Contacts of the helix formed by residues 367 - 382 (chain A) in PDB entry 5I35
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 SER 367 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A GLY 3.0 16.7 + - - -
364A VAL* 3.1 9.2 + - - +
366A GLN* 1.3 77.0 - - - +
368A ILE* 1.3 63.0 + - - +
369A ASN 3.2 2.9 + - - -
370A SER* 3.4 12.3 + - - -
371A ASP* 2.8 44.8 + - - +
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Residues in contact with ILE 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 VAL* 3.5 10.9 + - + +
365A ALA* 3.3 29.7 + - + +
366A GLN 3.4 1.0 - - - -
367A SER* 1.3 75.6 - - - +
369A ASN* 1.3 62.2 + - - +
371A ASP* 3.4 4.2 + - - +
372A VAL* 3.0 32.7 + - + +
399A ARG* 4.1 34.1 - - + +
402A LEU* 3.7 24.5 - - + +
403A ALA* 3.6 37.7 - - + +
406A CYS* 4.1 3.4 - - - -
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Residues in contact with ASN 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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366A GLN 4.8 3.9 + - - +
367A SER* 3.2 0.6 - - - +
368A ILE* 1.3 81.8 - - - +
370A SER* 1.3 62.9 + - - +
372A VAL* 3.9 2.7 - - - +
373A ASN* 3.1 29.7 + - - +
399A ARG* 2.8 50.3 + - - +
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Residues in contact with SER 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 GLN 5.5 0.2 + - - -
367A SER* 3.4 15.8 + - - +
369A ASN* 1.3 77.1 - - - +
371A ASP* 1.3 67.9 + - - +
373A ASN* 3.4 7.8 + - - +
374A ASN* 3.0 23.9 + - - +
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Residues in contact with ASP 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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269A LYS 4.6 4.0 - - - +
270A VAL* 3.5 38.2 - - + +
273A ALA* 4.3 11.2 + - + +
364A VAL 5.4 0.7 - - - +
367A SER* 2.8 41.8 + - - +
368A ILE* 3.8 5.0 - - - +
370A SER* 1.3 75.7 - - - +
372A VAL* 1.3 58.2 + - - +
374A ASN* 3.5 0.8 + - - -
375A LEU* 3.0 28.2 + - - +
402A LEU* 6.2 0.2 - - + -
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Residues in contact with VAL 372 (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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273A ALA* 4.2 4.5 - - + -
368A ILE* 3.0 26.2 + - + +
369A ASN* 3.9 4.7 - - - +
371A ASP* 1.3 73.2 - - - +
373A ASN* 1.3 69.5 + - - +
375A LEU* 3.4 6.7 + - - +
376A MSE 2.9 31.5 + - + +
395A ILE* 3.8 30.3 - - + +
398A LEU* 4.0 26.9 - - + -
399A ARG* 4.6 9.0 - - + +
402A LEU* 3.8 26.9 - - + -
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Residues in contact with ASN 373 (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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369A ASN* 3.1 20.7 + - - +
370A SER* 3.6 7.3 - - - +
372A VAL* 1.3 82.1 - - - +
374A ASN* 1.3 56.3 + - - +
376A MSE 3.2 8.4 + - - +
377A ALA* 2.9 28.4 + - - +
390A PHE* 5.6 0.7 - - - -
395A ILE* 5.3 3.8 - - - +
399A ARG* 4.9 11.3 + - - +
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Residues in contact with ASN 374 (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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266A THR* 4.9 6.7 + - - -
269A LYS* 5.4 5.1 - - - +
270A VAL* 3.8 22.5 - - + +
370A SER 3.0 16.8 + - - +
371A ASP* 3.7 4.7 - - - +
373A ASN* 1.3 73.8 - - - +
375A LEU* 1.3 58.7 + - - +
377A ALA* 3.3 10.2 + - - +
378A VAL* 3.0 37.9 + - - +
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Residues in contact with LEU 375 (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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267A LEU* 3.8 25.8 - - + -
