Contacts of the helix formed by residues 368 - 382 (chain A) in PDB entry 6M0X
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 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A GLN 4.1 1.6 + - - -
367A MET* 1.3 78.5 - - - +
369A ARG* 1.3 64.0 + - - +
370A GLU* 3.6 28.8 + - - +
371A THR* 3.0 20.5 + - - +
372A LEU* 3.4 19.6 + - - +
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Residues in contact with ARG 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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273A TYR* 3.0 34.8 - - + -
274A THR* 3.1 21.2 + - - +
277A GLU* 2.3 35.6 + - - +
368A ASP* 1.3 74.6 - - - +
370A GLU* 1.3 57.5 + - + +
371A THR 2.9 4.3 - - - -
372A LEU* 2.7 26.4 + - - +
373A ASP* 2.8 27.7 + - - +
429A VAL* 5.2 2.2 - - - -
433A MET* 3.2 34.0 - - - +
436A ILE* 4.4 0.2 - - - +
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Residues in contact with GLU 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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368A ASP* 3.6 14.5 + - - +
369A ARG* 1.3 81.4 - - + +
371A THR* 1.3 61.1 + - - +
373A ASP* 4.3 8.0 - - - +
374A LYS* 3.2 37.4 + - - +
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Residues in contact with THR 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 MET* 3.6 28.5 - - + -
368A ASP* 3.0 30.3 + - - +
369A ARG 2.9 0.8 - - - -
370A GLU* 1.3 81.7 - - - +
372A LEU* 1.3 58.9 + - - +
374A LYS* 3.8 6.8 - - - +
375A LEU* 3.0 26.0 + - - +
396A PHE* 3.9 21.5 - - + -
401A PHE* 6.0 1.1 - - + -
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Residues in contact with LEU 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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271A ALA 5.1 0.8 - - - +
272A SER* 4.6 1.0 - - - -
273A TYR* 4.3 23.1 - - + +
276A GLN* 6.3 1.1 - - - +
353A TYR* 4.0 33.2 - - + -
356A MET* 3.8 34.3 - - + -
364A ILE* 4.3 21.3 - - + +
367A MET* 3.4 20.9 - - + +
368A ASP 3.4 15.1 + - - +
369A ARG* 2.7 10.7 + - - +
371A THR* 1.3 73.8 - - - +
373A ASP* 1.3 63.5 + - - +
375A LEU* 3.5 1.5 + - + -
376A ALA* 3.1 22.7 + - - +
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Residues in contact with ASP 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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269A ALA* 5.2 0.7 + - - +
272A SER* 3.9 16.2 - - - -
273A TYR* 2.8 29.5 + - - +
274A THR* 2.3 33.9 + - - -
369A ARG* 2.8 30.2 + - - +
370A GLU* 4.3 7.2 - - - +
372A LEU* 1.3 71.6 - - - +
374A LYS* 1.3 57.4 + - - +
376A ALA* 3.3 3.8 + - - +
377A TYR* 3.0 25.7 + - - +
429A VAL* 3.9 17.0 - - + +
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Residues in contact with LYS 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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370A GLU* 3.2 28.6 + - - +
371A THR* 3.9 3.8 - - - +
372A LEU 3.3 0.2 - - - -
373A ASP* 1.3 73.8 - - - +
375A LEU* 1.3 66.4 + - - +
377A TYR* 3.1 22.8 + - + +
378A VAL* 3.1 16.3 + - + +
395A GLU* 3.7 35.0 + - + +
396A PHE* 3.5 35.9 - - + +
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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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356A MET* 3.5 26.0 - - + -
359A LEU* 5.6 2.9 - - + -
362A LEU* 5.7 2.9 - - + -
367A MET* 3.8 25.8 - - + -
371A THR 3.0 17.8 + - - +
372A LEU* 3.7 8.1 - - + +
373A ASP 3.3 0.2 - - - -
374A LYS* 1.3 76.7 - - - +
376A ALA* 1.3 62.0 + - - +
378A VAL* 3.3 3.0 + - - +
379A LEU* 3.1 38.0 + - + +
392A LEU* 4.1 26.0 - - + -
396A PHE* 3.8 6.2 - - + -
401A PHE* 4.3 12.6 - - + -
409A LEU* 4.3 24.7 - - + -
