Contacts of the helix formed by residues 286 - 297 (chain B) in PDB entry 3IO6
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 286 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281B GLU 4.3 4.3 - - - +
282B ASN* 3.8 24.2 + - - +
283B TYR* 2.9 19.8 + - - -
284B LEU 2.9 1.3 + - - +
285B LEU* 1.3 82.1 - - - +
287B ASP* 1.3 70.7 + - - +
288B GLU* 4.1 6.6 + - - +
289B GLY 3.0 8.5 + - - -
290B LEU* 2.9 20.6 + - - +
304B LEU* 3.6 7.0 - - - -
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Residues in contact with ASP 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B THR* 1.3 76.7 - - - +
288B GLU* 1.3 57.6 + - - +
290B LEU* 3.6 1.0 - - - +
291B GLU* 2.7 38.7 + - - +
304B LEU* 3.5 8.1 - - - +
306B SER* 3.8 17.5 + - - +
307B TYR* 3.7 36.4 - - + -
310B GLU* 5.0 6.3 - - - +
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Residues in contact with GLU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B VAL* 5.0 0.7 - - - +
26B LYS* 6.5 1.3 - - - -
286B THR* 3.2 6.9 + - - +
287B ASP* 1.3 81.9 + - - +
289B GLY* 1.3 65.8 + - - +
291B GLU* 3.2 30.5 - - - +
292B ALA* 3.9 14.9 + - - +
453B CA 3.6 5.7 - - - -
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Residues in contact with GLY 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 3.6 21.1 - - - +
283B TYR 3.4 20.8 + - - -
284B LEU* 3.6 7.0 - - - -
286B THR* 3.0 10.3 + - - -
288B GLU* 1.3 78.2 - - - +
290B LEU* 1.3 61.3 + - - +
292B ALA 3.2 10.7 + - - -
293B VAL* 3.4 17.3 + - - +
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ILE* 3.9 27.8 - - + +
284B LEU* 3.6 25.6 - - + +
285B LEU* 4.5 13.7 - - + -
286B THR 2.9 10.3 + - - +
287B ASP 4.1 1.1 - - - +
289B GLY* 1.3 72.0 - - - +
291B GLU* 1.3 60.1 + - - +
292B ALA 3.2 0.2 - - - -
293B VAL* 4.0 6.0 - - + +
294B ASN* 3.1 30.8 + - - +
299B LEU* 4.2 13.2 - - + +
302B VAL* 4.1 22.0 - - + -
304B LEU* 4.1 33.9 - - + +
307B TYR* 3.7 18.8 - - + -
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ASP* 2.7 23.3 + - - +
288B GLU* 3.2 22.6 - - - +
289B GLY 3.2 0.2 - - - -
290B LEU* 1.3 74.2 - - - +
292B ALA* 1.3 57.1 + - - +
294B ASN* 4.0 1.7 - - - +
295B LYS* 3.2 47.7 + - + +
307B TYR* 3.5 24.9 + - + +
310B GLU* 5.3 3.8 - - - +
453B CA 2.4 29.7 - - - -
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLY* 3.4 26.2 - - - +
22B GLU* 4.5 11.7 - - + -
23B VAL* 4.2 7.2 - - + -
288B GLU 3.9 8.9 + - - +
289B GLY 3.2 9.9 + - - +
291B GLU* 1.3 76.9 - - - +
293B VAL* 1.3 64.7 + - - +
295B LYS* 3.5 10.8 + - - +
296B ASP* 3.3 15.2 + - - +
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 5.9 5.4 - - + -
16B GLY* 3.8 19.6 - - - +
19B GLY* 4.0 8.5 - - - +
20B LEU* 4.2 17.9 - - + +
23B VAL* 4.7 0.7 - - + -
108B ILE* 6.2 0.4 - - + -
284B LEU* 3.9 23.1 - - + -
289B GLY 3.4 16.7 + - - +
290B LEU* 3.7 8.5 + - + +
292B ALA* 1.3 74.3 - - - +
294B ASN* 1.3 62.7 + - - +
296B ASP* 3.3 4.9 + - - +
297B LYS 3.2 23.6 + - - +
299B LEU* 3.8 31.9 - - + -
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Residues in contact with ASN 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B LEU 3.1 19.9 + - - +
291B GLU 4.0 1.3 - - - +
293B VAL* 1.3 77.7 - - - +
295B LYS* 1.3 62.0 + - - +
297B LYS 3.9 4.3 - - - -
298B PRO* 3.3 32.3 - - - +
299B LEU* 2.9 36.5 + - + +
300B GLY 4.3 1.2 + - - -
302B VAL* 5.3 0.2 - - - +
307B TYR* 3.4 23.2 + - + +
311B LEU* 3.4 30.8 - - - +
317B ILE* 6.1 0.6 - - - +
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Residues in contact with LYS 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B GLU* 3.2 42.6 + - + +
292B ALA* 3.9 9.2 - - - +
293B VAL 3.3 0.4 - - - -
294B ASN* 1.3 73.7 - - - +
296B ASP* 1.3 65.7 + - - +
298B PRO* 5.6 0.5 - - - +
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Residues in contact with ASP 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LYS 4.4 0.5 - - - +
16B GLY* 3.3 24.6 - - - -
17B TYR* 3.8 2.3 + - - -
18B ASN* 3.5 21.3 + - - +
19B GLY* 3.7 24.0 - - - +
292B ALA 3.3 2.6 + - - +
293B VAL 3.3 8.5 + - - +
295B LYS* 1.3 82.7 - - - +
297B LYS* 1.3 86.0 + - - +
298B PRO* 4.3 3.1 - - - +
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Residues in contact with LYS 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASP 3.9 18.8 - - - +
15B LYS* 4.3 5.1 - - + +
16B GLY* 4.0 17.6 + - - +
293B VAL 3.2 13.0 + - - +
294B ASN* 3.4 3.4 - - - -
296B ASP* 1.3 111.7 + - - +
298B PRO* 1.4 74.8 - - + +
299B LEU* 3.4 11.3 + - - +
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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