Contacts of the helix formed by residues 348 - 362 (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 ASN 348 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351M VAL* 3.5 23.8 - - - +
355M LEU* 4.1 17.0 - - + -
2N LEU* 3.8 15.6 - - - +
343O ALA* 2.7 17.3 + - - +
346O THR* 3.0 30.5 + - - +
347O LYS* 1.3 77.5 + - - +
349O ASP* 1.3 61.5 + - - -
350O LYS 3.4 2.7 - - - -
351O VAL* 3.2 30.2 - - + +
352O LEU* 3.3 9.7 + - - +
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Residues in contact with ASP 349 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18O THR* 2.9 38.0 + - - +
19O PHE* 3.6 21.0 - - + -
343O ALA* 3.4 3.7 + - - -
344O LEU* 3.6 36.0 - - + +
347O LYS* 3.6 8.0 - - - +
348O ASN* 1.3 82.4 + - - +
350O LYS* 1.3 63.2 + - - +
352O LEU 3.4 0.7 + - - -
353O ARG* 2.6 37.1 + - - +
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Residues in contact with LYS 350 (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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15O ASP* 3.1 36.7 + - - +
16O GLU* 4.4 12.0 - - - +
17O MET 5.0 0.9 - - - -
18O THR* 4.7 6.1 - - - +
348O ASN 3.4 0.8 - - - -
349O ASP* 1.3 89.6 - - - +
351O VAL* 1.3 64.5 + - - +
353O ARG* 3.5 31.8 - - - +
354O ASP* 3.0 30.1 + - - -
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Residues in contact with VAL 351 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348M ASN* 3.6 38.1 - - + +
351M VAL* 4.3 17.3 - - + -
355M LEU* 5.3 1.8 - - + -
348O ASN* 3.2 31.1 + - + +
350O LYS* 1.3 76.3 - - - +
352O LEU* 1.3 75.6 + - + +
354O ASP* 3.1 10.7 + - - +
355O LEU* 3.0 26.0 + - + +
2P LEU* 4.8 8.1 - - + -
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Residues in contact with LEU 352 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339M LEU* 4.5 11.9 - - + -
352M LEU* 4.0 25.6 - - + -
355M LEU* 4.7 7.0 - - + -
19O PHE* 3.6 22.9 - - + -
339O LEU* 4.4 15.5 - - + -
340O MET* 4.1 16.8 - - + -
343O ALA* 3.8 15.5 - - + -
348O ASN 3.3 13.8 + - - +
349O ASP 3.7 3.1 - - - +
351O VAL* 1.3 84.7 - - + +
353O ARG* 1.3 62.3 + - - +
355O LEU* 3.2 15.8 + - + +
356O MET* 3.1 40.7 + - + +
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Residues in contact with ARG 353 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15O ASP* 2.7 48.9 + - - +
17O MET 3.0 25.0 + - - +
18O THR* 4.3 3.4 - - - +
19O PHE* 4.0 4.0 - - + -
305O GLN* 3.4 27.9 - - + +
306O CYS* 4.7 1.3 - - - -
349O ASP 2.6 22.3 + - - +
350O LYS* 3.5 32.1 - - - +
352O LEU* 1.3 73.7 - - - +
354O ASP* 1.3 89.4 + - - +
356O MET* 3.1 15.8 + - - +
357O MET* 3.0 27.9 + - - +
372O TYR* 3.1 32.2 + - + -
1P MET* 5.5 0.2 - - - +
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Residues in contact with ASP 354 (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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350O LYS 3.0 15.7 + - - +
351O VAL* 3.4 9.9 - - - +
353O ARG* 1.3 90.3 + - - +
355O LEU* 1.3 55.3 + - - +
357O MET* 3.6 10.0 - - + +
358O LEU* 2.7 36.9 + - - +
372O TYR* 2.5 28.6 + - - -
1P MET* 3.3 21.2 - - - -
2P LEU* 3.5 30.5 + - + +
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Residues in contact with LEU 355 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339M LEU* 3.9 14.7 - - + +
342M THR* 3.6 15.6 - - + +
343M ALA* 4.1 28.9 - - + +
346M THR* 3.6 15.3 - - - +
348M ASN* 4.0 19.3 - - + +
351M VAL* 5.5 1.3 - - + -
352M LEU* 4.4 15.7 - - + -
355M LEU* 6.6 0.2 - - + -
351O VAL* 3.0 18.6 + - + +
352O LEU* 3.4 20.2 - - + +
354O ASP* 1.3 72.4 - - - +
356O MET* 1.3 61.2 + - - +
358O LEU 3.1 0.7 + - - -
359O SER* 2.8 30.3 + - - -
2P LEU* 3.2 29.4 - - + -
