Contacts of the helix formed by residues 273 - 284 (chain D) in PDB entry 2C11
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 SER 273 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187D GLU* 6.2 0.2 - - - -
190D GLN* 5.9 1.3 - - - -
261D ILE* 5.3 4.5 - - - -
264D VAL* 4.2 11.2 - - - -
271D TYR* 3.3 4.2 - - - +
272D ASP* 1.3 84.5 - - - +
274D LEU* 1.3 63.8 + - - +
275D ALA* 3.4 10.5 + - - +
276D GLN* 2.9 27.5 + - - +
277D LEU* 3.0 22.3 + - - +
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Residues in contact with LEU 274 (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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187D GLU* 2.9 69.2 + - + +
188D LEU* 3.5 7.0 - - + +
190D GLN* 4.2 4.9 + - + +
191D ALA* 3.8 18.1 - - + +
245D LEU* 4.8 9.2 - - + -
247D LEU* 3.7 21.5 - - + -
261D ILE* 5.2 3.3 - - + +
264D VAL* 3.7 25.7 - - + +
273D SER* 1.3 73.6 - - - +
275D ALA* 1.3 54.0 + - - +
277D LEU* 3.1 9.3 + - + +
278D GLU* 2.6 38.5 + - - +
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Residues in contact with ALA 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D GLN* 4.0 36.3 + - + +
273D SER* 3.6 9.4 - - - +
274D LEU* 1.3 80.4 - - - +
276D GLN* 1.3 52.8 + - - +
278D GLU* 3.1 2.1 + - - +
279D ALA* 2.6 37.9 + - - +
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Residues in contact with GLN 276 (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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270D TYR 5.2 1.0 + - - -
271D TYR* 4.1 18.8 - - - +
272D ASP* 2.6 43.4 + - - +
273D SER* 2.9 24.7 + - - +
275D ALA* 1.3 73.4 - - - +
277D LEU* 1.3 61.3 + - - +
279D ALA* 3.3 7.1 - - + +
280D GLN* 2.8 54.3 + - + +
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Residues in contact with LEU 277 (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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191D ALA* 5.5 4.3 - - + -
194D LEU* 3.7 25.6 - - + -
245D LEU* 4.2 7.6 - - + -
264D VAL* 4.1 17.0 - - + -
266D TYR* 3.7 24.2 - - + -
271D TYR* 3.5 43.9 - - + -
273D SER 3.0 14.1 + - - +
274D LEU* 3.3 11.2 - - + +
276D GLN* 1.3 73.3 - - - +
278D GLU* 1.3 68.4 + - - +
280D GLN* 2.7 15.8 + - - +
281D PHE* 2.8 11.3 + - - +
286D VAL* 3.9 17.3 - - + -
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Residues in contact with GLU 278 (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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190D GLN 3.0 28.7 - - - +
191D ALA* 2.6 37.3 - - - +
193D GLY* 3.7 9.0 - - - +
194D LEU* 2.7 21.7 + - - +
274D LEU 2.6 16.9 + - - +
275D ALA* 3.3 4.0 - - - +
277D LEU* 1.3 72.3 - - - +
279D ALA* 1.3 64.8 + - - +
281D PHE* 3.0 15.0 + - - +
282D GLU* 2.7 43.4 + - - +
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Residues in contact with ALA 279 (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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275D ALA 2.6 20.6 + - - +
276D GLN* 3.3 10.3 - - + +
278D GLU* 1.3 74.1 - - - +
280D GLN* 1.3 60.0 + - + +
281D PHE 3.1 0.5 + - - -
282D GLU* 3.2 11.0 + - - +
283D ALA* 2.8 29.1 + - - +
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Residues in contact with GLN 280 (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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271D TYR* 4.2 13.3 - - - -
276D GLN* 2.8 41.4 + - + +
277D LEU* 2.7 13.9 + - - +
279D ALA* 1.3 73.2 - - + +
281D PHE* 1.3 57.2 + - - +
283D ALA* 3.4 10.2 - - + +
284D GLY 3.1 2.9 + - - -
285D LEU* 3.0 49.7 + - + +
286D VAL* 3.5 15.9 + - + +
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Residues in contact with PHE 281 (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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193D GLY* 3.7 17.3 - - - -
194D LEU* 3.7 38.4 - - + -
197D HIS* 3.8 36.8 - + + -
277D LEU 2.8 10.0 + - - +
278D GLU* 3.0 23.8 + - - +
280D GLN* 1.3 78.4 - - - +
282D GLU* 1.3 67.1 + - + +
284D GLY* 3.0 19.4 + - - -
286D VAL* 3.7 28.8 + - + +
288D VAL* 4.4 5.4 - - + -
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Residues in contact with GLU 282 (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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193D GLY* 5.5 3.4 - - - -
278D GLU* 2.7 50.1 + - - +
279D ALA* 3.8 7.3 + - - +
281D PHE* 1.3 81.2 - - + +
283D ALA* 1.3 65.0 + - - +
284D GLY* 3.0 3.1 + - - -
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Residues in contact with ALA 283 (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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279D ALA 2.8 18.4 + - - +
280D GLN* 3.4 15.5 - - + +
282D GLU* 1.3 78.2 - - - +
284D GLY* 1.3 59.1 + - - +
285D LEU* 3.7 4.9 - - + +
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Residues in contact with GLY 284 (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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280D GLN 3.1 0.6 + - - -
281D PHE 3.0 15.2 + - - -
282D GLU 3.0 1.5 - - - -
283D ALA* 1.3 80.2 - - - +
285D LEU* 1.3 62.4 + - - +
286D VAL 3.5 4.1 + - - -
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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
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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