Contacts of the helix formed by residues 271 - 279 (chain D) in PDB entry 3IAD
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 HIS 271 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261D GLU* 3.6 16.3 + - - +
264D ASP* 5.3 1.0 + - - +
269D GLY 3.9 7.6 + - - -
270D LEU* 1.3 74.1 - - - +
272D VAL* 1.3 63.6 + - - +
274D ARG* 3.3 9.0 + - + +
275D ILE* 3.1 23.3 + - - +
493D GLN* 3.3 25.0 + - - -
494D LEU* 4.5 0.2 - - - -
804D EPE 3.2 52.4 - - - -
805D EPE 2.7 33.6 + - - +
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Residues in contact with VAL 272 (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 LEU* 2.9 21.3 + - + +
271D HIS* 1.3 69.8 - - - +
273D PHE* 1.3 81.5 + - + +
275D ILE* 3.2 6.8 + - - +
276D ALA* 2.9 26.9 + - - +
283D PRO* 4.6 2.4 - - + +
287D ILE* 4.0 24.5 - - + -
329D ILE* 4.3 12.5 - - + +
332D ALA* 4.1 16.6 - - + -
333D ASP* 4.4 16.6 - - + +
336D GLN* 6.1 0.4 - - + +
494D LEU* 4.1 9.1 - - + +
498D TRP* 4.2 15.7 - - + +
805D EPE 3.7 0.6 + - - -
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Residues in contact with PHE 273 (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 HIS 3.4 0.4 - - - -
272D VAL* 1.3 74.4 - - + +
274D ARG* 1.3 67.0 + - - +
276D ALA* 3.2 10.1 + - - +
277D GLU* 3.1 25.9 + - - +
329D ILE* 3.7 27.4 - - + -
494D LEU* 3.6 29.6 - - + -
497D GLN* 3.5 39.3 - - + +
498D TRP* 3.5 43.5 - + - -
501D ARG* 3.3 32.3 - - - -
805D EPE 3.4 19.0 + - + +
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Residues in contact with ARG 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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254D GLN* 5.9 0.2 - - - +
257D VAL* 4.5 9.1 - - - +
261D GLU* 4.1 13.9 - - - +
271D HIS* 3.5 16.6 - - + +
273D PHE* 1.3 74.4 - - - +
275D ILE* 1.3 57.9 + - - +
277D GLU* 3.2 31.0 + - - +
278D LEU* 2.9 77.6 + - + +
805D EPE 3.1 43.0 + - - +
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Residues in contact with ILE 275 (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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258D LEU* 4.1 11.8 - - + +
261D GLU* 4.0 23.1 - - + -
262D LEU* 3.9 18.4 - - + -
270D LEU* 3.4 45.8 - - + -
271D HIS 3.1 13.3 + - - +
272D VAL* 3.2 9.1 + - - +
274D ARG* 1.3 72.3 - - - +
276D ALA* 1.3 58.4 + - - +
278D LEU* 3.9 2.3 - - - +
279D SER* 2.8 34.1 + - - -
283D PRO* 4.4 4.7 - - + -
286D VAL* 4.0 25.6 - - + -
287D ILE* 4.2 14.1 - - + -
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Residues in contact with ALA 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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272D VAL 2.9 12.5 + - - +
273D PHE* 3.2 14.8 - - - +
275D ILE* 1.3 77.5 - - - +
277D GLU* 1.3 58.0 + - + +
279D SER* 3.2 6.6 + - - -
281D ASN* 2.7 38.1 + - - +
283D PRO* 4.0 24.7 - - + +
329D ILE* 4.3 19.1 - - + -
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Residues in contact with GLU 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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254D GLN* 4.5 6.5 + - - -
273D PHE* 3.1 13.0 + - - +
274D ARG* 3.2 22.8 + - - +
276D ALA* 1.3 76.4 - - + +
278D LEU* 1.3 64.3 + - - +
279D SER 3.2 1.1 + - - -
280D GLY* 3.5 10.2 + - - -
281D ASN 4.9 0.4 - - - +
805D EPE 2.9 62.6 - - - -
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Residues in contact with LEU 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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254D GLN* 4.1 40.2 + - + +
255D GLU* 5.2 1.4 + - - -
257D VAL* 3.8 29.8 - - + +
258D LEU* 3.8 31.9 - - + +
261D GLU* 3.7 30.3 - - + -
274D ARG* 2.9 59.0 + - + +
275D ILE 3.4 0.2 + - - -
277D GLU* 1.3 75.9 - - - +
279D SER* 1.3 58.0 + - - +
280D GLY 3.5 1.0 + - - -
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Residues in contact with SER 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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258D LEU* 4.0 18.6 - - - -
275D ILE 2.8 21.0 + - - -
276D ALA 3.2 3.1 + - - -
277D GLU 3.2 0.2 - - - -
278D LEU* 1.3 75.4 - - - +
280D GLY* 1.3 60.7 + - - +
282D ARG* 3.0 48.0 + - - +
283D PRO 3.6 0.9 - - - -
286D VAL* 4.2 13.4 - - - +
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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