Contacts of the helix formed by residues 284 - 296 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139D LEU* 4.0 28.0 - - + -
246D LEU* 5.4 0.2 - - + -
280D CYS* 4.9 2.1 - - - +
283D PHE* 1.4 98.4 - - + +
285D GLU* 1.3 64.9 + - - +
286D GLU* 3.8 7.9 - - + +
287D MET* 3.2 26.2 + - + +
288D ALA 4.0 1.4 + - - -
315D LEU* 3.7 36.6 - - + -
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Residues in contact with GLU 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D PHE 3.6 2.1 + - - -
284D PRO* 1.3 70.8 - - - +
286D GLU* 1.3 62.2 + - - +
288D ALA* 3.0 8.8 + - - +
289D THR* 2.7 54.5 + - - +
292D ARG* 3.0 33.8 + - - -
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Residues in contact with GLU 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D PRO* 3.8 5.5 - - + +
285D GLU* 1.3 91.5 + - - +
287D MET* 1.3 56.1 + - - +
289D THR* 3.8 8.6 - - - -
290D TYR* 2.8 31.4 + - - +
311D LEU* 3.8 34.1 - - + +
312D PHE* 3.8 9.2 - - + -
314D ASP* 5.4 0.7 - - - +
315D LEU* 3.3 44.9 - - + +
318D ARG* 3.6 25.1 + - - -
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Residues in contact with MET 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D LEU* 5.1 5.4 - - - -
142D VAL* 5.1 4.0 - - + -
143D LEU* 4.8 10.8 - - + -
146D ALA* 6.1 0.9 - - + -
239D GLY* 5.3 0.9 - - - +
242D PHE* 3.8 30.7 - - + -
243D MET* 3.7 22.0 - - - -
246D LEU* 3.9 24.2 - - + -
280D CYS* 4.1 7.9 - - + -
283D PHE* 4.6 1.8 - - + -
284D PRO* 3.4 24.2 - - + +
285D GLU 3.1 0.4 - - - -
286D GLU* 1.3 78.0 - - - +
288D ALA* 1.3 56.1 + - - +
290D TYR* 3.4 5.8 + - + +
291D LEU* 3.0 31.2 + - - +
312D PHE* 3.9 30.3 - - + -
315D LEU* 5.3 3.4 - - - -
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Residues in contact with ALA 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D ILE* 3.5 27.8 - - + +
277D GLU* 5.7 0.9 - - - -
280D CYS* 3.8 14.4 - - + -
284D PRO 4.0 0.2 + - - -
285D GLU* 3.0 16.6 + - - +
287D MET* 1.3 74.6 - - - +
289D THR* 1.3 61.0 + - - +
291D LEU* 3.1 1.8 + - - +
292D ARG* 2.8 54.8 + - - +
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Residues in contact with THR 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D GLU* 2.7 43.5 + - - +
286D GLU* 3.8 9.7 - - - -
288D ALA* 1.3 73.1 - - - +
290D TYR* 1.3 61.3 + - - +
292D ARG* 4.0 11.2 + - - +
293D TYR* 3.0 24.1 + - + +
307D TYR* 3.5 24.2 - - - +
311D LEU* 3.9 16.4 - - + -
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Residues in contact with TYR 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D ILE* 3.9 18.4 - - + +
235D LEU* 2.8 44.6 + - - +
238D LEU* 3.8 11.8 - - - +
239D GLY* 3.5 23.8 - - - -
242D PHE* 4.0 10.0 - + - -
286D GLU 2.8 22.1 + - - +
287D MET* 3.6 7.2 - - + +
289D THR* 1.3 73.9 - - - +
291D LEU* 1.3 66.5 + - + +
293D TYR* 3.4 1.4 + - - +
294D VAL* 3.1 35.9 + - + +
308D LEU* 3.5 38.8 - - + -
311D LEU* 3.8 9.1 - - + +
312D PHE* 3.7 26.7 - + + -
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Residues in contact with LEU 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D GLU* 4.1 25.1 - - + +
239D GLY* 4.1 17.7 - - - +
240D HIS* 4.4 12.1 - - + +
243D MET* 4.2 11.4 - - + -
276D ILE* 4.2 17.7 - - + -
279D LEU* 3.8 28.5 - - + -
280D CYS* 4.0 18.6 - - - -
287D MET 3.0 14.4 + - - +
288D ALA 3.1 3.8 + - - +
290D TYR* 1.3 75.3 - - + +
292D ARG* 1.3 59.5 + - - +
294D VAL* 3.2 9.9 - - + +
295D ARG* 2.9 42.2 + - - +
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Residues in contact with ARG 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D ILE* 3.3 23.5 - - + +
277D GLU* 2.9 34.7 + - - +
285D GLU* 3.0 28.9 + - - -
288D ALA* 2.8 37.3 + - - +
289D THR* 4.0 19.8 + - - +
291D LEU* 1.3 69.3 - - - +
293D TYR* 1.3 68.4 + - - +
295D ARG* 3.4 3.0 + - - +
296D ARG* 3.2 23.6 + - - +
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Residues in contact with TYR 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D THR* 3.0 19.5 + - + +
290D TYR 3.5 4.0 - - - +
291D LEU 3.3 0.2 - - - -
292D ARG* 1.3 79.2 - - - +
294D VAL* 1.3 70.4 + - + +
296D ARG* 3.1 12.3 + - - +
297D LEU* 3.4 45.9 + - + +
301D GLU* 4.7 4.2 + - - -
302D LYS 4.5 1.2 + - - -
303D PRO* 3.7 1.2 - - + +
304D ASP* 2.8 36.7 + - + +
307D TYR* 3.9 24.2 - + + +
308D LEU* 3.5 38.4 - - + -
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Residues in contact with VAL 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D ARG* 4.1 10.0 - - - +
235D LEU* 3.8 24.0 - - + +
236D GLU* 3.8 39.2 - - + +
290D TYR* 3.1 22.2 + - + +
291D LEU* 3.2 18.4 - - + +
293D TYR* 1.3 91.1 - - + +
295D ARG* 1.3 67.8 + - - +
296D ARG 3.3 0.3 + - - -
297D LEU* 3.3 29.4 + - + +
308D LEU* 4.1 11.7 - - + -
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Residues in contact with ARG 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D ILE* 3.4 31.6 - - - +
232D ARG* 5.7 0.2 + - - -
236D GLU* 2.9 42.0 + - + +
240D HIS* 3.0 28.3 + - - -
252D TRP* 5.0 2.8 - - - -
271D LYS* 4.7 8.9 + - - +
274D THR 5.1 5.3 + - - -
276D ILE* 3.7 27.8 - - + +
279D LEU* 4.8 9.9 - - - +
291D LEU* 2.9 34.0 + - - +
292D ARG* 3.8 6.3 - - - +
294D VAL* 1.3 77.0 - - - +
296D ARG* 1.3 58.9 + - - +
297D LEU 3.6 5.0 + - - +
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Residues in contact with ARG 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D ARG 3.2 16.1 + - - +
293D TYR* 3.1 7.6 + - - +
295D ARG* 1.3 74.5 - - + +
297D LEU* 1.3 64.7 + - - +
298D ASP* 3.6 1.6 + - - -
301D GLU* 4.6 1.6 - - - +
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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