Contacts of the helix formed by residues 348 - 362 (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 ASN 348 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A ALA* 2.6 12.0 + - - +
346A THR* 3.0 32.2 + - - +
347A LYS* 1.3 78.2 + - - +
349A ASP* 1.3 65.6 + - - +
350A LYS 3.3 2.7 - - - -
351A VAL* 3.1 29.9 - - + +
352A LEU* 3.4 8.1 + - - +
351C VAL* 3.6 22.3 - - - +
355C LEU* 4.2 15.3 - - + -
2D LEU* 3.9 16.5 - - - +
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Residues in contact with ASP 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR* 2.5 34.4 + - - +
19A PHE* 3.6 27.2 - - + -
343A ALA* 3.2 13.5 + - - +
344A LEU* 3.7 25.7 - - + +
347A LYS* 3.5 10.2 - - - -
348A ASN* 1.3 82.3 + - - +
350A LYS* 1.3 66.9 + - - +
352A LEU 3.2 0.7 + - - -
353A ARG* 2.7 31.7 + - - +
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Residues in contact with LYS 350 (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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15A ASP* 3.0 39.6 + - - +
16A GLU* 4.7 9.0 - - - +
17A MET 5.0 1.8 - - - -
18A THR* 4.4 5.2 - - - +
347A LYS 5.4 0.6 + - - -
348A ASN 3.3 1.0 - - - -
349A ASP* 1.3 90.7 - - - +
351A VAL* 1.3 58.6 + - - +
353A ARG* 3.4 31.6 - - - +
354A ASP* 2.9 32.8 + - - -
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Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ASN* 3.1 36.1 - - + +
350A LYS* 1.3 74.1 - - - +
352A LEU* 1.3 62.1 + - + +
354A ASP* 3.2 8.2 + - - +
355A LEU* 2.9 34.6 + - + +
2B LEU* 4.2 8.6 - - + +
348C ASN* 3.5 35.9 - - + +
351C VAL* 4.6 12.8 - - + -
355C LEU* 5.5 1.6 - - + -
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Residues in contact with LEU 352 (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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19A PHE* 3.8 16.4 - - + -
339A LEU* 4.2 26.2 - - + +
340A MET* 4.3 6.7 - - + -
343A ALA* 3.8 20.9 - - + -
348A ASN 3.4 8.7 + - - +
349A ASP 3.2 6.6 + - - +
351A VAL* 1.3 81.2 - - + +
353A ARG* 1.3 66.1 + - - +
355A LEU* 3.0 18.0 + - + +
356A MET* 2.9 40.8 + - + +
339C LEU* 4.4 11.4 - - + -
352C LEU* 3.9 24.7 - - + -
355C LEU* 4.9 9.9 - - + -
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Residues in contact with ARG 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA 4.0 0.6 + - - -
15A ASP* 2.6 51.1 + - - +
17A MET 2.9 24.8 + - - +
18A THR* 4.6 3.1 - - - +
19A PHE* 3.7 6.0 - - + -
305A GLN* 3.2 30.5 - - + +
306A CYS* 4.6 0.9 - - - -
349A ASP 2.7 22.4 + - - +
350A LYS* 3.4 29.6 + - - +
352A LEU* 1.3 72.9 - - - +
354A ASP* 1.3 88.1 + - - +
356A MET* 3.3 14.6 + - - +
357A MET* 3.0 22.2 + - - +
372A TYR* 3.1 36.7 + - + -
1B MET* 5.5 0.4 - - - +
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Residues in contact with ASP 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LYS 2.9 20.9 + - - +
351A VAL* 3.2 9.0 + - - +
353A ARG* 1.3 89.7 + - - +
355A LEU* 1.3 52.8 + - - +
357A MET* 3.2 8.5 + - + +
358A LEU* 2.7 37.6 + - - +
372A TYR* 2.6 28.9 + - - -
1B MET* 3.4 26.6 - - - +
2B LEU* 3.6 26.5 + - + +
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Residues in contact with LEU 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A VAL* 2.9 21.6 + - + +
352A LEU* 3.0 20.2 + - + +
354A ASP* 1.3 72.9 - - - +
356A MET* 1.3 66.9 + - - +
358A LEU 3.3 0.5 + - - -
359A SER* 3.0 24.6 + - - -
2B LEU* 3.6 17.0 - - + -
339C LEU* 3.9 15.3 - - + +
342C THR* 3.7 14.3 - - + +
343C ALA* 3.9 30.3 - - + +
346C THR* 3.4 25.8 - - - +
348C ASN* 4.0 21.5 - - + +
351C VAL* 5.3 2.2 - - + -
352C LEU* 4.7 8.3 - - + -
