Contacts of the helix formed by residues 355 - 369 (chain A) in PDB entry 1K6O
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 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A GLU* 3.7 15.0 - - - +
342A ALA* 3.4 14.6 - - - -
353A ASN 3.8 12.9 + - - -
354A MET* 1.3 81.4 - - - +
356A TYR* 1.3 63.2 + - - +
357A ASP* 2.9 24.9 + - - +
358A LYS* 3.0 28.7 + - - +
359A LEU* 3.0 18.7 + - - +
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Residues in contact with TYR 356 (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* 3.7 26.9 - - + -
338A ALA* 3.7 24.0 - - + -
339A GLU* 3.3 27.9 + - + +
342A ALA* 3.4 8.6 - - - +
355A ASN* 1.3 75.1 - - - +
357A ASP* 1.3 58.4 + - - +
358A LYS 3.0 0.2 - - - -
359A LEU* 4.1 9.0 - - + -
360A SER* 2.9 52.5 + - - -
380A PHE* 3.6 24.6 - + - -
382A TYR* 2.6 34.1 + + - -
102D A 4.8 6.7 - - + -
103D C 2.9 27.6 + + - -
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Residues in contact with ASP 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLU* 4.6 1.8 + - - +
355A ASN* 2.9 13.8 + - - +
356A TYR* 1.3 81.1 - - - +
358A LYS* 1.3 60.4 + - + +
360A SER* 3.7 11.3 + - - -
361A ARG* 4.2 8.7 - - - +
364A ARG* 4.6 5.5 + - - +
103D C 6.4 2.9 - - + +
217E T 5.4 0.2 - - - +
218E C 5.5 3.1 + - - -
219E C 5.4 5.9 + - - -
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Residues in contact with LYS 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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353A ASN* 3.1 30.8 + - - +
354A MET* 3.3 20.0 - - + +
355A ASN* 3.0 27.1 + - - +
357A ASP* 1.3 80.3 - - + +
359A LEU* 1.3 64.4 + - - +
360A SER 3.3 1.3 - - - -
361A ARG* 3.2 16.6 + - - +
362A ALA* 3.4 6.8 + - - +
216E A 4.5 3.8 + - + -
217E T 3.2 75.0 + - + +
218E C 3.8 20.1 + - + -
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Residues in contact with LEU 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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307A LEU* 3.8 28.3 - - + -
311A LEU* 5.1 2.5 - - + -
335A LEU* 4.8 12.8 - - + -
338A ALA 5.1 0.2 - - - +
341A VAL* 4.2 15.5 - - + -
342A ALA* 3.7 32.5 - - + +
345A TRP* 4.3 15.5 - - + -
354A MET* 4.0 11.2 - - - -
355A ASN 3.0 15.1 + - - +
356A TYR* 4.0 8.5 - - + +
358A LYS* 1.3 74.6 - - - +
360A SER* 1.3 67.4 + - - +
362A ALA* 3.0 18.0 + - - +
363A LEU* 3.1 25.8 + - + -
216E A 5.0 1.1 - - - -
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Residues in contact with SER 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 TYR* 2.9 45.9 + - - -
357A ASP* 3.7 7.6 + - - -
359A LEU* 1.3 78.7 - - - +
361A ARG* 1.3 53.3 + - - +
363A LEU* 2.8 14.9 + - - +
364A ARG* 2.6 58.9 + - - +
382A TYR* 4.0 8.5 - - - -
103D C 5.5 4.4 - - - -
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Residues in contact with ARG 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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357A ASP 4.2 8.3 - - - +
358A LYS 3.2 14.4 + - - +
359A LEU 3.1 0.2 - - - -
360A SER* 1.3 82.0 + - - +
362A ALA* 1.3 61.5 + - - +
364A ARG* 2.8 42.9 + - - +
365A TYR* 3.0 67.6 + - + +
105D G 3.3 41.8 + - - +
106D G 2.6 43.7 + - - -
217E T 3.8 24.0 - - + +
218E C 4.3 2.9 - - - +
219E C 6.2 0.2 - - - +
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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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307A LEU* 3.6 19.3 - - + -
