Contacts of the helix formed by residues 358 - 378 (chain A) in PDB entry 1KYO
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 THR 358 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A LYS* 4.9 7.0 + - - -
352A ARG* 4.6 4.5 - - - +
356A SER 3.7 12.8 - - - +
357A VAL* 1.3 73.9 - - - +
359A ASP* 1.3 62.4 + - - +
360A THR* 4.3 11.4 + - - +
361A GLU* 2.9 55.2 + - - +
362A VAL* 3.1 14.6 + - - +
414A VAL* 4.2 3.8 - - - -
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Residues in contact with ASP 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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358A THR* 1.3 72.7 - - - +
360A THR* 1.3 60.6 + - + +
362A VAL* 2.9 6.8 + - - +
363A GLU* 2.8 35.8 + - + +
414A VAL* 3.7 23.9 - - - +
125R VAL* 4.4 11.7 - - + +
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Residues in contact with THR 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A THR* 3.3 9.5 + - - +
359A ASP* 1.3 77.7 - - + +
361A GLU* 1.3 61.3 + - - +
363A GLU* 4.1 3.1 - - - -
364A ARG* 3.4 21.1 + - - +
73B LEU* 4.5 6.7 - - - +
121R ASP 6.1 0.5 - - - -
122R ASN* 5.3 3.5 - - - +
123R ILE* 3.2 33.1 + - - +
124R GLU* 4.1 13.2 - - + -
125R VAL* 3.8 22.8 - - + +
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Residues in contact with GLU 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ILE* 4.1 23.9 - - + +
300A LYS* 3.5 27.1 + - + +
349A GLN* 4.8 1.4 + - - -
352A ARG* 3.0 39.3 + - - -
357A VAL* 3.6 14.4 - - + +
358A THR* 2.9 43.7 + - - +
360A THR* 1.3 79.0 - - - +
362A VAL* 1.3 61.1 + - - +
364A ARG* 3.7 7.9 + - - +
365A ALA* 3.1 25.5 + - - +
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Residues in contact with VAL 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 4.0 15.9 - - + -
283A ILE* 4.8 4.0 - - + -
357A VAL* 4.4 14.1 - - + -
358A THR 3.3 13.9 - - - +
359A ASP* 3.3 7.4 - - - +
361A GLU* 1.3 74.9 - - - +
363A GLU* 1.3 63.7 + - - +
365A ALA* 2.9 9.2 + - - +
366A LYS* 2.8 50.4 + - - +
412A ILE 4.3 7.2 - - - +
413A THR* 4.8 4.9 - - - -
414A VAL* 3.7 19.5 - - + -
417A VAL* 4.4 17.5 - - + -
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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
----------------------------------------------------------
359A ASP* 2.8 24.6 + - + +
360A THR* 4.5 2.9 - - - -
362A VAL* 1.3 74.9 - - - +
364A ARG* 1.3 62.0 + - - +
366A LYS* 3.2 35.9 + - - +
367A SER* 3.2 27.2 + - - -
73B LEU* 4.6 9.4 - - + -
125R VAL* 3.7 28.7 - - + -
127R LYS* 3.6 33.2 + - + +
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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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282A GLN 3.4 22.8 + - - -
283A ILE* 4.0 5.7 + - - +
285A GLY* 5.0 1.6 - - - +
297A GLN* 4.3 4.8 + - - -
298A GLY* 3.6 26.3 + - - +
299A ILE* 3.5 24.7 - - - +
360A THR 3.4 19.3 + - - +
361A GLU* 3.7 7.1 + - - +
362A VAL 3.2 0.4 - - - -
363A GLU* 1.3 76.2 - - - +
365A ALA* 1.3 66.9 + - - +
367A SER* 3.2 6.2 + - - -
368A LEU* 2.9 45.1 + - + +
69B ARG* 6.3 0.2 - - - +
72B GLU* 2.8 67.3 + - + +
73B LEU* 4.1 20.1 - - + +
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Residues in contact with ALA 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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279A LEU* 3.5 35.4 - - + +
