Contacts of the helix formed by residues 356 - 371 (chain A) in PDB entry 5ID6
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 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A SER* 5.7 0.7 + - - -
354A GLU* 3.6 2.8 + - - +
355A TRP* 1.3 96.4 - - - +
357A LEU* 1.3 51.9 + - - +
358A ILE 3.5 0.9 - - - -
359A ARG* 3.2 14.9 + - + +
360A ASP* 2.5 54.4 + - - +
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Residues in contact with LEU 357 (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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348A SER* 3.6 11.0 - - - +
352A PHE* 3.5 39.9 - - + -
354A GLU* 4.1 25.0 + - + +
355A TRP 3.3 2.6 - - - -
356A ASN* 1.3 76.0 - - - +
358A ILE* 1.3 54.9 + - - +
360A ASP* 2.9 10.4 + - + +
361A LYS* 2.7 60.2 + - + +
405A ASP* 5.4 5.8 - - - +
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Residues in contact with ILE 358 (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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344A ILE* 3.5 37.2 - - + +
347A ILE* 4.9 4.5 - - + -
348A SER* 3.7 29.2 + - - +
351A ILE* 5.6 0.7 - - + -
352A PHE* 3.5 25.1 - - + -
355A TRP 5.3 0.2 - - - +
357A LEU* 1.3 76.4 - - - +
359A ARG* 1.3 64.3 + - - +
361A LYS* 3.5 2.1 + - - +
362A TRP* 3.0 24.1 + - - +
389A PHE* 5.0 1.3 - - + -
395A PHE* 4.8 12.1 - - + -
400A LEU* 3.9 29.8 - - + -
403A TYR* 4.0 22.7 - - + -
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Residues in contact with ARG 359 (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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344A ILE* 5.3 0.8 - - + +
355A TRP 5.2 0.6 + - - +
356A ASN* 3.2 19.6 + - + +
357A LEU 3.2 0.6 - - - -
358A ILE* 1.3 80.6 - - - +
360A ASP* 1.3 61.3 + - - +
362A TRP* 3.4 2.3 + - - +
363A ASN* 2.9 63.5 + - - +
382A GLU 5.4 0.2 + - - -
385A ARG* 4.1 4.0 + - - +
386A ARG* 3.5 46.5 - - - +
389A PHE* 3.3 57.7 - - + +
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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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356A ASN* 2.5 42.0 + - - +
357A LEU* 2.9 10.9 + - + +
359A ARG* 1.3 74.6 - - - +
361A LYS* 1.3 65.8 + - + +
363A ASN* 3.1 14.9 + - - +
364A ALA* 2.9 21.5 + - - +
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Residues in contact with LYS 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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352A PHE* 5.0 1.4 - - - -
357A LEU* 2.7 47.3 + - + +
358A ILE* 4.0 1.6 - - - +
360A ASP* 1.3 73.1 - - + +
362A TRP* 1.3 62.5 + - - +
364A ALA* 3.1 19.7 + - + +
365A GLU* 3.1 17.2 + - - +
403A TYR* 2.2 70.9 + - + +
405A ASP* 3.7 11.0 + - - -
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Residues in contact with TRP 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 ILE 3.0 18.2 + - - +
359A ARG 3.7 3.1 - - - +
360A ASP 3.1 0.2 - - - -
361A LYS* 1.3 77.9 - - - +
363A ASN* 1.3 72.3 + - - +
365A GLU* 3.5 6.0 + - + +
366A TYR* 3.0 43.9 + + + +
385A ARG* 3.7 10.1 - - + -
388A SER* 3.7 13.5 - - - -
389A PHE* 3.4 57.0 - + + -
392A ILE* 3.9 29.6 - - + +
395A PHE* 3.9 19.3 - + + -
403A TYR* 3.1 27.8 + - + +
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Residues in contact with ASN 363 (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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359A ARG* 2.9 54.1 + - - +
360A ASP* 3.1 14.5 + - - +
362A TRP* 1.3 82.7 - - - +
364A ALA* 1.3 57.3 + - - +
365A GLU 3.1 0.4 - - - -
366A TYR* 3.9 2.9 - - - +
367A ASP* 3.0 36.6 + - - +
