Contacts of the helix formed by residues 276 - 285 (chain D) in PDB entry 3IKH
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 GLY 276 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49D ARG* 4.1 9.6 - - - -
274D PHE 3.8 0.8 + - - -
275D PRO* 1.3 74.1 - - - +
277D SER* 1.3 68.3 - - - -
278D ARG* 2.9 18.0 + - - -
279D GLU* 3.0 16.0 + - - -
280D LEU* 3.0 24.2 + - - +
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Residues in contact with SER 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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49D ARG* 3.3 43.7 + - - +
276D GLY* 1.3 69.8 - - - -
278D ARG* 1.3 56.9 + - - +
280D LEU* 3.2 4.9 + - - +
281D ALA* 2.8 37.7 + - - +
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Residues in contact with ARG 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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276D GLY* 4.2 12.8 - - - -
277D SER* 1.3 84.4 - - - +
279D GLU* 1.3 76.2 + - - +
281D ALA* 3.2 11.3 + - - +
282D ALA* 3.3 12.6 + - - +
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Residues in contact with GLU 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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263D ILE* 4.0 19.3 - - + +
267D ARG* 2.9 40.7 + - - -
275D PRO* 3.3 7.7 - - + +
276D GLY* 3.0 26.2 + - - +
278D ARG* 1.3 91.1 + - + +
280D LEU* 1.3 58.3 + - - +
282D ALA* 3.5 6.5 + - - +
283D LEU* 2.9 31.7 + - - +
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Residues in contact with LEU 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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46D ILE* 4.2 6.1 - - + +
49D ARG* 3.5 36.1 - - + +
50D CYS* 3.7 24.5 - - - -
237D VAL* 3.8 29.2 - - + -
275D PRO* 3.8 29.6 - - + +
276D GLY 3.0 15.2 + - - +
277D SER* 3.4 7.6 - - - +
279D GLU* 1.3 74.3 - - - +
281D ALA* 1.3 54.7 + - - +
283D LEU* 3.2 15.9 + - + +
284D LEU* 2.6 44.0 + - + +
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Residues in contact with ALA 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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277D SER 2.8 19.7 + - - +
278D ARG* 3.2 6.3 + - - +
280D LEU* 1.3 74.4 - - - +
282D ALA* 1.3 63.6 + - - +
284D LEU* 3.2 14.5 + - - +
285D THR* 3.2 16.4 + - - -
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Residues in contact with ALA 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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278D ARG 3.3 8.9 + - - +
279D GLU* 3.8 9.0 - - - +
280D LEU 3.3 0.2 - - - -
281D ALA* 1.3 78.3 - - - +
283D LEU* 1.3 63.3 + - - +
285D THR* 3.1 23.7 + - - -
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Residues in contact with LEU 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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237D VAL* 4.2 3.8 - - + -
256D HIS* 3.4 46.0 + - + +
259D ARG* 3.9 16.9 - - + +
260D ALA* 3.4 39.7 - - + +
263D ILE* 4.6 10.3 - - + -
279D GLU 2.9 18.5 + - - +
280D LEU* 3.3 13.7 - - + +
282D ALA* 1.3 77.7 - - - +
284D LEU* 1.3 73.8 + - + +
285D THR 3.1 3.7 + - - -
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Residues in contact with LEU 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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50D CYS* 4.0 30.5 - - + +
237D VAL* 4.1 9.6 - - + -
240D ALA* 5.0 0.2 - - + -
241D SER* 3.9 33.2 - - - +
244D LEU* 3.6 28.5 - - + -
245D ARG* 5.5 3.5 - - - -
256D HIS* 3.4 22.4 - - + +
280D LEU* 2.6 27.2 + - - +
281D ALA* 3.2 8.7 + - - +
283D LEU* 1.3 84.8 - - + +
285D THR* 1.3 65.7 + - - +
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Residues in contact with THR 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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252D LEU* 5.8 2.3 - - - +
256D HIS* 4.4 9.6 + - - -
281D ALA 3.2 13.5 + - - -
282D ALA* 3.1 16.3 + - - -
283D LEU 3.1 6.8 - - - -
284D LEU* 1.3 81.9 - - - +
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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