Contacts of the helix formed by residues 278 - 287 (chain A) in PDB entry 1IDO
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 GLU 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A SER* 1.3 72.0 + - - +
279A LYS* 1.3 68.1 + - - +
281A ARG* 2.9 30.5 + - - +
282A GLN* 3.1 53.6 + - + +
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A GLY 2.7 27.0 + - - -
244A GLU* 3.2 27.7 + - + +
245A LYS 5.0 3.8 - - - +
277A SER* 3.1 9.5 + - - +
278A GLU* 1.3 81.4 - - - +
280A SER* 1.3 80.9 + - - +
282A GLN* 3.3 4.6 + - - +
283A GLU* 3.0 41.4 + - - +
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Residues in contact with SER 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ASP 3.6 16.2 - - - -
243A GLY 3.3 17.7 - - - -
244A GLU* 4.3 7.4 + - - -
273A ASP 3.7 3.8 + - - -
274A ALA 2.9 25.4 + - - -
277A SER* 3.4 20.2 + - - -
279A LYS* 1.3 86.3 - - - +
281A ARG* 1.3 65.4 + - - +
283A GLU* 3.1 3.0 + - - +
284A LEU* 3.1 27.5 + - - +
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Residues in contact with ARG 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ALA 3.4 2.9 + - - -
275A PHE* 3.1 50.2 + - + +
276A ARG* 3.6 4.0 + - - +
277A SER* 3.1 35.0 + - - +
278A GLU* 2.9 39.9 + - - +
280A SER* 1.3 75.0 - - - +
282A GLN* 1.3 74.5 + - - +
284A LEU* 3.4 10.6 + - - +
285A ASN* 3.1 26.1 + - - +
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Residues in contact with GLN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A GLU* 3.1 41.6 + - + +
279A LYS* 3.7 4.5 - - - +
281A ARG* 1.3 87.9 + - - +
283A GLU* 1.3 59.1 + - - +
285A ASN* 3.1 30.8 + - - +
286A THR* 2.8 36.6 + - - +
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Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A THR* 4.5 1.9 + - - +
241A THR* 5.1 1.2 + - - +
243A GLY* 3.0 32.9 - - - +
244A GLU 3.5 0.2 + - - -
245A LYS* 2.9 28.8 + - - +
252A TYR* 2.6 45.1 + - + +
279A LYS* 3.0 25.2 + - - +
280A SER 3.1 9.1 + - - +
282A GLN* 1.3 76.7 - - - +
284A LEU* 1.3 63.3 + - - +
286A THR* 3.2 7.7 + - - -
287A ILE* 3.1 31.1 + - + +
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A THR* 4.0 14.8 - - + +
243A GLY* 3.8 23.6 - - - +
268A VAL* 3.7 29.6 - - + +
270A GLY* 4.1 5.2 - - - +
274A ALA* 3.9 19.5 - - + +
275A PHE* 3.5 38.6 - - + -
280A SER 3.1 15.8 + - - +
281A ARG* 3.6 7.9 - - - +
283A GLU* 1.3 75.4 - - - +
285A ASN* 1.3 64.9 + - - +
287A ILE* 3.3 4.2 + - + -
288A ALA* 3.0 25.6 + - - +
296A VAL* 4.1 13.0 - - + -
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Residues in contact with ASN 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ARG* 3.1 13.0 + - - +
282A GLN* 3.1 37.5 + - - +
284A LEU* 1.3 77.9 - - - +
286A THR* 1.3 59.7 + - - +
288A ALA 3.6 14.9 + - - +
290A LYS* 5.9 0.7 - - - +
292A PRO* 3.6 39.0 - - + +
293A ARG* 4.9 1.4 - - - +
296A VAL* 3.7 17.2 - - - +
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Residues in contact with THR 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A TYR* 3.6 34.5 - - + -
253A GLU 5.7 0.2 - - - +
256A ILE* 4.1 16.0 - - + +
282A GLN* 2.8 21.2 + - - +
283A GLU* 3.2 8.2 + - - -
285A ASN* 1.3 78.5 - - - +
287A ILE* 1.3 61.9 + - - +
288A ALA 4.1 3.3 - - - +
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Residues in contact with ILE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A THR* 4.3 11.7 - - + -
215A ILE* 3.8 18.2 - - + -
239A VAL* 3.9 23.3 - - + -
241A THR* 4.6 9.9 - - + -
252A TYR* 3.6 41.7 - - + +
256A ILE* 3.9 6.4 - - - +
266A ARG* 3.0 39.4 + - + -
268A VAL* 3.7 16.4 - - + -
283A GLU* 3.1 22.9 + - + +
284A LEU* 3.8 8.3 - - - +
286A THR* 1.3 78.1 - - - +
288A ALA* 1.3 59.2 + - - +
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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