Contacts of the helix formed by residues 371 - 384 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A LEU* 3.9 11.4 - - + +
305A GLN* 3.7 6.3 - - - -
357A MET* 3.7 15.0 - - + -
361A ARG* 3.5 28.3 - - + +
367A ALA 3.1 5.0 + - - +
368A TYR* 3.4 16.6 - - - +
369A MET 3.2 0.8 - - - -
370A LEU* 1.3 74.9 - - - +
372A TYR* 1.3 52.7 + - - +
373A ASP* 3.1 1.8 - - - +
374A ASN* 2.8 27.3 + - - +
375A ALA 2.8 14.0 + - - -
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Residues in contact with TYR 372 (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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14A ALA* 3.4 37.4 - - + +
15A ASP* 4.3 4.4 + - + -
17A MET* 4.8 8.2 - - + +
274A ILE* 4.0 7.0 - - + -
305A GLN* 2.9 37.7 + - - +
306A CYS* 4.0 15.9 - - - -
353A ARG* 3.1 36.3 + - + -
354A ASP* 2.6 30.5 + - - -
357A MET* 4.0 16.6 - - + -
370A LEU 3.4 0.6 + - - -
371A ALA* 1.3 70.7 - - - +
373A ASP* 1.3 61.1 + - - +
375A ALA* 3.8 9.6 - - - +
376A TYR* 3.0 24.3 + - - +
1B MET* 3.3 34.6 - - + +
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Residues in contact with ASP 373 (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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14A ALA* 3.7 16.0 - - + +
357A MET* 5.0 0.3 - - - +
361A ARG* 2.5 41.0 + - - -
371A ALA* 3.5 5.0 - - - +
372A TYR* 1.3 78.5 - - - +
374A ASN* 1.3 71.2 + - - +
376A TYR* 3.5 4.9 + - - +
377A ARG* 3.2 20.4 + - - +
1B MET* 3.3 29.2 - - + +
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Residues in contact with ASN 374 (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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361A ARG* 3.6 21.3 + - - +
368A TYR* 2.9 41.5 + - - +
369A MET 3.4 16.2 - - - +
371A ALA 2.8 9.0 + - - +
373A ASP* 1.3 81.6 + - - +
375A ALA* 1.3 64.7 + - - +
376A TYR 3.2 0.2 - - - -
377A ARG* 3.2 13.1 + - - +
378A VAL* 2.9 26.9 + - - +
403A ILE* 3.6 28.3 - - + +
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Residues in contact with ALA 375 (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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17A MET* 6.4 0.2 - - - -
274A ILE* 3.6 34.3 - - + +
275A ILE* 3.7 30.7 - - + +
278A ALA* 4.9 0.4 - - + -
369A MET 3.3 7.9 + - - +
370A LEU* 3.8 6.3 - - - +
371A ALA 2.8 17.6 + - - +
372A TYR 3.8 2.5 - - - +
374A ASN* 1.3 71.4 - - - +
376A TYR* 1.3 52.2 + - - +
378A VAL* 3.2 5.3 + - - +
379A GLY* 2.8 30.1 + - - -
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Residues in contact with TYR 376 (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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9A MET* 3.5 29.9 - - + +
11A TYR* 2.6 35.8 + - + -
12A ALA* 2.9 15.1 + - - -
13A ASN* 3.5 23.1 - - + -
14A ALA* 3.7 24.5 - - + -
17A MET* 4.3 5.2 - - - -
278A ALA* 3.9 17.7 - - + +
372A TYR 3.0 18.4 + - - +
373A ASP 3.5 6.3 - - - +
374A ASN 3.2 0.2 - - - -
375A ALA* 1.3 75.5 - - - +
377A ARG* 1.3 59.9 + - - +
379A GLY* 3.0 3.8 + - - -
380A GLN* 2.9 57.8 + - + +
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Residues in contact with ARG 377 (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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373A ASP 3.2 10.1 + - - +
374A ASN* 3.2 16.5 + - - +
376A TYR* 1.3 80.8 - - + +
378A VAL* 1.3 61.6 + - - +
380A GLN* 3.0 30.9 + - - +
381A SER* 3.1 13.0 + - - -
399A GLU* 2.7 28.9 + - - +
402A ASN* 3.7 19.2 - - - +
403A ILE* 3.5 28.1 - - + +
406A GLU* 2.7 45.7 + - - -