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Residues in contact with MET 356 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339M LEU* 3.8 23.3 - - + -
19O PHE* 3.2 26.2 - - + -
301O ASN* 3.6 18.6 - - - +
302O LEU* 3.4 15.0 + - - -
304O MET* 3.5 34.3 - - + +
305O GLN* 3.7 10.8 - - - +
339O LEU* 6.5 0.2 - - - -
340O MET* 4.6 4.3 - - - -
352O LEU* 3.1 24.4 + - + +
353O ARG* 3.1 32.3 - - - +
355O LEU* 1.3 79.5 - - - +
357O MET* 1.3 66.6 + - - +
359O SER* 3.3 14.0 + - - -
360O ASP 3.9 0.5 + - - -
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Residues in contact with MET 357 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302O LEU* 3.5 15.9 - - + +
305O GLN* 3.4 24.1 - - + +
353O ARG 3.0 17.6 + - - +
354O ASP* 3.6 17.0 - - + +
356O MET* 1.3 76.5 - - - +
358O LEU* 1.3 67.4 + - + +
360O ASP 3.2 3.5 + - - -
361O ARG* 3.0 53.3 + - - +
371O ALA* 3.7 15.9 - - + -
372O TYR* 4.1 15.3 - - + -
1P MET* 3.6 29.8 - - + -
2P LEU 4.0 13.0 - - - +
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Residues in contact with LEU 358 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342M THR* 3.9 9.4 - - + -
346M THR* 3.8 16.2 - - + -
354O ASP 2.7 21.6 + - - +
355O LEU 3.1 0.2 + - - -
357O MET* 1.3 79.7 - - + +
359O SER* 1.3 68.7 + - - +
360O ASP 2.9 1.2 + - - -
361O ARG* 3.5 13.3 + - + +
362O TYR* 3.9 17.9 + - + -
2P LEU* 3.9 9.9 - - + +
3P ASP* 3.6 35.2 - - - +
4P PHE* 3.6 52.0 - - + +
13P LEU* 5.5 0.2 - - - +
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Residues in contact with SER 359 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338M ALA* 3.6 15.4 - - - +
339M LEU* 4.5 2.0 - - - -
342M THR* 3.4 20.7 - - - +
301O ASN* 3.0 26.6 + - - -
355O LEU 2.8 12.8 + - - -
356O MET* 3.4 12.6 - - - -
357O MET 3.3 0.4 - - - -
358O LEU* 1.3 76.9 - - - +
360O ASP* 1.3 80.7 + - - +
363O ARG* 3.4 12.0 + - - -
4P PHE* 5.1 0.2 - - - -
12P VAL* 4.3 4.7 - - - +
13P LEU* 3.4 13.3 - - - +
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Residues in contact with ASP 360 (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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335M TYR* 3.4 7.9 - - - -
298O VAL 4.1 11.7 - - - +
299O MET* 4.1 2.7 - - - -
300O GLY 3.2 6.7 + - - -
301O ASN 2.8 30.7 + - - -
302O LEU* 3.1 22.2 + - + -
356O MET 3.9 0.2 + - - -
357O MET 3.2 3.2 + - - -
358O LEU 3.0 0.2 - - - -
359O SER* 1.3 97.6 + - - +
361O ARG* 1.3 66.1 + - - +
362O TYR 2.8 6.2 + - - -
363O ARG* 2.8 44.3 + - - +
367O ALA* 3.3 13.1 - - + +
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Residues in contact with ARG 361 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302O LEU* 4.2 9.0 - - - -
357O MET* 3.0 44.6 + - - +
358O LEU* 3.5 9.2 + - + +
360O ASP* 1.3 76.0 - - - +
362O TYR* 1.3 92.1 + - + +
363O ARG 3.8 0.2 + - - -
364O ASP 4.0 0.2 - - - +
368O TYR* 3.2 61.1 + - + +
371O ALA* 3.8 4.8 - - + +
373O ASP* 2.6 46.0 + - - -
374O ASN* 3.6 18.1 + - - +
1P MET* 3.8 9.7 - - - -
2P LEU 5.7 1.0 + - - -
3P ASP* 5.0 2.0 - - - -
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Residues in contact with TYR 362 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358O LEU* 3.9 17.9 + - + -
360O ASP 3.0 0.8 - - - -
361O ARG* 1.3 100.2 + - + +
363O ARG* 1.3 63.7 + - - +
364O ASP 3.3 3.2 + - - -
368O TYR* 4.0 12.5 - + - -
407O GLY 5.6 0.2 - - - -
411O LYS* 3.6 37.6 + - + +
412O LEU* 3.8 30.5 - - - +
413O GLU* 5.1 1.7 + - - +
3P ASP* 2.7 32.8 + - - -
4P PHE* 4.0 12.8 - + + -
9P LEU* 3.8 36.1 - - + -
13P LEU* 4.0 8.8 - - + +
15P ARG* 3.7 14.4 - - - +
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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
------------------------------------------------------------
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