Contacts of the helix formed by residues 282 - 293 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A ASP* 3.2 6.9 - - - +
279A ASN* 3.0 36.4 + - + +
280A ILE 3.7 0.6 - - - -
281A ASN* 1.3 77.9 - - - +
283A GLU* 1.3 59.5 + - - +
285A TYR* 3.7 1.9 - - - +
286A ARG* 3.1 27.4 + - - +
218B ILE* 3.8 21.6 - - + +
219B ASP* 2.7 31.1 + - - +
285B TYR* 3.2 22.7 - - + +
289B LEU* 4.3 9.4 - - + -
324B PHE* 5.3 0.2 - - + -
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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
----------------------------------------------------------
211A LEU 5.2 0.7 - - - +
212A LEU* 4.1 9.7 - - + +
274A VAL* 3.5 24.7 - - + +
275A THR* 4.2 1.2 - - - +
278A ASP* 2.2 45.9 - - - +
280A ILE 4.6 6.4 - - - +
281A ASN 4.5 1.0 - - - -
282A THR* 1.3 75.2 + - - +
284A ALA* 1.4 58.4 + - - +
286A ARG* 3.2 9.4 + - - +
287A GLY 2.9 22.9 + - - -
422A ASN* 4.7 4.2 + - - +
472A LEU* 3.7 26.2 - - + +
476A VAL* 3.8 27.0 - - + +
219B ASP* 3.6 14.1 - - - +
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ASN* 3.2 7.2 + - + +
283A GLU* 1.4 80.1 + - - +
285A TYR* 1.3 55.2 + - - +
287A GLY* 3.1 0.7 + - - -
288A ALA* 2.8 31.0 + - - +
327A ILE* 5.0 5.2 - - + -
422A ASN* 4.4 8.0 + - - +
425A PHE* 3.6 42.2 - - + -
426A ALA 5.7 0.2 - - - +
429A LEU* 4.4 11.6 - - + +
472A LEU* 4.1 12.5 - - + +
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Residues in contact with TYR 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ILE* 4.4 6.5 - - + -
281A ASN* 2.8 22.2 + - - +
282A THR 3.7 4.3 - - - +
284A ALA* 1.3 69.1 - - - +
286A ARG* 1.4 68.3 + - + +
288A ALA* 3.2 6.9 + - - +
289A LEU* 2.9 49.7 + - + +
324A PHE* 3.7 17.7 - + + -
327A ILE* 4.1 21.5 - - + +
218B ILE* 5.4 4.7 - - + -
279B ASN 4.1 0.3 + - - -
281B ASN* 2.7 35.7 + - - -
282B THR* 3.2 32.8 + - + +
285B TYR* 3.7 49.3 - + + +
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU 4.4 8.4 + - - +
212A LEU* 3.4 51.5 + - - +
214A ASN 5.6 0.4 + - - -
216A PHE* 3.2 46.5 - - + +
225A PRO* 3.7 17.2 - - - +
274A VAL* 4.4 7.1 - - - +
282A THR 3.1 15.3 + - - +
283A GLU* 3.5 8.4 - - - +
285A TYR* 1.4 78.5 - - + +
287A GLY* 1.3 63.7 + - - +
289A LEU* 3.3 8.6 + - + +
290A ILE* 3.1 26.3 + - + +
218B ILE* 4.0 11.3 - - + +
219B ASP* 2.7 40.6 + - - +
221B ILE* 3.9 9.2 - - - +
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Residues in contact with GLY 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 4.0 31.8 + - - -
283A GLU 2.9 14.9 + - - -
284A ALA 3.1 4.2 + - - -
286A ARG* 1.3 79.1 - - - +
288A ALA* 1.3 54.0 + - - +
290A ILE* 3.2 3.3 + - - +
291A LEU* 2.9 40.5 + - - +
429A LEU* 5.1 1.6 - - - -
472A LEU* 4.5 2.5 - - - -
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Residues in contact with ALA 288 (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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284A ALA 2.8 19.0 + - - +
285A TYR* 3.4 9.6 - - - +
287A GLY* 1.3 71.3 - - - +
289A LEU* 1.3 57.6 + - - +
291A LEU* 4.4 0.8 - - - +
292A LEU* 3.0 19.8 + - - +
323A TYR* 2.7 36.5 + - + +
324A PHE* 4.2 11.4 - - + -
327A ILE* 4.6 9.0 - - + -
429A LEU* 3.8 20.6 - - + +
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Residues in contact with LEU 289 (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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216A PHE* 4.3 18.4 - - + -
217A THR 3.9 26.4 + - - +
218A ILE* 4.0 18.8 - - + -
285A TYR* 2.9 38.7 + - + +
286A ARG* 3.8 4.9 - - + +
288A ALA* 1.3 74.5 - - - +
290A ILE* 1.4 63.9 + - - +
292A LEU* 3.4 6.5 + - + +
293A GLY* 3.0 19.4 + - - -
324A PHE* 3.8 25.8 - - + -
279B ASN* 3.9 21.1 - - - +
282B THR* 4.3 10.1 - - + -
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Residues in contact with ILE 290 (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 LEU* 3.5 38.1 - - + +
214A ASN* 3.8 23.1 - - + +
215A SER 3.5 18.4 - - - +
216A PHE* 3.7 16.6 - - + +
286A ARG* 3.1 18.0 + - + +
287A GLY* 3.6 5.8 - - - +
289A LEU* 1.4 74.9 - - - +
291A LEU* 1.3 64.5 + - - +
293A GLY* 3.1 3.7 + - - -
294A LEU* 2.9 32.8 + - + +
442A TYR* 3.3 25.1 - - - +
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 4.0 18.6 - - + -
287A GLY 2.9 26.4 + - - +
290A ILE* 1.3 76.0 - - - +
292A LEU* 1.3 62.2 - - - +
294A LEU* 3.2 4.2 + - - +
295A ASP 3.0 4.2 + - - -
296A ALA* 3.0 38.7 + - + -
297A PHE 4.3 1.8 - - - -
323A TYR* 3.6 12.8 - - - +
429A LEU* 4.2 12.6 - - + -
433A ILE* 4.1 9.0 - - + -
442A TYR* 5.1 1.1 - - + -
465A PHE* 3.6 35.0 - - + +
468A GLU* 6.6 0.2 - - + -
469A ILE* 3.8 36.3 - - + -
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Residues in contact with LEU 292 (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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288A ALA 3.0 17.7 + - - +
289A LEU* 3.6 7.4 - - + +
291A LEU* 1.3 75.6 - - - +
293A GLY* 1.3 56.5 + - - +
295A ASP* 2.9 20.3 + - - +
297A PHE* 3.5 25.9 - - + +
299A ARG* 3.6 48.4 + - + +
320A ILE* 3.7 12.3 - - + -
323A TYR* 3.8 6.4 + - + +
324A PHE* 4.2 15.7 - - + -
279B ASN* 3.4 39.0 - - - +
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Residues in contact with GLY 293 (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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289A LEU 3.0 14.9 + - - -
290A ILE* 3.1 4.9 + - - -
292A LEU* 1.3 78.3 - - - +
294A LEU* 1.3 60.9 + - - +
295A ASP* 3.2 2.4 + - - +
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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