385A ARG* 3.3 46.5 + - - +
1054A ARG* 5.5 0.7 - - - +
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Residues in contact with ALA 364 (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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360A ASP 2.9 12.1 + - - +
361A LYS* 3.1 15.0 + - + +
363A ASN* 1.3 77.0 - - - +
365A GLU* 1.3 62.4 + - + +
367A ASP* 4.0 6.8 + - - +
368A ASP* 3.7 18.7 + - - +
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Residues in contact with GLU 365 (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 LYS 3.1 16.6 + - - +
362A TRP* 3.5 8.3 + - + +
363A ASN 3.1 0.2 - - - -
364A ALA* 1.3 79.8 - - + +
366A TYR* 1.3 62.9 + - - +
367A ASP 3.3 0.4 + - - -
368A ASP* 3.7 5.8 + - - +
369A ILE* 3.7 26.5 + - + +
402A GLU* 5.7 3.5 - - - +
403A TYR* 4.2 22.8 + - + +
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Residues in contact with TYR 366 (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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362A TRP* 3.0 46.1 + + + +
363A ASN* 3.4 4.2 + - - +
365A GLU* 1.3 74.8 - - - +
367A ASP* 1.3 69.8 + - - +
369A ILE* 3.4 6.0 + - - -
370A HIS* 3.0 68.1 + + + +
381A TYR* 3.8 22.5 + + - -
384A ASP* 4.2 6.8 - - - +
385A ARG* 3.3 46.4 + - + -
388A SER* 3.6 23.1 + - - -
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Residues in contact with ASP 367 (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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363A ASN 3.0 21.0 + - - +
364A ALA* 4.1 7.5 - - - +
365A GLU 3.3 0.2 - - - -
366A TYR* 1.3 76.0 - - - +
368A ASP* 1.3 55.6 + - - +
370A HIS 2.7 8.8 + - - -
371A LEU* 2.5 50.9 + - + +
377A VAL* 5.9 1.0 - - - +
381A TYR* 2.5 33.6 + - - +
385A ARG* 3.2 24.0 + - - -
1054A ARG* 3.8 10.7 + - - -
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Residues in contact with ASP 368 (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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364A ALA 3.7 11.6 + - - +
365A GLU* 3.7 10.0 + - - +
366A TYR 3.4 0.4 - - - -
367A ASP* 1.3 78.3 - - - +
369A ILE* 1.3 62.6 + - + +
371A LEU* 4.4 10.8 + - - +
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Residues in contact with ILE 369 (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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365A GLU* 3.7 16.1 + - + +
366A TYR* 3.4 4.7 + - - +
367A ASP 2.8 1.6 + - - -
368A ASP* 1.3 81.4 - - + +
370A HIS* 1.3 89.4 + - + +
371A LEU 3.9 0.9 + - - -
372A LYS* 5.8 1.0 - - - +
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Residues in contact with HIS 370 (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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366A TYR* 3.0 65.3 + + + +
367A ASP 2.7 8.5 + - - -
369A ILE* 1.3 98.7 - - + +
371A LEU* 1.3 57.0 + - - +
372A LYS* 3.3 19.1 + - - +
381A TYR* 4.1 14.0 - - + -
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Residues in contact with LEU 371 (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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367A ASP* 2.5 39.5 + - + +
368A ASP* 4.5 9.2 - - - +
369A ILE 3.6 1.5 - - - -
370A HIS* 1.3 69.8 - - - +
372A LYS* 1.3 67.3 + - - +
373A LYS* 3.7 3.6 + - - +
375A ALA* 4.6 20.4 - - + -
376A VAL 5.9 0.2 - - - -
377A VAL* 4.1 26.5 - - + -
381A TYR* 3.8 17.4 + - + +
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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
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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