Contacts of the helix formed by residues 368 - 379 (chain A) in PDB entry 2R8K
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 ALA 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A ALA* 5.6 0.2 - - - +
343A LYS* 3.6 33.5 - - + +
365A LEU 5.6 1.1 - - - +
366A LYS* 3.1 2.6 - - - -
367A THR* 1.3 80.4 - - + +
369A ASP* 1.3 70.7 + - - +
371A ALA* 3.1 14.5 - - - +
372A GLU* 3.2 11.6 + - - +
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Residues in contact with ASP 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 LYS* 2.9 51.9 + - - +
368A ALA* 1.3 77.8 - - - +
370A LEU* 1.3 56.5 + - - +
371A ALA 2.7 14.9 + - - -
372A GLU* 3.2 5.9 + - - +
373A LYS* 2.9 28.7 + - + +
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Residues in contact with LEU 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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308A LEU* 5.1 6.7 - - + -
312A LEU* 5.1 9.4 - - + -
316A LEU* 4.0 15.7 - - + -
346A LEU* 4.4 21.1 - - + -
362A ILE* 3.5 46.9 - - + -
363A ASP 6.1 0.2 - - - +
366A LYS 4.0 9.8 + - - +
367A THR* 4.9 2.9 - - - +
368A ALA 3.6 0.2 - - - -
369A ASP* 1.3 78.1 - - - +
371A ALA* 1.3 64.4 + - - +
373A LYS* 3.6 14.8 - - + +
374A LEU* 3.4 39.0 + - + +
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Residues in contact with ALA 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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339A ALA* 4.1 19.5 - - + +
342A LEU* 4.1 16.6 - - + +
343A LYS* 4.2 14.6 - - + -
346A LEU* 4.3 2.7 - - + -
367A THR 3.6 15.3 + - - +
368A ALA* 3.1 15.5 + - - +
369A ASP 2.7 4.9 + - - -
370A LEU* 1.3 71.0 - - - +
372A GLU* 1.3 67.0 + - - +
373A LYS 2.7 5.0 + - - -
374A LEU* 3.0 14.7 + - - +
375A PHE* 3.1 12.2 + - - +
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Residues in contact with GLU 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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339A ALA* 3.7 26.1 - - + +
368A ALA 3.2 10.2 + - - +
369A ASP* 3.2 4.6 + - - +
371A ALA* 1.3 79.0 - - - +
373A LYS* 1.3 52.3 + - - +
375A PHE* 3.7 2.2 - - + +
376A LYS* 2.7 78.2 + - + +
382A TYR* 5.9 2.9 - - + -
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Residues in contact with LYS 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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307A THR* 5.3 13.1 + - - -
308A LEU* 5.8 7.2 - - + -
312A LEU* 6.3 1.2 - - - +
369A ASP* 2.9 21.6 + - + +
370A LEU* 3.6 18.2 - - + +
371A ALA 2.7 4.8 + - - -
372A GLU* 1.3 74.5 - - - +
374A LEU* 1.3 55.4 + - + +
376A LYS* 3.5 1.4 - - - +
377A LEU* 2.8 47.7 + - + +
382A TYR* 3.0 52.6 - - + +
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Residues in contact with LEU 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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302A ILE* 3.8 17.7 - - + -
308A LEU* 3.7 31.9 - - + -
316A LEU* 3.8 33.7 - - + -
320A LEU* 4.5 20.0 - - + -
322A LEU* 6.3 0.4 - - + -
331A ILE* 4.2 18.6 - - + +
342A LEU* 4.7 11.2 - - + -
346A LEU* 5.7 1.1 - - + -
370A LEU* 3.5 23.6 - - + +
371A ALA 3.0 5.1 + - - +
373A LYS* 1.3 78.5 - - + +
375A PHE* 1.3 57.5 + - - +
377A LEU* 3.9 3.8 - - + +
378A SER* 2.9 33.5 + - - -
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Residues in contact with PHE 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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331A ILE* 5.0 6.5 - - - +
335A TRP* 3.3 22.0 - - + -
336A PRO 5.5 0.2 - - - -
337A ASP 4.6 2.9 - - - -
338A ASN* 3.7 21.5 - - + +
339A ALA* 3.6 31.9 - - + -
342A LEU* 5.1 8.0 - - + +
371A ALA 3.1 14.9 + - - +
372A GLU* 3.7 7.2 - - + +
374A LEU* 1.3 76.7 - - - +
376A LYS* 1.3 72.3 + - + +
378A SER* 2.6 22.3 + - - -
379A ARG* 2.8 57.5 - - - +
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Residues in contact with LYS 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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372A GLU* 2.7 66.1 + - + +
373A LYS 3.5 2.5 - - - +
375A PHE* 1.3 82.5 - - + +
377A LEU* 1.3 67.9 + - - +
379A ARG* 2.9 17.3 + - - +
380A GLY 2.9 9.0 + - - -
381A ARG* 3.2 34.9 + - + +
382A TYR* 3.9 23.5 - - + -
383A GLY 5.8 0.6 - - - +
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Residues in contact with LEU 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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269A ASN* 3.9 28.5 - - + +
270A VAL* 6.5 0.2 - - + -
295A LEU* 3.5 9.2 - - - +
302A ILE* 5.5 0.9 - - + -
305A PHE* 3.6 36.5 - - + -
306A TRP 5.9 0.9 - - - +
308A LEU* 3.6 32.1 - - + -
373A LYS* 2.8 35.2 + - + +
374A LEU* 3.9 6.3 - - + +
376A LYS* 1.3 71.2 - - - +
378A SER* 1.3 57.4 + - - +
380A GLY* 2.7 27.2 + - - +
382A TYR* 3.7 27.8 - - + +
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Residues in contact with SER 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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295A LEU* 3.6 8.1 - - - +
305A PHE* 4.6 0.9 - - - -
328A ILE* 3.9 32.2 - - - +
331A ILE* 4.2 13.5 + - - -
332A ARG* 3.5 38.7 + - - +
374A LEU 2.9 15.5 + - - -
375A PHE* 2.6 26.3 + - - -
377A LEU* 1.3 76.2 - - - +
379A ARG* 1.3 64.2 + - - +
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Residues in contact with ARG 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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291A LEU* 3.9 14.9 - - - +
292A LEU* 3.8 22.3 - - + +
295A LEU* 4.2 2.2 - - - -
332A ARG* 2.8 49.0 + - + +
335A TRP 3.3 13.3 + - - -
336A PRO* 3.8 9.5 - - - +
375A PHE* 2.8 53.8 - - - +
376A LYS* 2.9 8.5 + - - +
378A SER* 1.3 84.9 - - - +
380A GLY* 1.3 62.4 + - - +
381A ARG* 4.2 18.4 + - + +
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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