Contacts of the helix formed by residues 272 - 281 (chain M) in PDB entry 2I2X
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 272 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218M THR* 4.0 0.9 - - - -
219M ASP* 3.0 22.8 + - - +
247M ARG* 3.0 34.6 + - + +
250M SER* 3.4 30.3 - - - +
251M ALA* 3.9 14.8 - - + +
254M SER* 2.8 32.7 + - - +
270M GLY* 3.4 12.3 - - - -
271M TYR* 1.3 72.3 + - - +
273M ASN* 1.3 54.6 + - - +
274M ILE* 3.0 6.5 - - - -
275M ILE* 2.6 37.5 + - + +
276M VAL* 3.1 9.3 + - + +
370M LEU* 4.8 0.4 - - - -
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Residues in contact with ASN 273 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217M ASP 4.6 5.0 - - - +
254M SER* 5.2 3.1 - - - -
258M TYR* 4.4 6.2 + - - -
266M GLY 3.7 9.9 - - - -
267M LYS 2.7 32.1 + - - -
270M GLY* 2.8 23.2 + - - +
272M GLU* 1.3 80.2 - - - +
274M ILE* 1.3 53.9 + - - +
276M VAL* 3.5 11.9 - - - +
277M LYS* 2.7 35.2 + - - +
284M MET* 3.5 25.7 - - + +
285M THR 3.2 11.9 + - - -
286M MET* 3.6 13.0 - - - -
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Residues in contact with ILE 274 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M MET* 3.8 14.1 - - + -
271M TYR 3.4 18.4 + - - +
272M GLU 2.9 1.4 + - - -
273M ASN* 1.3 80.0 - - - +
275M ILE* 1.3 63.4 + - - +
277M LYS* 3.4 3.7 + - + +
278M ALA* 3.3 20.6 + - - +
286M MET* 4.1 14.3 - - + +
302M LEU* 6.0 0.2 - - + -
305M GLN* 3.7 22.4 - - + +
306M CYS* 3.8 36.6 - - + +
370M LEU* 3.7 30.3 - - + +
372M TYR* 4.1 5.2 - - + -
375M ALA* 3.7 19.0 - - + +
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Residues in contact with ILE 275 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247M ARG 4.8 0.2 - - - +
248M ALA* 4.7 3.1 - - - -
251M ALA* 3.6 30.7 - - + -
272M GLU* 2.6 21.2 + - + +
274M ILE* 1.3 76.2 - - + +
276M VAL* 1.3 60.2 + - - +
278M ALA* 3.3 5.7 + - - +
279M ILE* 3.3 23.6 + - + +
369M MET* 3.8 29.4 - - + -
370M LEU* 4.3 6.7 - - + -
375M ALA* 3.7 36.8 - - + +
378M VAL* 3.9 10.3 - - + -
379M GLY* 3.7 19.3 - - - +
382M ILE* 4.0 7.6 - - + -
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Residues in contact with VAL 276 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251M ALA* 3.8 26.2 - - + +
254M SER* 4.5 9.2 - - - -
255M LEU* 4.1 12.3 - - + +
258M TYR* 3.5 35.7 - - + -
272M GLU 3.1 13.8 + - - +
273M ASN* 3.2 14.6 + - - +
275M ILE* 1.3 76.0 - - - +
277M LYS* 1.3 58.9 + - - +
279M ILE* 3.3 7.3 + - + +
280M THR* 2.9 43.5 + - + +
284M MET* 3.9 9.0 - - + -
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Residues in contact with LYS 277 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M TYR* 3.3 27.4 - - + +
17M MET* 3.9 9.2 - - + -
18M THR 3.1 13.3 + - - +
21M VAL 3.0 27.3 + - - -
22M SER* 4.0 5.2 - - - -
273M ASN 2.7 21.2 + - - +
274M ILE* 3.9 7.0 - - + +
275M ILE 3.4 0.4 - - - -
276M VAL* 1.3 72.2 - - - +
278M ALA* 1.3 58.6 + - - +
280M THR* 4.0 6.1 - - - -
281M GLY 2.8 24.8 + - - -
282M MET 3.4 18.6 - - - +
284M MET* 4.0 8.6 - - + +
306M CYS* 2.8 37.1 + - + +
307M CYS 4.4 0.4 + - - -
308M ASP* 2.8 25.4 + - - +
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Residues in contact with ALA 278 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M MET* 3.5 24.5 - - + +
10M ALA 3.5 14.2 + - - -
11M TYR* 3.7 13.5 + - - +
17M MET* 3.5 29.0 - - + +
274M ILE 3.3 8.5 + - - +
275M ILE 3.6 9.6 - - - +
276M VAL 3.3 0.2 - - - -
277M LYS* 1.3 78.6 - - - +
279M ILE* 1.3 60.6 + - - +
375M ALA* 4.8 0.7 - - + +
376M TYR* 3.7 18.4 - - + +
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Residues in contact with ILE 279 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6M TYR* 3.7 37.4 - - + -
8M SER 3.8 5.0 - - - +
9M MET* 3.7 23.3 - - + -
10M ALA* 3.0 22.3 + - - +
251M ALA* 5.9 0.9 - - + +
255M LEU* 3.8 22.2 - - + -
275M ILE* 3.6 17.5 - - + +
276M VAL* 3.3 7.1 + - + +
277M LYS 3.2 0.4 - - - -
278M ALA* 1.3 77.7 - - - +
280M THR* 1.3 59.2 + - - +
379M GLY* 3.8 22.2 - - - +
382M ILE* 4.1 26.5 - - + -
383M VAL* 3.9 8.5 - - + -
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Residues in contact with THR 280 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6M TYR* 3.7 33.3 + - + +
10M ALA* 3.5 3.9 - - - +
24M TYR* 3.2 23.4 - - - -
255M LEU* 3.3 30.1 - - + -
258M TYR* 4.1 8.3 - - + -
276M VAL* 2.9 37.1 + - + +
277M LYS* 4.0 0.9 - - - -
279M ILE* 1.3 73.8 - - - +
281M GLY* 1.3 61.2 + - - +
282M MET* 3.1 27.8 + - - +
284M MET* 4.1 3.1 - - - +
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Residues in contact with GLY 281 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M ALA* 3.5 14.5 - - - +
11M TYR* 3.7 12.8 - - - -
22M SER* 3.3 3.7 - - - -
23M LYS* 3.0 16.4 + - - -
24M TYR* 3.0 29.8 + - - -
277M LYS 2.8 18.0 + - - -
280M THR* 1.3 76.8 - - - +
282M MET* 1.3 59.3 + - - +
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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