Contacts of the helix formed by residues 371 - 384 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302O LEU* 3.8 10.5 - - + +
305O GLN* 3.5 7.6 - - - -
357O MET* 3.7 19.5 - - + -
361O ARG* 3.8 13.0 - - + +
367O ALA 3.2 5.5 + - - -
368O TYR 3.4 14.8 - - - +
369O MET 3.3 0.2 - - - -
370O LEU* 1.3 74.8 - - - +
372O TYR* 1.3 61.9 + - - +
373O ASP* 3.0 15.3 + - - +
374O ASN* 3.0 5.2 + - - +
375O ALA 2.8 24.4 + - - -
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Residues in contact with TYR 372 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14O ALA* 3.3 36.5 - - + +
15O ASP* 4.4 3.8 + - + +
17O MET* 4.8 8.7 - - + +
274O ILE* 4.1 5.8 - - + +
305O GLN* 2.7 32.7 + - - +
306O CYS* 3.9 17.7 - - - -
353O ARG* 3.1 36.8 + - + -
354O ASP* 2.5 29.9 + - - -
357O MET* 4.1 18.2 - - + -
370O LEU 3.2 2.4 + - - -
371O ALA* 1.3 71.3 - - - +
373O ASP* 1.3 57.1 + - - +
375O ALA* 3.9 5.5 - - - +
376O TYR* 2.9 29.1 + - - +
1P MET* 3.3 34.4 - - + +
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Residues in contact with ASP 373 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14O ALA* 3.6 16.8 - - + +
357O MET* 5.1 0.5 - - - +
361O ARG* 2.6 41.3 + - - -
371O ALA* 3.5 8.1 - - - +
372O TYR* 1.3 76.6 - - - +
374O ASN* 1.3 66.5 + - - +
376O TYR* 3.4 6.2 + - - +
377O ARG* 3.1 24.1 + - - +
1P MET* 3.4 28.2 - - + +
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Residues in contact with ASN 374 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361O ARG* 3.6 18.3 + - - +
368O TYR* 2.8 40.5 + - - -
369O MET* 3.3 17.3 - - - +
371O ALA* 3.0 2.6 + - - +
373O ASP* 1.3 88.6 + - - +
375O ALA* 1.3 61.6 + - - +
377O ARG* 2.9 16.0 + - - +
378O VAL* 2.9 31.4 + - - +
403O ILE* 3.6 27.5 - - + +
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Residues in contact with ALA 375 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274O ILE* 3.7 29.8 - - + +
275O ILE* 3.7 34.0 - - + +
278O ALA* 4.6 0.6 - - - +
369O MET 3.2 8.6 + - - +
370O LEU 3.7 6.1 - - - +
371O ALA 2.8 15.8 + - - +
372O TYR 3.9 1.6 - - - +
374O ASN* 1.3 76.9 - - - +
376O TYR* 1.3 61.7 + - - +
378O VAL* 3.3 4.6 + - - +
379O GLY* 2.9 19.4 + - - -
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Residues in contact with TYR 376 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9O MET* 3.5 29.1 - - + +
11O TYR* 2.6 36.6 + - + -
12O ALA* 3.2 13.0 + - - -
13O ASN* 3.4 21.5 - - + -
14O ALA* 3.7 23.8 - - + -
17O MET* 4.2 5.4 - - - -
278O ALA* 3.9 18.7 - - + +
372O TYR 2.9 19.5 + - - +
373O ASP 3.4 6.3 - - - +
375O ALA* 1.3 76.3 - - - +
377O ARG* 1.3 58.4 + - - +
379O GLY* 3.2 3.5 + - - -
380O GLN* 3.0 53.8 + - + +
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Residues in contact with ARG 377 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373O ASP 3.1 12.5 + - - +
374O ASN* 2.9 20.0 + - - +
376O TYR* 1.3 75.5 - - + +
378O VAL* 1.3 62.2 + - - +
380O GLN* 3.2 28.3 + - + +
381O SER* 3.3 12.8 + - - -
399O GLU* 2.6 28.9 + - - +
402O ASN* 4.0 18.4 - - - +
403O ILE* 3.5 25.9 - - + +
