Contacts of the helix formed by residues 282 - 293 (chain B) in PDB entry 1QI9
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 282 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A ILE* 3.7 24.5 - - + +
219A ASP* 2.6 30.0 + - - +
285A TYR* 3.2 22.9 - - + +
289A LEU* 4.3 9.0 - - + -
278B ASP* 3.3 4.4 - - - +
279B ASN* 3.0 38.3 + - + +
280B ILE 3.8 0.8 - - - -
281B ASN* 1.3 74.9 - - - +
283B GLU* 1.4 57.0 + - - +
285B TYR* 3.6 2.0 - - - +
286B ARG* 3.0 34.1 + - - +
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Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ASP* 3.6 14.1 - - - +
211B LEU 5.1 0.3 - - - +
212B LEU* 4.1 11.8 - - + +
274B VAL* 3.5 26.5 - - + +
275B THR* 4.3 0.2 - - - -
278B ASP* 2.4 46.4 - - - +
280B ILE 4.7 5.2 - - - +
281B ASN* 4.5 1.6 - - - -
282B THR* 1.4 77.6 + - - +
284B ALA* 1.3 57.6 + - - +
286B ARG* 3.4 6.3 + - - +
287B GLY 3.0 22.2 + - - -
422B ASN* 4.7 4.5 + - - +
472B LEU* 3.7 19.8 - - + +
476B VAL* 3.7 34.5 - - + +
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Residues in contact with ALA 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ASN* 3.3 7.5 + - + +
283B GLU* 1.3 78.8 + - - +
285B TYR* 1.3 54.4 + - - +
287B GLY 3.6 0.3 - - - -
288B ALA* 2.7 34.0 + - - +
327B ILE* 4.9 6.4 - - + +
422B ASN* 4.6 7.3 + - - +
425B PHE* 3.8 40.2 - - + -
429B LEU* 4.2 13.1 - - + +
472B LEU* 4.0 13.2 - - + +
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Residues in contact with TYR 285 (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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218A ILE* 5.3 4.9 - - + -
279A ASN 4.1 0.9 + - - -
281A ASN* 2.6 33.7 + - - -
282A THR* 3.2 37.6 - - + +
285A TYR* 3.7 50.7 - + + +
218B ILE* 4.5 6.5 - - + -
281B ASN* 2.9 19.4 + - - +
282B THR* 3.6 4.7 - - - +
284B ALA* 1.3 72.4 - - - +
286B ARG* 1.3 68.6 + - - +
288B ALA* 3.2 6.6 + - - +
289B LEU* 3.0 42.5 + - + +
324B PHE* 3.7 18.8 - + - -
327B ILE* 4.2 19.9 - - + +
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Residues in contact with ARG 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ILE* 3.8 20.0 - - + -
219A ASP* 2.7 50.2 + - - +
221A ILE* 4.0 10.8 - - - +
211B LEU 4.2 7.1 + - - +
212B LEU* 3.1 54.5 + - - +
214B ASN 5.3 0.2 + - - -
216B PHE* 3.6 40.9 - - + +
225B PRO* 3.5 17.4 - - - +
274B VAL* 4.8 4.9 - - - +
282B THR 3.0 14.0 + - - +
283B GLU* 3.5 7.5 - - - +
285B TYR* 1.3 78.6 - - + +
287B GLY* 1.3 62.0 + - - +
289B LEU* 3.2 6.7 + - - +
290B ILE* 3.1 27.1 + - + +
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Residues in contact with GLY 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LEU* 3.9 35.1 + - - -
283B GLU 3.0 15.1 + - - -
284B ALA 3.7 3.1 - - - -
286B ARG* 1.3 75.5 - - - +
288B ALA* 1.3 57.6 + - - +
290B ILE* 3.2 2.6 + - - +
291B LEU* 2.8 40.1 + - - +
429B LEU* 5.2 0.9 - - - -
472B LEU* 4.6 1.8 - - - -
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Residues in contact with ALA 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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284B ALA 2.7 21.8 + - - +
285B TYR* 3.2 8.7 + - - +
287B GLY* 1.3 72.1 - - - +
289B LEU* 1.3 62.3 + - - +
291B LEU* 4.4 0.8 - - - +
292B LEU* 3.0 14.7 + - - +
323B TYR* 2.9 30.1 + - + +
324B PHE* 4.4 6.5 - - + -
327B ILE* 3.5 30.5 - - + -
429B LEU* 3.8 10.0 - - + +
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Residues in contact with LEU 289 (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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279A ASN* 3.9 20.6 - - - +
282A THR* 4.3 10.1 - - + -
216B PHE* 4.3 19.3 - - + -
217B THR 3.8 26.0 - - - +
218B ILE* 4.2 18.4 - - + -
285B TYR* 3.0 37.5 + - + +
286B ARG* 3.7 5.2 - - - +
288B ALA* 1.3 73.0 - - - +
290B ILE* 1.3 66.6 + - - +
292B LEU* 3.4 6.9 + - + +
293B GLY* 3.0 20.3 + - - -
324B PHE* 3.9 26.7 - - + -
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Residues in contact with ILE 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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211B LEU* 3.5 44.6 - - + +
214B ASN* 3.6 26.5 - - + +
215B SER 3.6 16.8 - - - +
216B PHE* 3.7 12.8 - - + +
286B ARG 3.1 15.1 + - - +
287B GLY 3.6 6.1 - - - +
289B LEU* 1.3 76.1 - - - +
291B LEU* 1.3 63.0 + - - +
293B GLY* 3.2 3.5 + - - -
294B LEU* 3.1 31.9 + - + +
442B TYR* 3.4 23.3 - - - +
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Residues in contact with LEU 291 (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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211B LEU* 4.0 19.5 - - + -
287B GLY 2.8 30.0 + - - +
290B ILE* 1.3 72.8 - - - +
292B LEU* 1.3 62.1 + - - +
294B LEU* 3.3 4.9 + - - +
295B ASP 3.1 3.6 + - - -
296B ALA* 3.0 33.2 + - + +
297B PHE 3.6 1.7 + - - +
323B TYR* 3.7 13.7 - - - +
429B LEU* 4.2 12.8 - - + -
433B ILE* 4.1 16.8 - - + -
442B TYR* 5.5 0.2 - - + -
465B PHE* 3.5 37.2 - - + +
468B GLU* 6.5 0.4 - - + -
469B ILE* 3.9 29.4 - - + -
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ASN* 3.3 38.8 - - - +
288B ALA 3.0 18.0 + - - +
289B LEU* 3.6 7.2 - - + +
291B LEU* 1.3 76.2 - - - +
293B GLY* 1.3 58.9 + - - +
295B ASP* 3.0 16.5 + - - +
297B PHE* 3.4 45.0 - - + +
299B ARG* 3.6 38.1 + - + +
320B ILE* 3.8 6.1 - - + -
323B TYR* 3.9 5.5 + - + +
324B PHE* 4.1 16.8 - - + -
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Residues in contact with GLY 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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289B LEU 3.0 14.7 + - - -
290B ILE* 3.7 4.0 - - - -
292B LEU* 1.3 78.4 - - - +
294B LEU* 1.3 60.9 + - - +
295B ASP* 3.3 2.2 + - - +
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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