Contacts of the helix formed by residues 356 - 370 (chain A) in PDB entry 6IRT
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 ASP 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A LEU 3.5 1.8 + - - -
355A LYS* 1.3 79.1 - - + +
357A ALA* 1.3 63.8 + - - +
358A SER* 4.2 6.2 + - - -
359A SER* 2.9 37.2 + - - -
360A PHE* 3.2 23.8 - - + -
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Residues in contact with ALA 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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351A ILE* 3.3 35.9 - - + +
354A LEU* 3.7 29.0 + - + +
356A ASP* 1.3 76.6 - - - +
358A SER* 1.3 62.2 + - - +
359A SER 3.1 1.6 + - - -
360A PHE 3.5 5.4 + - - -
361A LEU* 3.4 24.0 + - - +
392A LEU* 5.2 9.2 - - + -
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Residues in contact with SER 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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356A ASP* 4.2 6.8 + - - -
357A ALA* 1.3 77.1 - - - +
359A SER* 1.3 60.7 + - - +
361A LEU* 4.4 10.1 - - - -
362A ALA* 4.3 5.5 + - - +
391A SER 4.0 20.9 + - - -
392A LEU* 4.1 22.1 - - - +
394A GLU* 6.3 0.4 - - - -
395A SER* 5.7 3.6 - - - -
396A ASN* 4.0 15.6 + - - +
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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
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356A ASP* 2.9 37.2 + - - -
357A ALA 3.1 1.0 - - - -
358A SER* 1.3 79.1 + - - +
360A PHE* 1.3 69.3 - - - +
361A LEU 3.2 2.7 + - - -
362A ALA* 3.5 12.9 + - - +
363A GLU* 3.6 10.0 + - - +
1D NAG 5.6 0.3 + - - -
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Residues in contact with PHE 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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324A VAL* 5.1 13.9 - - + -
325A ASP* 5.7 5.2 - - + -
328A ALA* 4.1 27.4 - - + -
354A LEU* 4.2 18.8 - - + -
355A LYS* 3.2 24.5 - - - -
356A ASP* 3.2 25.4 - - + -
357A ALA 3.5 1.4 + - - -
359A SER* 1.3 78.4 - - - +
361A LEU* 1.3 60.4 + - - +
362A ALA 3.4 0.2 - - - -
363A GLU* 3.5 20.6 + - - +
364A TRP* 3.0 54.8 + + + -
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Residues in contact with LEU 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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348A VAL* 4.3 17.7 - - + -
351A ILE* 3.7 30.5 - - + -
354A LEU* 5.4 1.8 - - + -
357A ALA 3.4 16.8 - - - +
358A SER* 4.8 4.9 - - - +
359A SER 3.2 1.0 - - - -
360A PHE* 1.3 76.3 - - - +
362A ALA* 1.3 54.8 + - - +
364A TRP* 2.9 27.5 + - + +
365A GLN* 2.4 39.4 + - - +
377A LEU* 4.4 10.5 - - + +
379A ALA* 4.4 5.2 - - + -
392A LEU* 5.2 6.5 - - + +
396A ASN* 3.8 15.0 - - - +
399A LEU* 3.9 26.7 - - + -
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Residues in contact with ALA 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 SER 4.3 5.8 + - - +
359A SER* 3.5 9.7 + - - +
360A PHE 3.4 0.2 - - - -
361A LEU* 1.3 78.0 - - - +
363A GLU* 1.3 60.8 + - - +
365A GLN* 3.9 2.7 - - - +
366A ASN* 2.8 33.6 + - - +
395A SER* 4.9 10.8 - - - +
396A ASN* 3.3 28.7 - - - +
1D NAG 3.9 19.7 - - - +
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Residues in contact with GLU 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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332A LYS* 3.8 31.4 + - - +
359A SER 3.6 8.1 + - - +
360A PHE* 3.5 28.9 + - - +
361A LEU 3.2 0.6 - - - -
362A ALA* 1.3 77.3 - - - +
