -
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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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283A PHE 3.6 2.1 + - - +
284A PRO* 1.3 69.4 - - - +
286A GLU* 1.3 61.1 + - - +
288A ALA* 2.9 14.5 + - - +
289A THR* 2.7 42.3 + - - +
292A ARG* 3.2 35.2 + - - -
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Residues in contact with GLU 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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284A PRO* 3.2 9.0 - - - +
285A GLU* 1.3 86.6 + - - +
287A MET* 1.3 56.0 + - - +
289A THR* 3.7 9.6 - - - -
290A TYR* 2.8 30.3 + - - +
311A LEU* 3.4 35.2 - - + +
312A PHE* 3.7 19.2 - - + -
315A LEU* 3.9 21.0 - - + +
318A ARG* 2.6 32.8 + - - -
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Residues in contact with MET 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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139A LEU* 4.4 7.4 - - + -
142A VAL* 5.3 2.9 - - + -
143A LEU* 3.6 24.9 - - + -
242A PHE* 4.9 8.3 - - - -
243A MET* 3.2 40.8 - - + +
246A LEU* 3.8 15.9 - - + -
280A CYS* 4.2 7.4 - - + -
283A PHE* 4.6 2.0 - - + -
284A PRO* 3.4 22.0 - - + +
285A GLU 3.0 0.2 + - - -
286A GLU* 1.3 78.6 - - - +
288A ALA* 1.3 57.3 + - - +
290A TYR* 3.4 6.0 + - - +
291A LEU* 3.0 29.8 + - - +
312A PHE* 3.3 35.9 - - + -
315A LEU* 4.1 12.6 - - + -
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Residues in contact with ALA 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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276A ILE* 3.4 28.7 - - + +
277A GLU* 5.7 0.9 - - - -
280A CYS* 3.9 14.0 - - + -
284A PRO 4.0 0.6 + - - -
285A GLU* 2.9 18.6 + - - +
287A MET* 1.3 76.1 - - - +
289A THR* 1.3 57.3 + - - +
291A LEU* 3.1 1.0 + - - +
292A ARG* 2.8 58.9 + - - +
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Residues in contact with THR 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 GLU* 2.7 36.8 + - - +
286A GLU* 3.7 9.8 - - - -
288A ALA* 1.3 72.6 - - - +
290A TYR* 1.3 61.8 + - - +
292A ARG* 3.9 12.7 + - - +
293A TYR* 3.0 23.4 + - + +
307A TYR* 3.3 26.0 - - - +
311A LEU* 3.6 17.7 - - + -
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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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150A ILE* 4.0 20.5 - - + +
235A LEU* 2.7 47.5 + - + +
238A LEU* 3.9 10.2 - - - +
239A GLY* 3.7 22.0 - - - -
242A PHE* 4.2 7.1 - + - -
286A GLU 2.8 20.7 + - - +
287A MET 3.5 6.5 - - - +
289A THR* 1.3 73.3 - - - +
291A LEU* 1.3 69.1 + - + +
293A TYR* 3.3 2.8 + - - +
294A VAL* 3.1 34.7 + - + +
308A LEU* 3.7 34.5 - - + -
311A LEU* 3.7 10.5 - - + +
312A PHE* 3.7 28.0 - + + -
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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
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236A GLU* 4.2 17.0 - - + +
239A GLY* 4.3 12.6 - - - +
240A HIS* 4.2 22.0 - - + +
243A MET* 4.2 12.3 - - + -
276A ILE* 3.9 16.2 - - + -
279A LEU* 3.8 28.7 - - + -
280A CYS* 3.9 19.1 - - - -
287A MET 3.0 11.9 + - - +
288A ALA 3.1 6.7 + - - +
290A TYR* 1.3 78.3 - - + +
292A ARG* 1.3 59.6 + - - +
294A VAL* 3.4 10.0 + - + +
295A ARG* 2.9 42.7 + - - +
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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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276A ILE* 3.3 22.5 - - + +
277A GLU* 3.0 37.1 + - - +
285A GLU* 3.2 29.9 + - - -
288A ALA* 2.8 40.2 + - - +
289A THR* 3.9 10.7 + - - +
291A LEU* 1.3 69.9 - - - +
293A TYR* 1.3 69.5 + - - +
295A ARG* 3.8 2.4 - - - +
296A ARG* 3.1 58.9 + - - +
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Residues in contact with TYR 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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289A THR 3.0 19.0 + - - +
290A TYR 3.5 3.1 - - - +
292A ARG* 1.3 80.5 - - - +
294A VAL* 1.3 67.9 + - + +
296A ARG* 3.1 13.0 + - - +
297A LEU* 3.5 37.0 + - + +
301A GLU* 4.9 4.4 + - - -
302A LYS 4.6 1.2 + - - -
303A PRO* 3.7 4.5 - - - +
304A ASP* 2.8 38.0 + - + +
307A TYR* 4.1 22.7 - + + +
308A LEU* 3.4 39.9 - - + -
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Residues in contact with VAL 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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232A ARG* 4.2 9.3 - - - +
235A LEU* 3.8 24.9 - - + -
236A GLU* 3.6 37.6 - - + +
290A TYR* 3.1 29.7 + - + +
291A LEU* 3.5 12.8 - - + +
293A TYR* 1.3 93.8 - - + +
295A ARG* 1.3 64.5 + - - +
296A ARG 3.4 0.3 + - - -
297A LEU* 3.4 27.4 + - + +
308A LEU* 4.0 12.8 - - + -
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Residues in contact with ARG 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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221A ILE* 3.4 31.4 - - - +
222A ASN* 4.8 10.9 + - - -
232A ARG* 6.1 0.3 - - - -
236A GLU* 3.0 40.2 + - + +
240A HIS* 3.3 24.7 + - - -
252A TRP* 5.0 4.4 - - - -
271A LYS* 4.4 10.9 + - - +
274A THR 4.7 6.3 + - - -
276A ILE* 3.9 25.9 - - + +
279A LEU* 4.6 13.5 - - - +
291A LEU* 2.9 35.0 + - + +
292A ARG* 3.8 5.4 - - - +
294A VAL* 1.3 76.4 - - - +
296A ARG* 1.3 62.0 + - + +
297A LEU 3.6 4.3 + - - +
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Residues in contact with ARG 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* 3.1 52.6 + - - +
293A TYR* 3.1 8.2 + - - +
295A ARG* 1.3 77.1 - - + +
297A LEU* 1.3 66.2 + - - +
298A ASP* 3.5 8.0 + - - +
301A GLU* 4.6 1.7 - - - +
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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