406O GLU* 3.0 42.2 + - - -
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Residues in contact with VAL 378 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248O ALA* 4.5 7.9 - - + +
275O ILE* 4.3 16.8 - - + -
369O MET* 4.0 22.4 - - + -
374O ASN 2.9 18.8 + - - +
375O ALA* 3.3 6.3 + - - +
377O ARG* 1.3 72.5 - - - +
379O GLY* 1.3 65.6 + - - +
381O SER* 2.7 23.1 + - - -
382O ILE* 3.1 16.5 + - + +
396O ALA* 4.0 30.7 - - + +
399O GLU* 4.6 2.5 - - + -
400O CYS* 4.8 7.2 - - - +
403O ILE* 3.6 18.6 - - + -
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Residues in contact with GLY 379 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O MET* 3.7 15.5 - - - +
275O ILE* 3.9 10.1 - - - +
278O ALA* 5.4 0.2 - - - -
279O ILE* 3.9 22.2 - - - +
375O ALA 2.9 14.8 + - - -
376O TYR 3.2 5.6 + - - -
378O VAL* 1.3 77.4 - - - +
380O GLN* 1.3 59.3 + - - +
382O ILE* 3.2 4.7 + - - +
383O VAL* 3.1 21.0 + - - +
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Residues in contact with GLN 380 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O MET* 3.8 14.2 - - + +
376O TYR* 3.0 40.6 + - + +
377O ARG* 3.4 25.4 - - - +
378O VAL 3.2 0.4 - - - -
379O GLY* 1.3 74.5 - - - +
381O SER* 1.3 63.9 + - - +
383O VAL* 3.2 6.7 + - - +
384O LYS* 3.2 26.5 + - - +
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Residues in contact with SER 381 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377O ARG 3.3 2.0 + - - -
378O VAL 2.7 17.1 + - - -
380O GLN* 1.3 79.7 - - - +
382O ILE* 1.3 59.8 + - - +
384O LYS* 3.6 18.5 - - - +
395O ASN* 2.9 39.9 + - - +
396O ALA* 3.6 12.0 - - - -
399O GLU* 3.6 42.1 - - - +
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Residues in contact with ILE 382 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6O TYR 5.9 0.2 - - - +
251O ALA* 4.1 1.6 - - + -
252O PRO* 3.7 38.1 - - + -
255O LEU* 4.2 11.2 - - + -
275O ILE* 3.9 23.8 - - + -
279O ILE* 4.0 18.2 - - + -
378O VAL* 3.1 17.1 + - + +
379O GLY 3.4 5.8 - - - +
381O SER* 1.3 83.1 + - - +
383O VAL* 1.3 65.9 + - + +
385O ASP 3.3 10.2 + - - -
386O GLY* 3.3 8.6 + - - -
392O ARG* 3.3 32.7 - - + +
396O ALA* 3.8 22.0 - - + -
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Residues in contact with VAL 383 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6O TYR* 3.8 15.9 - - + +
7O THR* 3.6 28.1 - - - +
8O SER* 3.8 29.4 - - - +
9O MET* 3.8 17.9 - - + -
255O LEU* 5.6 0.2 - - + -
279O ILE* 3.9 26.9 - - + -
379O GLY 3.1 15.5 + - - +
380O GLN* 3.2 10.1 + - - +
382O ILE* 1.3 73.5 - - + +
384O LYS* 1.3 60.0 + - - +
385O ASP 2.9 11.6 + - - -
386O GLY* 3.0 11.4 + - - +
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Residues in contact with LYS 384 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7O THR 5.3 0.9 - - - -
380O GLN 3.2 10.8 + - - +
381O SER* 3.6 28.5 - - - +
383O VAL* 1.3 76.1 - - - +
385O ASP* 1.3 71.9 + - - +
395O ASN* 3.5 25.0 - - - +
399O GLU* 4.8 7.1 + - - -
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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