Contacts of the helix formed by residues 371 - 384 (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 ALA 371 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302M LEU* 3.6 17.3 - - + -
305M GLN* 3.7 1.8 - - - -
357M MET* 3.6 21.8 - - + -
361M ARG* 3.9 12.8 - - + +
367M ALA 3.0 6.4 + - - +
368M TYR 3.4 15.0 - - - +
369M MET 3.2 0.6 - - - -
370M LEU* 1.3 75.0 - - - +
372M TYR* 1.3 55.3 + - - +
373M ASP* 3.2 11.9 - - - +
374M ASN* 3.0 7.0 + - - +
375M ALA 2.8 29.6 + - - -
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Residues in contact with TYR 372 (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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14M ALA* 3.7 35.8 - - + +
15M ASP* 4.3 3.2 + - - -
17M MET* 4.8 6.0 - - + +
274M ILE* 4.1 6.5 - - + -
305M GLN* 2.9 40.4 + - - +
306M CYS* 4.0 19.1 - - - -
353M ARG* 2.9 41.0 + - + -
354M ASP* 2.4 24.8 + - - -
357M MET* 4.1 15.7 - - + -
370M LEU 3.2 1.9 + - - -
371M ALA* 1.3 70.1 - - - +
373M ASP* 1.3 55.4 + - - +
375M ALA* 3.7 7.3 - - - +
376M TYR* 3.0 28.4 + - - +
1N MET* 3.2 33.5 - - + +
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Residues in contact with ASP 373 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M ALA* 3.7 16.2 - - + +
357M MET* 4.9 1.0 - - - +
361M ARG* 2.3 39.1 + - - -
371M ALA* 3.7 7.4 - - - +
372M TYR* 1.3 78.2 + - - +
374M ASN* 1.3 67.1 + - - +
376M TYR* 3.5 4.5 - - - +
377M ARG* 3.1 23.6 + - - +
1N MET* 3.4 29.1 - - + +
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Residues in contact with ASN 374 (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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361M ARG* 3.7 18.2 + - - +
368M TYR* 2.8 44.1 + - - +
369M MET 3.3 16.2 - - - +
371M ALA* 3.0 4.5 + - - +
373M ASP* 1.3 87.6 + - - +
375M ALA* 1.3 61.0 + - - +
377M ARG* 3.1 16.7 + - - +
378M VAL* 2.9 32.2 + - - +
403M ILE* 3.5 26.0 - - + +
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Residues in contact with ALA 375 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M MET* 6.4 0.4 - - - -
274M ILE* 3.7 34.1 - - + +
275M ILE* 3.7 31.7 - - + +
278M ALA* 4.8 1.1 - - + +
369M MET 3.3 7.1 + - - +
370M LEU 4.0 2.2 - - - +
371M ALA 2.8 15.9 + - - +
372M TYR 3.7 3.6 - - - +
373M ASP 3.4 0.2 - - - -
374M ASN* 1.3 75.1 - - - +
376M TYR* 1.3 64.0 + - - +
378M VAL* 3.2 6.2 + - - +
379M GLY* 3.0 18.4 + - - -
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Residues in contact with TYR 376 (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* 3.6 30.7 - - + +
11M TYR* 2.5 38.0 + - + -
12M ALA 3.1 13.6 + - - -
13M ASN* 3.5 21.1 - - + -
14M ALA* 3.8 23.6 - - + -
17M MET* 4.2 3.8 - - - -
278M ALA* 3.7 19.0 - - + +
372M TYR 3.0 19.2 + - - +
373M ASP 3.5 6.3 - - - +
375M ALA* 1.3 75.6 - - - +
377M ARG* 1.3 63.3 + - - +
379M GLY* 2.9 13.2 + - - -
380M GLN* 3.0 41.4 + - + +
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Residues in contact with ARG 377 (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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373M ASP 3.1 13.8 + - - +
374M ASN* 3.1 18.9 + - - +
376M TYR* 1.3 75.4 - - - +
378M VAL* 1.3 60.5 + - - +
380M GLN* 3.2 29.2 + - + +