282A GLN* 3.7 13.0 - - + +
283A ILE* 3.8 14.6 - - + +
361A GLU 3.1 12.5 + - - +
362A VAL 2.9 10.2 + - - +
364A ARG* 1.3 80.1 - - - +
366A LYS* 1.3 51.7 - - - +
368A LEU* 3.2 2.1 + - - -
369A LEU* 2.7 37.4 + - - +
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Residues in contact with LYS 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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279A LEU* 3.6 16.4 - - + -
362A VAL* 2.8 27.1 + - + +
363A GLU* 3.2 42.5 + - - +
365A ALA* 1.3 69.9 - - - +
367A SER* 1.3 66.9 + - - +
369A LEU* 2.8 4.2 + - - +
370A LYS* 2.8 29.9 + - - +
409A ILE* 3.4 30.7 - - + +
410A ASP* 3.0 32.8 + - - +
412A ILE* 2.8 31.3 + - - -
413A THR* 5.7 1.0 - - - +
127R LYS* 4.6 6.5 - - - +
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Residues in contact with SER 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 GLU 3.2 12.1 + - - -
364A ARG 3.6 4.5 - - - -
366A LYS* 1.3 77.4 - - - +
368A LEU* 1.3 61.0 + - - +
370A LYS* 3.6 17.3 + - - +
371A LEU* 3.2 22.5 + - - +
72B GLU 3.4 20.6 - - - -
73B LEU 2.8 20.7 + - - -
74B LEU 3.9 4.4 + - - -
75B GLY* 3.6 17.2 - - - -
94B LEU* 4.5 1.3 - - - +
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Residues in contact with LEU 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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282A GLN* 3.5 23.2 - - + +
297A GLN* 5.2 2.9 - - - +
364A ARG* 2.9 62.7 + - + +
365A ALA 3.9 2.5 - - - +
367A SER* 1.3 72.6 - - - +
369A LEU* 1.3 60.7 + - - +
371A LEU* 3.5 12.5 + - + +
372A GLN* 3.0 29.1 + - - +
72B GLU* 3.4 39.3 - - + +
75B GLY* 4.4 7.4 - - - -
76B GLY 4.6 6.1 - - - +
77B THR* 5.5 3.8 - - + -
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Residues in contact with LEU 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A PHE* 4.4 8.1 - - + +
278A LYS* 4.5 19.1 - - + +
279A LEU* 4.0 38.6 - - + +
282A GLN* 4.0 12.3 - - + +
365A ALA 2.7 22.6 + - - +
366A LYS* 2.8 6.2 + - - +
368A LEU* 1.3 68.5 - - - +
370A LYS* 1.3 59.5 + - - +
371A LEU 3.1 0.7 - - - -
372A GLN* 4.5 10.8 - - + +
373A LEU* 2.8 61.4 + - + +
409A ILE* 3.5 25.8 - - + -
412A ILE* 5.9 0.2 - - + -
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Residues in contact with LYS 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 LYS* 2.8 20.3 + - - +
367A SER* 3.8 19.6 + - - +
369A LEU* 1.3 71.4 - - - +
371A LEU* 1.3 57.7 + - - +
373A LEU* 4.5 0.9 - - - -
374A GLY* 3.0 22.7 + - - -
406A PHE* 3.2 59.7 - - + -
409A ILE* 4.0 15.3 - - + -
410A ASP* 3.0 39.6 + - - +
28B ILE* 4.2 0.9 - - - +
74B LEU 5.9 0.2 - - - -
94B LEU* 4.1 22.4 - - + +
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Residues in contact with LEU 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 SER 3.2 17.1 + - - +
368A LEU* 3.6 13.5 - - + +
369A LEU 3.1 0.8 - - - -
370A LYS* 1.3 76.2 - - - +
372A GLN* 1.3 60.2 + - + +
374A GLY* 3.2 2.4 + - - -
375A GLN* 3.0 37.4 + - - +
28B ILE* 3.9 10.7 - - + +
75B GLY 3.9 17.0 - - - +
76B GLY* 3.8 15.3 - - - +
77B THR* 3.6 31.9 - - + +
92B THR* 4.0 31.0 - - + +
93B PHE* 4.2 5.8 - - - -
94B LEU* 4.2 7.4 - - + +
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Residues in contact with GLN 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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278A LYS* 5.3 9.3 - - - +