358A LYS 3.4 5.1 + - - +
359A LEU 3.0 13.1 + - - +
361A ARG* 1.3 78.5 - - - +
363A LEU* 1.3 63.8 + - - +
365A TYR* 3.2 14.4 + - - +
366A TYR* 3.1 26.7 + - + -
215E C 4.0 33.9 - - + +
216E A 4.4 3.8 - - + +
217E T 5.8 0.2 - - - +
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Residues in contact with LEU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU* 3.9 15.0 - - + -
311A LEU* 4.0 21.1 - - + -
333A PHE* 5.2 0.2 - - + -
335A LEU* 5.0 4.3 - - + -
356A TYR* 5.2 0.2 - - + -
359A LEU* 3.1 27.6 + - + +
360A SER* 2.8 15.3 + - - +
362A ALA* 1.3 78.0 - - - +
364A ARG* 1.3 59.7 + - - -
366A TYR* 2.9 34.8 + - + +
367A TYR* 2.9 17.8 - - + -
372A ILE* 4.0 12.6 - - + +
382A TYR* 3.2 52.9 - - + +
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Residues in contact with ARG 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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357A ASP* 4.6 6.1 + - - +
360A SER* 2.6 35.8 + - - +
361A ARG* 2.8 66.3 - - - +
363A LEU* 1.3 73.4 - - - +
365A TYR* 1.3 57.5 + - - +
367A TYR* 2.9 46.2 - - + +
368A VAL* 4.0 1.6 + - - +
382A TYR* 5.7 0.7 - - - +
103D C 4.0 16.0 - - - +
104D A 3.1 72.7 + - - +
105D G 3.4 21.3 + - + +
219E C 5.3 0.4 - - - +
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Residues in contact with TYR 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 ARG* 3.0 66.9 + - + -
362A ALA* 3.2 12.3 + - - +
364A ARG* 1.3 76.1 - - - +
366A TYR* 1.3 62.7 + - + +
367A TYR 3.1 1.0 + - - -
368A VAL* 3.3 23.8 - - + +
369A LYS* 3.5 7.0 + - - +
155B LEU* 4.6 28.1 - - + +
106D G 4.2 0.5 + - - -
107D A 2.8 32.7 + - - -
108D T 4.3 2.1 + - - -
215E C 5.0 16.8 - + - -
216E A 3.7 20.7 + - - -
217E T 4.6 0.2 - - - -
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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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307A LEU* 3.3 26.3 - - + +
308A TRP* 3.3 31.6 + + + -
362A ALA 3.1 21.2 + - - -
363A LEU* 2.9 26.3 + - + +
365A TYR* 1.3 74.6 - - + +
367A TYR* 1.3 66.4 + - - +
369A LYS* 3.2 7.8 + - + -
370A ASN 3.2 14.6 + - - -
371A ILE* 3.2 42.8 + - + -
372A ILE* 3.7 21.9 + - + +
215E C 2.6 45.2 + - - -
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Residues in contact with TYR 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 LEU* 2.9 31.0 - - + -
364A ARG* 2.9 31.9 + - + +
366A TYR* 1.3 80.5 - - - +
368A VAL* 1.3 61.0 + - + +
370A ASN* 3.1 13.2 + - - +
371A ILE 4.5 0.2 + - - -
372A ILE 3.1 19.6 - - - +
373A LYS* 4.3 22.7 - - + +
374A LYS* 3.3 23.3 - - + +
382A TYR* 3.3 20.3 + + - -
104D A 2.6 46.1 + - - -
105D G 4.1 17.9 - - - +
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Residues in contact with VAL 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 ARG 5.0 0.9 - - - +
365A TYR* 3.3 16.2 - - + +
367A TYR* 1.3 75.4 - - + +
369A LYS* 1.3 60.1 + - - +
370A ASN* 3.0 12.5 + - - +
153B ASN* 6.2 2.2 - - - +
155B LEU* 4.0 28.9 - - + -
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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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365A TYR 3.5 10.1 + - - +
366A TYR* 3.2 14.8 + - + +
367A TYR 3.2 1.2 - - - -
368A VAL* 1.3 79.6 - - + +
370A ASN* 1.3 69.8 + - - +
371A ILE* 3.4 19.3 + - + +
155B LEU* 5.9 3.6 - - + -
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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