Contacts of the helix formed by residues 279 - 286 (chain D) in PDB entry 2IHU
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 279 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273D ASP* 4.1 5.2 - - - +
278D PHE* 1.4 97.9 - - + +
280D ALA* 1.3 54.7 + - - +
281D LEU 3.7 1.3 - - - -
282D GLN* 4.2 17.3 - - + -
283D THR* 2.3 41.8 + - - +
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Residues in contact with ALA 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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272D MET* 3.7 31.0 - - + +
273D ASP* 2.8 16.0 + - - +
276D LEU* 4.2 10.5 - - + -
278D PHE* 2.8 15.0 + - + +
279D PRO* 1.3 69.8 - - - +
281D LEU* 1.3 59.6 + - - +
283D THR* 3.3 4.2 + - - -
284D MET* 2.9 30.4 + - - +
364D LEU* 3.7 21.5 - - + +
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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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268D VAL* 4.1 8.3 - - + -
269D THR 4.2 7.9 - - - +
270D GLY* 4.5 13.7 - - - +
272D MET* 3.7 33.4 - - + -
273D ASP* 3.0 24.2 + - - +
280D ALA* 1.3 72.5 - - - +
282D GLN* 1.3 61.8 + - - +
284D MET* 3.4 2.4 + - - -
285D PHE* 2.8 60.6 + - + +
306D MET* 3.8 16.6 - - + +
309D LYS* 3.9 29.6 - - + +
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Residues in contact with GLN 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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273D ASP* 5.1 1.0 + - - -
279D PRO* 3.9 21.0 + - + +
281D LEU* 1.3 78.1 - - - +
283D THR* 1.3 58.0 + - - +
286D ALA* 2.8 51.0 + - + +
287D PRO* 4.2 0.2 - - - +
309D LYS* 3.6 22.3 - - - +
310D GLY* 3.4 26.5 + - - +
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Residues in contact with THR 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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278D PHE* 3.5 10.7 - - + -
279D PRO* 2.3 32.6 + - - +
280D ALA 3.5 5.2 - - - -
282D GLN* 1.3 76.1 - - - +
284D MET* 1.3 62.1 + - - +
287D PRO* 4.2 4.5 - - - +
359D HIS* 3.9 8.3 - - - -
360D ASP 4.2 7.2 - - - +
361D ILE* 3.7 25.8 - - + +
363D PRO* 5.0 6.7 - - + -
364D LEU* 3.8 30.5 - - + +
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Residues in contact with MET 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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248D ILE* 3.9 29.6 - - + +
265D TYR* 3.7 36.3 - - - +
266D GLY 5.3 0.2 - - - +
267D ALA 4.9 2.9 - - - +
268D VAL* 3.8 20.4 - - + -
272D MET* 4.4 9.9 - - + -
280D ALA 2.9 14.3 + - - +
281D LEU* 3.6 7.2 - - - +
283D THR* 1.3 77.4 - - - +
285D PHE* 1.3 81.5 + - + +
288D VAL* 3.5 4.2 - - - +
359D HIS* 2.8 26.5 + - - -
361D ILE* 4.3 7.9 - - - -
364D LEU* 3.9 21.7 - - + +
368D ILE* 6.4 0.7 - - + -
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Residues in contact with PHE 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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220D VAL* 4.6 10.5 - - + -
222D VAL* 4.6 8.3 - - + -
248D ILE* 3.7 27.6 - - + -
268D VAL* 3.9 17.3 - - + -
281D LEU* 2.8 41.9 + - + +
284D MET* 1.3 92.9 - - + +
286D ALA* 1.3 62.1 + - - +
287D PRO* 3.4 4.3 - - - -
288D VAL* 3.1 19.6 + - + +
291D VAL* 5.2 0.9 - - + -
302D LEU* 5.4 3.8 - - + -
306D MET 3.5 24.2 - - - -
307D TRP* 3.7 39.9 - - + +
309D LYS* 3.9 7.2 - - + -
313D LYS* 2.8 26.0 + - - -
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Residues in contact with ALA 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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282D GLN* 2.8 54.1 + - + +
285D PHE* 1.3 72.6 - - - +
287D PRO* 1.4 60.7 - - + +
309D LYS* 3.5 11.5 + - - +
310D GLY* 3.8 3.5 - - - -
311D ILE* 3.1 34.1 + - - +
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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