381M SER* 3.3 12.1 + - - -
399M GLU* 2.5 34.4 + - - +
402M ASN* 4.1 15.6 - - - +
403M ILE* 3.6 21.0 - - + +
406M GLU* 2.8 43.8 + - - -
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Residues in contact with VAL 378 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248M ALA* 4.7 4.9 - - + +
275M ILE* 3.9 17.9 - - + -
369M MET* 4.0 23.8 - - + -
374M ASN 2.9 20.6 + - - +
375M ALA 3.2 6.9 + - - +
377M ARG* 1.3 68.8 - - - +
379M GLY* 1.3 65.9 + - - +
381M SER* 2.6 25.7 + - - +
382M ILE* 3.1 24.7 + - + +
396M ALA* 4.1 18.6 - - + +
399M GLU* 4.3 3.1 - - + -
400M CYS* 4.7 10.5 - - - +
403M ILE* 3.6 17.3 - - + -
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Residues in contact with GLY 379 (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* 3.4 12.5 - - - +
275M ILE* 3.7 7.4 - - - +
279M ILE* 3.8 25.7 - - - +
375M ALA 3.0 7.8 + - - -
376M TYR 2.9 8.6 + - - -
378M VAL* 1.3 78.0 - - - +
380M GLN* 1.3 61.3 + - - +
382M ILE* 3.3 3.0 + - - +
383M VAL* 3.2 26.2 + - - +
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Residues in contact with GLN 380 (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* 4.1 11.0 - - + +
376M TYR* 3.0 41.2 + - + +
377M ARG* 3.2 29.9 + - - +
379M GLY* 1.3 75.4 - - - +
381M SER* 1.3 62.4 + - - +
383M VAL* 3.5 9.5 - - + +
384M LYS* 3.2 27.0 + - - +
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Residues in contact with SER 381 (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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377M ARG 3.3 2.0 + - - -
378M VAL 2.6 21.3 + - - -
380M GLN* 1.3 76.0 - - - +
382M ILE* 1.3 61.1 + - - +
384M LYS* 3.5 17.5 - - - +
395M ASN* 2.9 38.3 + - - +
396M ALA* 3.6 18.7 - - - -
399M GLU* 3.6 33.5 - - - +
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Residues in contact with ILE 382 (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 5.8 0.2 - - - +
251M ALA* 4.0 2.0 - - + -
252M PRO* 3.8 28.0 - - + -
255M LEU* 4.1 21.3 - - + -
275M ILE* 4.0 16.6 - - + -
279M ILE* 4.1 10.5 - - + -
378M VAL* 3.1 30.4 + - + +
379M GLY 3.7 5.4 - - - +
380M GLN 3.2 0.2 - - - -
381M SER* 1.3 80.8 + - - +
383M VAL* 1.3 66.1 + - + +
385M ASP 3.3 4.9 + - - -
386M GLY* 3.3 14.2 + - - -
392M ARG* 3.3 39.3 - - + +
396M ALA* 3.8 17.3 - - + -
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Residues in contact with VAL 383 (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* 3.9 15.0 - - + +
7M THR* 3.6 26.4 - - - +
8M SER* 3.8 28.9 - - - +
9M MET* 3.9 14.6 - - + -
255M LEU* 5.6 0.2 - - + -
279M ILE* 3.9 25.6 - - + -
379M GLY 3.2 16.8 + - - +
380M GLN* 3.5 9.4 - - + +
382M ILE* 1.3 75.1 - - + +
384M LYS* 1.3 63.5 + - - +
385M ASP 3.0 2.5 - - - -
386M GLY* 2.8 19.9 + - - +
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Residues in contact with LYS 384 (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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7M THR 5.2 1.6 - - - -
380M GLN 3.2 13.2 + - - +
381M SER* 3.5 26.8 - - - +
383M VAL* 1.3 78.9 - - + +
385M ASP* 1.3 71.6 + - - +
395M ASN* 3.7 23.2 - - - +
399M GLU* 5.2 5.3 + - - -
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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