Contacts of the helix formed by residues 268 - 277 (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 ALA 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A MET* 4.7 5.4 - - + +
147A ALA 4.6 1.8 + - - +
148A ARG* 3.3 18.6 + - + +
150A VAL 4.4 2.0 + - - -
152A PHE* 3.6 6.9 - - - -
155A TYR* 4.2 12.1 + - - +
195A PHE* 5.7 1.3 - - + -
267A ASN* 1.3 73.6 - - - +
269A ARG* 1.3 61.0 + - - +
271A LEU* 3.3 1.1 + - - +
272A ALA* 2.9 31.1 + - - +
482A MET* 3.4 43.6 - - + +
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Residues in contact with ARG 269 (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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145A ALA 5.0 1.2 + - - -
148A ARG* 3.0 40.3 + - + +
149A ASP* 2.7 40.8 + - - +
229A THR* 4.7 0.4 - - - -
230A PHE* 3.6 29.8 - - + +
231A ALA 3.2 24.9 + - - -
232A PRO* 3.9 0.4 - - - +
233A ASP* 3.7 8.9 - - - +
234A VAL 3.1 22.8 + - - -
235A ASN* 3.1 27.5 + - - +
236A TYR* 5.5 0.6 - - - -
267A ASN* 2.9 10.3 + - - +
268A ALA* 1.3 74.9 - - - +
270A ASP* 1.3 59.0 + - - +
272A ALA* 3.4 6.5 + - - +
273A ARG* 2.8 27.4 + - - +
403A ALA* 4.2 15.8 + - + +
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Residues in contact with ASP 270 (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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227A GLN* 3.2 20.6 + - - +
229A THR* 2.6 34.8 + - - +
230A PHE 4.8 2.1 - - - +
263A ARG* 5.5 0.2 - - - -
264A PHE 3.5 8.3 - - - +
265A VAL* 3.9 4.7 - - - -
266A ARG* 2.7 61.3 + - - +
267A ASN* 2.8 18.0 + - - +
269A ARG* 1.3 75.0 - - - +
271A LEU* 1.3 63.3 + - - +
273A ARG 3.2 1.6 + - - -
274A VAL* 3.1 19.1 + - - +
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Residues in contact with LEU 271 (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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152A PHE* 4.6 0.4 - - + -
207A PHE* 3.9 14.4 - - + -
208A ILE* 3.7 24.2 - - + -
212A LEU* 4.5 10.5 - - + -
265A VAL* 3.7 14.1 - - + +
267A ASN 3.2 12.4 + - - +
268A ALA* 3.3 4.4 + - - +
270A ASP* 1.3 75.0 - - - +
272A ALA* 1.3 64.9 + - - +
274A VAL* 3.3 23.2 + - + +
275A THR* 3.3 14.9 + - + +
475A ASN* 3.5 44.0 - - + +
476A VAL* 4.7 1.1 - - + +
478A PHE* 4.8 0.9 - - + -
479A GLY* 3.8 6.3 - - - +
482A MET* 3.8 20.9 - - + -
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PHE* 4.9 0.2 - - + -
268A ALA 2.9 17.1 + - - +
269A ARG* 3.5 7.4 - - - +
271A LEU* 1.3 76.3 - - - +
273A ARG* 1.3 62.9 + - - +
275A THR* 3.0 17.4 + - - -
276A PHE 3.0 6.9 + - - -
403A ALA* 4.9 3.8 - - + -
479A GLY* 3.3 24.6 + - - +
482A MET 3.8 6.3 - - - +
483A LEU* 3.5 34.4 - - + +
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Residues in contact with ARG 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLN* 3.9 9.2 - - - +
228A GLU* 2.8 46.4 + - - +
229A THR* 3.8 13.8 - - - +
230A PHE* 3.5 43.4 - - + +
256A GLU* 5.3 1.8 + - - -
258A LEU* 3.5 31.8 - - - +
269A ARG 2.8 15.3 + - - +
270A ASP 3.2 10.1 + - - +
272A ALA* 1.3 74.3 - - - +
274A VAL* 1.3 64.2 + - - +
276A PHE* 3.0 14.9 + - - +
277A THR* 3.1 32.7 + - - +
220B SER* 3.4 16.2 + - - +
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Residues in contact with VAL 274 (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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212A LEU* 5.0 7.6 - - + -
227A GLN* 3.4 20.6 - - - +
265A VAL* 3.5 27.4 - - + -
270A ASP 3.1 4.7 + - - +
271A LEU* 3.4 17.0 - - + +
273A ARG* 1.3 75.2 - - - +
275A THR* 1.4 60.8 + - + +
277A THR* 3.1 7.9 + - - -
278A ASP* 3.0 27.0 + - - +
283A GLU* 3.5 31.6 - - + +
286A ARG* 4.4 13.9 - - - +
476A VAL* 5.8 0.9 - - + -
219B ASP* 4.5 7.9 - - + +
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Residues in contact with THR 275 (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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271A LEU* 3.3 13.9 + - + +
272A ALA 3.0 13.0 + - - -
274A VAL* 1.4 77.8 - - + +
276A PHE* 1.3 59.3 + - - +
277A THR 3.3 0.2 - - - -
278A ASP* 3.3 23.8 - - - +
283A GLU* 4.4 1.8 - - - +
418A HIS* 3.4 1.8 + - - -
475A ASN 4.5 0.2 - - - +
476A VAL* 3.3 39.5 - - + +
479A GLY* 3.4 18.8 + - - -
480A ARG* 3.0 42.4 + - - -
483A LEU* 3.5 3.5 - - - +
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Residues in contact with PHE 276 (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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230A PHE* 3.8 20.0 - + + -
256A GLU* 3.8 18.2 - - - -
272A ALA 3.0 11.5 + - - +
273A ARG* 3.0 11.4 + - - +
275A THR* 1.3 77.9 + - - +
277A THR* 1.3 70.6 + - + +
278A ASP 3.7 0.7 - - - -
404A ILE* 3.6 42.6 - - + -
406A GLU* 3.6 30.5 - - - -
480A ARG* 4.2 8.5 - - - +
483A LEU* 4.0 12.3 - - + -
299B ARG* 3.3 21.4 + - - -
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Residues in contact with THR 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ARG* 3.1 40.6 + - - +
274A VAL* 3.5 3.9 + - - -
276A PHE* 1.3 91.2 - - + +
278A ASP* 1.3 61.8 + - - +
279A ASN* 4.1 8.1 + - - -
219B ASP* 3.7 17.9 + - - -
220B SER* 2.8 37.0 + - - +
299B ARG* 3.8 7.2 - - - +
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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