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Residues in contact with VAL 378 (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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248A ALA* 4.6 5.6 - - + +
275A ILE* 4.0 22.0 - - + -
369A MET* 4.1 20.6 - - + -
374A ASN 2.9 17.1 + - - +
375A ALA 3.6 6.3 - - - +
377A ARG* 1.3 74.2 - - - +
379A GLY* 1.3 63.2 + - - +
381A SER* 2.8 23.9 + - - -
382A ILE* 3.2 14.1 + - + +
396A ALA* 3.9 27.1 - - + +
399A GLU* 4.4 6.1 - - + -
400A CYS* 4.6 8.3 - - + +
403A ILE* 3.6 20.4 - - + -
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Residues in contact with GLY 379 (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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9A MET* 3.6 10.5 - - - -
275A ILE* 3.8 9.5 - - - +
279A ILE* 4.0 19.6 - - - +
375A ALA 2.8 15.0 + - - -
376A TYR 3.0 6.9 + - - -
378A VAL* 1.3 76.6 - - - +
380A GLN* 1.3 59.7 + - - +
382A ILE* 3.2 12.5 + - - +
383A VAL* 3.3 19.4 + - - +
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Residues in contact with GLN 380 (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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9A MET* 4.0 15.7 - - + -
12A ALA 5.6 0.8 + - - -
376A TYR* 2.9 45.8 + - + +
377A ARG* 3.0 27.4 + - - +
379A GLY* 1.3 69.9 - - - +
381A SER* 1.3 63.3 + - - +
383A VAL* 3.5 6.3 + - + +
384A LYS* 3.3 27.2 + - - +
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Residues in contact with SER 381 (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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377A ARG 3.1 3.6 + - - -
378A VAL 2.8 16.8 + - - -
380A GLN* 1.3 78.2 - - - +
382A ILE* 1.3 60.3 + - - +
384A LYS* 3.3 17.4 - - - +
395A ASN* 3.2 37.5 + - - +
396A ALA* 3.5 21.5 - - - -
399A GLU* 3.6 36.5 - - - +
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Residues in contact with ILE 382 (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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6A TYR 5.7 0.2 - - - +
251A ALA* 4.0 3.1 - - + -
252A PRO* 3.8 31.0 - - + -
255A LEU* 4.2 9.2 - - + -
275A ILE* 3.9 23.3 - - + -
279A ILE* 4.0 18.6 - - + -
378A VAL* 3.2 19.9 + - + +
379A GLY 3.5 5.8 - - - +
380A GLN 3.2 0.4 - - - -
381A SER* 1.3 77.6 + - - +
383A VAL* 1.3 67.5 + - + +
384A LYS 3.2 0.2 - - - -
385A ASP 3.2 10.2 + - - -
386A GLY* 3.3 8.8 + - - -
392A ARG* 3.4 39.7 - - + +
396A ALA* 3.8 16.8 - - + -
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Residues in contact with VAL 383 (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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6A TYR* 3.9 13.9 - - + +
7A THR* 3.6 30.6 - - - +
8A SER* 3.7 29.6 - - - +
9A MET* 4.0 18.6 - - + -
279A ILE* 3.9 23.6 - - + -
379A GLY 3.3 12.8 + - - +
380A GLN* 3.6 13.0 - - - +
382A ILE* 1.3 73.7 - - + +
384A LYS* 1.3 62.7 + - + +
385A ASP 3.0 11.3 + - - -
386A GLY 3.0 9.4 + - - -
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Residues in contact with LYS 384 (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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7A THR 5.6 0.4 - - - -
380A GLN 3.3 15.7 + - - +
381A SER* 3.3 30.9 - - - +
382A ILE 3.2 1.6 - - - -
383A VAL* 1.3 78.1 - - + +
385A ASP* 1.3 68.9 + - - +
386A GLY 3.8 0.2 - - - -
395A ASN* 3.8 23.4 - - - +
399A GLU* 4.3 9.1 + - - -
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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