Contacts of the helix formed by residues 275 - 286 (chain D) in PDB entry 6IY6
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 THR 275 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D PHE* 3.6 14.4 - - + -
225D HIS* 3.4 29.6 - - + +
233D ILE* 3.7 14.1 - - + +
270D ALA* 3.3 33.6 + - + +
273D GLU 3.7 2.5 - - - +
274D LEU* 1.3 77.6 - - - +
276D VAL* 1.3 57.8 + - - +
277D ALA* 3.8 14.1 - - - +
278D ASP* 2.8 43.0 + - - +
279D VAL* 3.4 7.3 + - - +
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Residues in contact with VAL 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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138D LEU* 4.7 3.8 - - + -
214D ALA* 3.6 33.4 - - + +
215D ARG* 3.8 14.4 - - + +
218D PHE* 3.6 34.0 - - + -
233D ILE* 3.4 22.7 - - + -
234D ASP* 5.3 0.9 - - - +
237D VAL* 4.3 10.8 - - + -
275D THR* 1.3 70.3 - - - +
277D ALA* 1.3 64.8 + - - +
279D VAL* 3.1 6.3 + - - +
280D VAL* 2.9 38.7 + - + +
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Residues in contact with ALA 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D ILE* 3.7 18.6 - - + +
236D TRP* 3.6 34.8 - - + +
237D VAL* 4.1 12.5 - - - +
269D LEU* 4.0 9.2 - - + +
270D ALA 5.5 0.4 - - - +
275D THR* 3.8 13.0 + - - +
276D VAL* 1.3 80.7 - - - +
278D ASP* 1.3 60.4 + - - +
280D VAL* 4.3 1.0 - - - +
281D LEU* 3.2 28.4 + - - +
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Residues in contact with ASP 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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268D TRP* 3.6 16.2 - - - +
269D LEU* 3.0 36.0 + - - +
274D LEU* 3.4 21.0 - - + +
275D THR* 2.8 40.4 + - - +
277D ALA* 1.3 72.5 - - - +
279D VAL* 1.3 64.9 + - - +
282D TRP* 3.0 29.6 + - - +
302D TRP* 3.3 25.2 + - + +
306D CYS* 4.8 1.3 - - - -
312D PHE* 5.0 1.6 - - - -
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Residues in contact with VAL 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D SER 3.7 19.3 - - - +
137D VAL* 3.6 24.0 - - + -
138D LEU* 3.8 19.3 - - + -
141D LEU* 4.2 17.7 - - + -
218D PHE* 4.4 6.3 - - + -
274D LEU* 4.7 4.3 - - + -
275D THR 3.9 11.0 - - - +
276D VAL* 3.1 10.9 + - - +
278D ASP* 1.3 76.1 - - - +
280D VAL* 1.3 55.8 + - + +
282D TRP* 3.8 3.1 - - - +
283D SER* 2.6 37.2 + - - +
312D PHE* 3.7 25.8 - - + -
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Residues in contact with VAL 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D SER* 4.0 17.9 - - - -
214D ALA* 3.5 33.0 - - + -
237D VAL* 4.4 15.7 - - + -
240D ALA* 4.2 11.4 - - + -
241D ILE* 3.7 34.3 - - + -
276D VAL* 2.9 24.8 + - + +
277D ALA 4.3 2.0 - - - +
279D VAL* 1.3 77.9 - - + +
281D LEU* 1.3 58.3 + - - +
283D SER* 3.2 4.0 + - - -
284D VAL* 2.9 34.1 + - + +
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Residues in contact with LEU 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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236D TRP* 3.7 23.6 - - + +
239D ILE* 5.4 0.4 - - + -
240D ALA* 3.4 24.2 - - + +
244D LEU* 3.2 34.8 - - + -
255D VAL* 4.7 3.4 - - + -
259D MET* 3.6 34.1 - - + -
269D LEU* 3.5 25.4 - - + -
277D ALA 3.2 16.4 + - - +
278D ASP 4.0 1.6 - - - +
280D VAL* 1.3 74.3 - - - +
282D TRP* 1.3 66.0 + - - +
284D VAL* 3.1 6.1 + - - +
285D LEU* 3.0 22.8 + - + +
302D TRP* 4.2 2.5 - - + -
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Residues in contact with TRP 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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133D LEU* 4.2 9.0 - - + -
137D VAL* 4.0 17.5 - - + -
278D ASP 3.0 19.7 + - - +
279D VAL 3.8 1.1 - - - +
281D LEU* 1.3 73.6 - - - +
283D SER* 1.3 78.8 + - - +
285D LEU* 3.1 7.1 + - - +
286D GLN* 3.0 66.7 + - + +
302D TRP* 3.4 17.8 - + + -
303D MET* 3.6 33.5 + - + -
306D CYS* 3.6 20.1 - - + +
307D GLU* 3.6 21.4 + - + +
312D PHE* 3.4 50.3 - + + -
313D ASN* 6.2 0.2 - - - -
316D LEU* 3.8 17.9 - - + -
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Residues in contact with SER 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D LEU* 3.7 15.4 + - - +
134D SER* 3.4 37.5 + - - -
137D VAL* 3.9 5.9 - - - +
210D GLU* 5.7 0.2 - - - -
279D VAL* 2.6 23.2 + - - +
280D VAL 3.2 5.4 + - - -
282D TRP* 1.3 90.5 - - - +
284D VAL* 1.3 62.1 + - - +
286D GLN 3.4 1.6 + - - -
287D GLN* 3.4 29.4 + - - +
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Residues in contact with VAL 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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210D GLU* 4.9 6.7 - - - +
240D ALA* 3.5 35.7 - - + +
241D ILE* 4.6 9.4 - - + -
244D LEU* 4.0 16.2 - - + -
245D LYS* 3.9 34.5 - - + +
280D VAL* 2.9 25.4 + - + +
281D LEU* 3.1 8.7 + - - +
283D SER* 1.3 72.6 - - - +
285D LEU* 1.3 65.3 + - - +
287D GLN* 3.2 14.9 + - - +
288D ILE* 3.5 16.6 - - + +
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Residues in contact with LEU 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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244D LEU* 3.9 20.2 - - + -
256D PHE* 3.6 32.8 - - + -
259D MET* 3.9 18.4 - - + -
281D LEU* 3.0 16.4 + - + +
282D TRP* 3.4 7.6 - - - +
284D VAL* 1.3 75.8 - - - +
286D GLN* 1.3 61.1 + - + +
287D GLN 3.2 0.2 - - - -
288D ILE* 3.3 33.9 + - + +
299D VAL* 4.8 0.7 - - + -
302D TRP* 3.8 29.4 - - + -
303D MET* 3.9 26.6 - - + +
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Residues in contact with GLN 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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133D LEU* 3.9 13.2 - - + +
282D TRP* 3.0 56.0 + - + +
283D SER 3.8 5.8 - - - +
284D VAL 3.3 0.4 - - - -
285D LEU* 1.3 76.3 - - - +
287D GLN* 1.3 60.0 + - - +
288D ILE 3.6 3.7 + - - +
303D MET* 4.1 14.5 - - - +
307D GLU* 2.9 28.6 + - - -
316D LEU* 3.9 22.0 - - + +
319D LEU* 6.0 0.9 - - - +
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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