270A VAL* 4.2 11.8 - - + +
273A ALA* 3.6 35.7 - - + +
274A ALA* 4.1 14.8 - - + -
277A LEU* 4.0 10.5 - - + -
297A PHE* 4.9 1.8 - - + -
371A ASP 3.0 19.1 + - - +
372A VAL* 3.5 3.6 - - - +
374A ASN* 1.3 77.3 - - - +
376A MSE 1.4 80.4 + - + +
378A VAL* 3.3 3.8 + - - +
379A LEU* 3.0 42.2 + - + +
398A LEU* 4.2 6.5 - - + -
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Residues in contact with MSE 376 (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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277A LEU* 3.8 20.2 - - + -
372A VAL* 2.9 23.1 + - + +
373A ASN* 3.7 7.2 - - - +
375A LEU* 1.4 112.4 - - + +
377A ALA* 1.3 53.1 + - - +
379A LEU* 3.4 7.5 + - + +
380A ASN* 2.7 36.7 + - - +
385A LEU* 4.6 10.9 - - + +
390A PHE* 3.7 23.9 - - + -
391A PRO* 4.6 12.8 - - - -
394A LEU* 5.3 2.7 - - - -
395A ILE* 3.4 34.8 - - + -
398A LEU* 4.1 15.0 - - + -
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Residues in contact with ALA 377 (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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373A ASN 2.9 13.5 + - - +
374A ASN* 3.4 17.9 - - - +
376A MSE 1.3 77.3 - - - +
378A VAL* 1.3 56.4 + - + +
380A ASN* 3.8 6.6 + - - +
381A MSE 2.9 42.6 + - + +
390A PHE* 4.5 7.1 - - + -
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Residues in contact with VAL 378 (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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263A ILE* 4.2 16.4 - - + -
266A THR* 3.9 29.4 - - + +
267A LEU* 3.4 29.6 - - + -
270A VAL* 6.1 0.4 - - + -
374A ASN* 3.0 33.2 + - - +
375A LEU* 3.3 5.4 + - - +
377A ALA* 1.3 74.1 - - + +
379A LEU* 1.3 67.5 + - + +
381A MSE 4.0 12.9 - - + +
382A SER* 3.3 26.4 + - - +
384A MSE 6.1 0.4 - - + -
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Residues in contact with LEU 379 (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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267A LEU* 5.0 6.3 - - + -
277A LEU* 3.5 32.8 - - + -
293A LEU* 4.3 16.4 - - + -
297A PHE* 4.3 14.1 - - + -
375A LEU* 3.0 31.6 + - + +
376A MSE 3.8 13.0 - - + +
378A VAL* 1.3 78.6 - - + +
380A ASN* 1.3 67.4 + - - +
382A SER* 3.5 7.2 + - - -
384A MSE 3.3 49.1 + - + +
385A LEU* 4.7 9.9 - - + -
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Residues in contact with ASN 380 (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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376A MSE 2.7 21.9 + - - +
377A ALA* 3.3 6.4 + - - +
379A LEU* 1.3 69.8 - - - +
381A MSE 1.3 54.5 + - - +
383A ASN* 2.6 34.8 + - - +
385A LEU* 3.3 33.7 - - + +
388A GLY 4.9 2.9 - - - +
390A PHE* 4.1 22.3 - - + -
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Residues in contact with MSE 381 (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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377A ALA* 2.9 27.8 + - + +
378A VAL* 4.0 13.7 - - + +
380A ASN* 1.3 79.8 - - - +
382A SER* 1.3 58.1 + - - +
383A ASN* 3.3 3.3 + - - -
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Residues in contact with SER 382 (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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261A GLU* 5.7 0.2 + - - -
263A ILE* 3.5 22.9 - - - +
378A VAL* 3.3 17.0 + - - +
379A LEU 3.6 1.1 - - - -
380A ASN 3.0 1.8 + - - -
381A MSE 1.3 75.8 - - - +
383A ASN* 1.3 73.5 + - - +
384A MSE 3.3 39.6 + - - +
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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