364A TRP* 1.3 56.6 + - + +
366A ASN* 2.9 9.8 + - - +
367A ILE* 2.8 49.1 + - + +
1D NAG 5.1 2.2 + - - -
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Residues in contact with TRP 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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319A TRP* 4.4 25.1 - + - -
328A ALA* 4.1 23.3 + - + +
331A VAL* 3.6 34.5 - - + -
332A LYS* 4.0 19.6 - - - +
335A LEU* 3.5 27.0 - - + +
348A VAL* 4.8 11.0 - - + -
354A LEU* 4.6 9.2 - - + -
360A PHE* 3.0 33.9 + + + +
361A LEU* 2.9 27.2 + - + +
363A GLU* 1.3 79.2 + - + +
365A GLN* 1.3 64.6 + - - +
367A ILE* 3.7 12.9 - - + +
368A THR* 2.8 28.8 + - - -
377A LEU* 4.1 15.3 - - + +
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Residues in contact with GLN 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 LEU 2.4 30.1 + - - +
362A ALA* 3.9 10.8 - - - +
364A TRP* 1.3 69.1 - - - +
366A ASN* 1.3 54.3 + - - +
368A THR* 3.1 7.8 + - - +
369A LYS* 2.7 62.7 + - + +
375A ARG 5.1 0.5 - - - +
376A LEU* 5.4 0.5 - - - -
377A LEU* 4.1 16.6 + - + +
396A ASN* 4.2 10.6 + - + +
398A ASP* 2.9 40.9 + - + +
399A LEU* 3.5 24.0 - - + +
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Residues in contact with ASN 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 ALA* 2.8 15.5 + - - +
363A GLU* 2.9 6.7 + - + +
365A GLN* 1.3 80.7 - - - +
367A ILE* 1.3 62.4 - - + +
369A LYS* 3.7 7.2 - - - +
370A GLY* 2.7 25.9 + - - -
1D NAG 1.5 87.1 + - + +
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Residues in contact with ILE 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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332A LYS* 4.2 26.0 - - + +
335A LEU* 3.8 32.3 - - + -
336A GLU* 4.5 17.9 - - + +
339A LEU* 4.9 3.1 - - + +
363A GLU* 2.8 23.9 + - + +
364A TRP* 3.7 28.9 - - + +
365A GLN 3.3 0.4 - - - -
366A ASN* 1.3 77.7 - - - +
368A THR* 1.3 57.2 + - - +
370A GLY* 3.0 16.4 + - - -
371A PHE* 3.3 13.7 + - - +
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Residues in contact with THR 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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335A LEU* 4.3 15.4 - - - +
339A LEU* 4.7 12.9 - - + +
345A GLY* 5.5 1.1 - - - -
346A PHE* 4.9 4.1 - - + -
364A TRP 2.8 17.3 + - - -
365A GLN* 3.1 11.1 + - - +
367A ILE* 1.3 78.3 - - - +
369A LYS* 1.3 60.7 + - - +
370A GLY 3.5 0.2 + - - -
371A PHE* 3.5 2.4 + - - +
372A SER 3.4 18.4 + - - +
375A ARG* 3.5 42.6 - - + +
376A LEU* 3.9 14.6 - - - +
377A LEU* 4.6 9.3 - - - +
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Residues in contact with LYS 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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218A LYS* 5.6 1.4 - - - +
220A TRP* 4.2 8.5 - - - -
365A GLN* 2.7 46.1 + - + +
366A ASN* 4.3 9.2 - - - +
368A THR* 1.3 72.5 - - - +
370A GLY* 1.3 55.9 + - - +
371A PHE 3.1 5.9 + - - -
372A SER 2.9 22.6 + - - +
373A GLU* 3.5 26.6 + - + +
375A ARG 3.5 20.1 + - - +
376A LEU* 5.8 0.4 - - - +
398A ASP* 3.3 30.1 + - - -
1D NAG 5.6 5.4 - - + -
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Residues in contact with GLY 370 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A ASN 2.7 23.5 + - - -
367A ILE* 3.0 7.4 + - - -
369A LYS* 1.3 74.0 - - - +
371A PHE* 1.3 59.8 + - - +
1D NAG 6.0 2.7 - - - -
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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