282A GLN* 4.3 23.5 - - - +
368A LEU 3.0 16.1 + - - +
369A LEU* 4.1 11.7 - - + +
371A LEU* 1.3 79.0 - - + +
373A LEU* 1.3 72.2 + - - +
375A GLN* 3.5 17.4 + - - +
376A LEU* 3.4 25.6 + - - +
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Residues in contact with LEU 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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274A TYR* 6.3 1.3 - - + -
275A PHE* 4.2 19.5 - - + -
278A LYS* 4.8 15.5 - - + +
369A LEU* 2.8 29.1 + - + +
370A LYS 4.0 2.5 - - - +
372A GLN* 1.3 82.8 - - - +
374A GLY* 1.3 63.4 + - - +
376A LEU* 3.3 12.1 + - + +
377A TYR* 3.3 44.9 + - + +
402A LEU* 4.4 11.4 - - + -
405A ALA* 4.2 14.4 - - + -
406A PHE* 4.6 2.9 - - + -
409A ILE* 3.7 29.4 - - + -
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Residues in contact with GLY 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 LYS 3.0 19.1 + - - -
371A LEU 3.2 1.8 + - - -
373A LEU* 1.3 74.4 - - - +
375A GLN* 1.3 57.3 + - - +
376A LEU 3.0 10.3 + - - -
377A TYR 3.5 0.2 + - - -
378A GLU* 3.0 28.2 + - - +
402A LEU* 4.1 17.9 - - - +
28B ILE* 3.6 19.3 - - - -
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Residues in contact with GLN 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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371A LEU* 3.0 35.8 + - - +
372A GLN* 3.5 15.4 + - - +
373A LEU 3.4 0.4 - - - -
374A GLY* 1.3 73.7 - - - +
376A LEU* 1.3 59.4 + - - +
378A GLU 4.4 6.1 - - - -
379A SER* 3.9 17.0 + - - -
28B ILE* 4.4 8.3 - - + -
77B THR* 5.3 3.9 + - - +
92B THR* 4.0 34.6 + - + +
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Residues in contact with LEU 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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278A LYS* 6.1 2.9 - - - +
372A GLN* 3.4 14.8 + - - +
373A LEU* 3.3 17.2 + - + +
374A GLY 3.0 1.8 + - - -
375A GLN* 1.3 78.9 - - - +
377A TYR* 1.3 83.3 + - + +
378A GLU 3.1 2.3 + - - -
379A SER* 3.8 11.4 + - - -
384A ASN* 5.3 12.6 - - + +
385A ASP* 5.1 1.4 - - - +
388A LEU* 3.8 30.2 - - + +
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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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41A GLU* 4.9 1.2 - - - +
274A TYR* 5.0 11.4 + - - -
275A PHE* 5.8 4.1 - + - -
373A LEU* 3.3 31.9 + - + +
374A GLY 4.5 0.4 - - - +
376A LEU* 1.3 92.6 - - + +
378A GLU* 1.3 59.3 + - - +
379A SER 3.9 0.4 - - - -
385A ASP* 2.8 22.7 - - - +
388A LEU* 3.6 32.0 - - + +
392A GLU* 3.6 21.0 + - - -
399A LYS* 4.4 21.8 + - - +
400A LEU* 4.1 19.1 - - + -
402A LEU* 4.0 35.4 - - + -
405A ALA* 5.6 3.4 - - + -
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Residues in contact with GLU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLY 3.0 22.8 + - - +
375A GLN* 4.4 5.6 - - - +
376A LEU 4.2 0.7 - - - -
377A TYR* 1.3 80.3 - - - +
379A SER* 1.3 60.9 + - - +
385A ASP* 4.5 1.6 - - - -
402A LEU* 3.1 27.2 - - + +
26B THR* 3.0 36.1 + - + +
27B LYS* 3.1 16.9 + - - +
28B ILE* 3.3 25.5 + - + +
191B ASN* 5.1 0.3 + - - -
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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
------------------------------------------------------------
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