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Residues in contact with ALA 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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269A ALA* 3.9 4.5 - - + -
271A ALA* 3.5 32.3 - - + +
272A SER* 3.5 21.5 - - - +
356A MET* 5.2 4.9 - - - +
372A LEU 3.1 12.0 + - - +
373A ASP 3.7 2.0 - - - +
374A LYS 3.2 0.2 - - - -
375A LEU* 1.3 73.8 - - - +
377A TYR* 1.3 63.6 + - - +
379A LEU* 4.4 5.8 - - - +
380A THR* 2.6 32.2 + - - -
420A PHE* 4.7 4.7 - - + -
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Residues in contact with TYR 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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253A GLY* 4.3 9.0 - - - -
256A ILE* 3.8 20.1 - - + +
266A PHE* 6.3 3.4 - + + -
267A ARG 5.6 2.5 - - - -
269A ALA* 4.2 2.2 - - + +
373A ASP 3.0 12.7 + - - +
374A LYS* 3.1 18.6 + - + +
376A ALA* 1.3 77.6 - - - +
378A VAL* 1.3 80.6 + - + +
381A LEU* 3.2 47.3 + - + +
382A ASN* 5.6 1.3 - - - -
391A ALA* 6.0 1.6 - - + -
395A GLU* 4.6 16.6 + - + -
424A TRP* 3.8 27.3 - + + -
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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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374A LYS* 3.1 12.8 + - + +
375A LEU 3.3 6.3 + - - +
377A TYR* 1.3 89.8 - - + +
379A LEU* 1.3 61.7 + - + +
382A ASN* 3.1 39.1 + - - +
388A ILE* 4.1 17.3 - - + +
391A ALA* 3.7 36.3 - - + +
392A LEU* 3.9 21.3 - - + -
395A GLU* 4.9 4.9 - - + -
396A PHE* 4.2 18.2 - - + -
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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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356A MET* 4.1 10.3 - - + -
375A LEU* 3.1 37.5 + - + +
376A ALA 4.4 0.2 - - - +
378A VAL* 1.3 77.4 - - + +
380A THR* 1.3 59.8 + - - +
382A ASN 4.2 1.3 - - - -
388A ILE* 4.2 23.3 - - + -
392A LEU* 5.8 0.2 - - + -
409A LEU* 4.4 24.9 - - + +
412A PHE* 4.8 4.9 - - + -
413A ARG* 2.7 54.9 + - + -
420A PHE* 3.2 39.6 - - + +
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Residues in contact with THR 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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269A ALA* 3.4 10.3 - - + +
271A ALA* 4.4 4.3 + - - +
376A ALA 2.6 25.4 + - - -
377A TYR 3.9 2.0 - - - -
379A LEU* 1.3 78.4 - - - +
381A LEU* 1.3 60.6 + - - +
383A THR* 5.2 0.5 - - - +
413A ARG* 3.2 17.8 + - - -
420A PHE* 3.3 31.5 + - - +
423A GLY* 3.4 29.1 + - - +
424A TRP* 3.7 24.0 + - + +
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Residues in contact with LEU 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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225A TYR* 4.6 3.1 + - - -
250A ASN* 3.7 31.5 + - + +
252A PHE* 3.9 14.4 - - + +
253A GLY* 3.7 38.6 - - - +
256A ILE* 4.3 8.7 - - + -
377A TYR* 3.2 36.5 + - + +
380A THR* 1.3 81.5 - - - +
382A ASN* 1.3 68.2 + - - +
383A THR* 4.0 7.2 + - - +
424A TRP* 3.8 15.0 - - + +
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Residues in contact with ASN 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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226A TYR* 4.8 2.8 - - + -
249A ASP* 5.1 1.2 - - - +
250A ASN* 3.3 24.1 + - - +
377A TYR* 5.6 1.0 - - - -
378A VAL* 3.1 27.0 + - - +
379A LEU 3.6 2.6 - - - +
381A LEU* 1.3 93.4 - - - +
383A THR* 1.3 62.4 + - - +
384A GLU 3.7 0.4 - - - +
387A GLY* 3.3 28.0 - - - +
388A ILE* 3.5 25.4 - - + +
391A ALA* 4.0 18.6 - - - +
413A ARG* 2.9 24.6 + - - -
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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