Contacts of the helix formed by residues 358 - 378 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300L LYS* 4.7 9.6 - - - -
352L ARG* 3.9 7.0 - - - +
356L SER 3.8 9.9 - - - +
357L VAL* 1.3 76.2 - - - +
359L ASP* 1.3 62.3 + - - +
360L THR* 3.8 9.1 + - - -
361L GLU* 3.0 46.3 + - - +
362L VAL* 3.5 15.2 + - - +
414L VAL* 4.1 1.8 - - - -
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Residues in contact with ASP 359 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G VAL* 4.4 16.7 - - + +
127G LYS* 4.9 6.8 - - - -
358L THR* 1.3 73.7 - - - +
360L THR* 1.3 65.0 + - + +
362L VAL* 3.3 5.0 + - - +
363L GLU* 3.0 33.6 + - - +
414L VAL* 3.6 23.2 - - - +
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Residues in contact with THR 360 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G ASP 5.4 3.3 + - - -
122G ASN 5.3 1.1 - - - +
123G ILE* 2.9 34.7 + - - +
124G GLU* 3.8 14.4 - - - -
125G VAL* 4.0 20.4 - - + +
358L THR* 3.4 8.6 + - - +
359L ASP* 1.3 77.6 - - + +
361L GLU* 1.3 62.7 + - - +
363L GLU* 3.8 7.2 - - - +
364L ARG* 2.9 31.0 + - - +
73M LEU* 4.6 6.8 - - - +
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Residues in contact with GLU 361 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283L ILE* 4.0 27.7 - - + +
284L PHE* 5.4 0.5 - - - -
298L GLY 5.6 5.2 - - - +
299L ILE* 6.0 0.2 - - - -
300L LYS* 3.6 24.2 + - + +
349L GLN* 4.9 0.5 + - - -
352L ARG* 2.8 45.9 + - - -
357L VAL* 3.8 13.8 - - + +
358L THR* 3.0 33.0 + - - +
359L ASP 3.2 0.2 - - - -
360L THR* 1.3 80.2 + - - +
362L VAL* 1.3 62.4 + - - +
364L ARG* 3.8 8.2 - - - +
365L ALA* 3.2 22.0 + - - +
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Residues in contact with VAL 362 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279L LEU* 4.2 13.7 - - + -
283L ILE* 4.9 2.7 - - + -
357L VAL* 4.3 12.3 - - + -
358L THR 3.7 12.8 - - - +
359L ASP* 3.3 9.6 + - - +
360L THR 3.2 0.4 - - - -
361L GLU* 1.3 77.3 - - - +
363L GLU* 1.3 67.0 + - - +
365L ALA* 3.2 9.6 + - - +
366L LYS* 3.1 40.4 + - - +
412L ILE 4.3 8.5 - - - +
413L THR* 4.6 2.0 - - - -
414L VAL* 3.8 32.3 - - + +
417L VAL* 4.1 15.3 - - + -
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Residues in contact with GLU 363 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G VAL* 3.8 31.0 - - + -
127G LYS* 3.7 29.5 + - + +
359L ASP* 3.0 23.7 + - - +
360L THR* 3.3 8.5 + - - +
362L VAL* 1.3 75.8 - - - +
364L ARG* 1.3 64.9 + - - +
366L LYS* 3.2 48.9 + - - +
367L SER* 3.3 17.5 + - - -
410L ASP* 5.6 0.3 - - - +
73M LEU* 4.6 5.6 - - + -
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Residues in contact with ARG 364 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282L GLN* 3.2 26.5 + - - -
283L ILE* 3.8 12.7 + - - +
285L GLY* 5.0 1.6 - - - +
297L GLN* 4.1 6.1 + - - -
298L GLY* 3.6 28.3 + - - +
299L ILE* 3.9 20.6 - - - +
360L THR 2.9 18.3 + - - +
361L GLU* 3.8 6.7 + - - +
363L GLU* 1.3 76.3 - - - +
365L ALA* 1.3 64.4 + - - +
367L SER* 3.5 3.4 + - - -
368L LEU* 3.1 43.0 + - + +
72M GLU* 2.5 66.1 + - + +
73M LEU* 4.2 21.9 - - + +
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Residues in contact with ALA 365 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279L LEU* 3.6 36.6 - - + +