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Residues in contact with MET 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.3 24.2 - - + -
301A ASN* 3.4 17.7 - - - +
302A LEU* 3.2 16.8 + - - +
304A MET* 3.5 28.7 - - + +
305A GLN* 3.0 39.7 - - - +
340A MET* 4.6 6.1 - - - -
352A LEU* 2.9 23.2 + - + +
353A ARG* 3.3 20.0 - - - -
355A LEU* 1.3 74.7 - - - +
357A MET* 1.3 65.5 + - - +
359A SER* 3.2 14.9 - - - -
339C LEU* 3.7 21.5 - - + +
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Residues in contact with MET 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 3.6 14.7 - - + +
305A GLN* 3.5 24.2 - - + +
353A ARG 3.0 16.2 + - - +
354A ASP* 3.6 10.8 - - + +
356A MET* 1.3 77.9 - - - +
358A LEU* 1.3 75.3 + - + +
360A ASP 3.1 4.5 + - - -
361A ARG* 3.0 51.0 + - - +
371A ALA* 3.7 15.0 - - + -
372A TYR* 4.0 16.2 - - + -
1B MET* 3.5 31.6 - - + -
2B LEU 3.8 14.8 - - - +
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Residues in contact with LEU 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ASP 2.7 21.4 + - - +
355A LEU* 4.7 0.2 - - - -
357A MET* 1.3 83.0 - - + +
359A SER* 1.3 62.5 + - - +
360A ASP 3.1 1.2 + - - -
361A ARG* 3.5 15.4 + - + +
362A TYR* 4.0 10.6 + - + -
2B LEU* 4.0 9.0 - - + +
3B ASP* 3.6 34.8 - - - +
4B PHE* 3.5 65.8 - - + +
13B LEU* 5.6 0.3 - - - +
342C THR* 3.8 7.9 - - + -
346C THR* 3.6 16.2 - - + -
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Residues in contact with SER 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ASN* 3.2 24.2 + - - -
355A LEU 3.0 13.2 + - - -
356A MET* 3.2 15.7 - - - -
358A LEU* 1.3 76.6 - - - +
360A ASP* 1.3 73.1 + - - +
363A ARG* 3.4 13.7 + - - -
4B PHE* 5.0 0.4 - - - -
12B VAL* 4.5 5.2 - - - +
13B LEU* 3.8 10.9 - - - +
338C ALA* 3.9 12.6 - - - +
339C LEU* 4.7 2.9 - - - -
342C THR* 3.3 21.1 + - - -
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Residues in contact with ASP 360 (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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298A VAL 4.2 2.9 - - - +
299A MET* 3.0 14.5 - - - -
300A GLY 3.0 7.2 + - - -
301A ASN 2.7 31.4 + - - -
302A LEU* 2.8 26.1 + - + -
357A MET 3.1 2.4 + - - -
358A LEU 3.1 0.4 - - - -
359A SER* 1.3 92.0 + - - +
361A ARG* 1.3 69.0 + - - +
362A TYR 2.9 5.5 + - - -
363A ARG* 2.9 38.4 + - - +
367A ALA* 3.4 13.7 - - + +
335C TYR* 3.4 6.2 - - - -
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Residues in contact with ARG 361 (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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302A LEU* 4.0 8.7 - - + +
357A MET* 3.0 39.6 + - - +
358A LEU* 3.5 11.0 + - - +
360A ASP* 1.3 76.7 - - - +
362A TYR* 1.3 91.9 + - + +
363A ARG 3.9 0.2 + - - -
364A ASP 4.1 0.9 - - - +
368A TYR* 3.3 63.7 + - + +
371A ALA* 3.5 12.2 - - + +
373A ASP* 2.5 43.6 + - - -
374A ASN* 3.6 14.0 + - - +
412A LEU* 4.4 0.3 - - - +
1B MET* 4.0 6.9 - - - -
2B LEU 5.7 0.6 + - - -
3B ASP* 4.5 4.3 - - - -
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Residues in contact with TYR 362 (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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358A LEU* 4.0 9.6 + - + -
360A ASP 3.0 0.6 - - - -
361A ARG* 1.3 105.1 + - + +
363A ARG* 1.3 65.1 + - - +
364A ASP 3.3 3.6 + - - -
368A TYR* 4.0 10.4 + + - -
407A GLY 5.6 0.2 - - - -
411A LYS* 3.4 39.6 + - + +
412A LEU* 3.6 34.1 - - + +
413A GLU* 5.2 1.7 + - - +
3B ASP* 2.7 31.3 + - - -
4B PHE* 4.0 14.4 - + - -
9B LEU* 3.7 37.2 - - + -
13B LEU* 3.9 8.9 - - + +
15B ARG* 3.5 17.7 - - - +
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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