282L GLN* 3.8 12.3 - - + +
283L ILE* 3.8 13.5 - - + +
361L GLU 3.2 11.2 + - - +
362L VAL 3.2 10.5 + - - +
363L GLU 3.2 0.4 - - - -
364L ARG* 1.3 80.8 - - - +
366L LYS* 1.3 51.6 - - - +
368L LEU* 3.2 2.2 + - - -
369L LEU* 2.6 38.2 + - - +
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Residues in contact with LYS 366 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G LYS* 4.8 6.3 - - - +
279L LEU* 3.5 17.0 - - + +
362L VAL* 3.1 18.7 + - - +
363L GLU* 3.2 38.4 + - - +
365L ALA* 1.3 75.6 - - - +
367L SER* 1.3 55.9 + - - +
369L LEU* 3.0 1.1 + - - +
370L LYS* 2.8 42.2 + - - +
409L ILE* 3.3 30.1 - - + +
410L ASP* 2.9 39.6 + - - +
412L ILE* 3.0 26.4 + - - -
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Residues in contact with SER 367 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363L GLU* 3.3 11.0 + - - -
364L ARG 3.8 3.1 - - - -
366L LYS* 1.3 77.3 - - - +
368L LEU* 1.3 57.9 + - - +
370L LYS* 3.7 11.3 + - - +
371L LEU* 3.0 27.5 + - - +
72M GLU 3.2 21.8 - - - -
73M LEU* 2.7 22.4 + - - -
74M LEU 4.2 1.5 - - - -
75M GLY* 3.6 18.2 - - - -
94M LEU* 5.0 4.0 - - - +
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Residues in contact with LEU 368 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282L GLN* 3.9 19.6 - - + +
297L GLN* 5.3 2.0 - - - +
364L ARG* 3.1 57.0 + - - +
365L ALA* 3.9 2.2 - - - +
367L SER* 1.3 75.5 - - - +
369L LEU* 1.3 63.6 + - - +
371L LEU* 3.8 25.9 - - + +
372L GLN* 3.1 26.9 + - - +
72M GLU* 4.0 32.8 - - + +
76M GLY 4.5 4.9 - - - +
77M THR* 4.6 9.2 - - + -
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Residues in contact with LEU 369 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275L PHE* 4.5 7.0 - - + +
278L LYS* 4.3 17.9 - - + +
279L LEU* 3.8 43.1 - - + +
282L GLN* 3.8 9.2 - - + +
365L ALA 2.6 21.1 + - - +
366L LYS* 3.4 4.3 - - - +
368L LEU* 1.3 69.9 - - - +
370L LYS* 1.3 58.5 + - - +
371L LEU 3.2 0.2 + - - -
372L GLN* 3.2 20.3 + - - +
373L LEU* 2.7 51.0 + - + +
409L ILE* 3.6 33.0 - - + -
412L ILE* 5.6 0.2 - - + -
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Residues in contact with LYS 370 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366L LYS* 2.8 22.6 + - - +
367L SER* 3.7 7.6 - - - +
369L LEU* 1.3 77.0 - - - +
371L LEU* 1.3 56.8 + - - +
373L LEU* 3.6 2.9 - - - +
374L GLY* 2.8 28.4 + - - -
406L PHE* 3.9 55.5 - - + +
409L ILE* 4.2 15.7 - - + +
410L ASP* 2.7 46.0 + - - -
28M ILE* 4.6 0.9 - - - +
94M LEU* 4.6 20.5 - - + +
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Residues in contact with LEU 371 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367L SER 3.0 16.7 + - - +
368L LEU* 3.8 15.3 - - + +
369L LEU 3.1 0.2 - - - -
370L LYS* 1.3 83.0 - - - +
372L GLN* 1.3 66.1 + - + +
374L GLY* 3.1 7.6 + - - -
375L GLN* 3.1 25.5 + - - +
28M ILE* 3.9 23.4 - - + +
75M GLY 4.4 2.5 - - - -
76M GLY* 3.9 18.6 - - - +
77M THR* 3.4 34.3 - - + +
92M THR* 3.8 29.4 - - + +
93M PHE* 4.1 6.3 - - - -
94M LEU* 4.8 3.1 - - + +
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Residues in contact with GLN 372 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278L LYS* 5.2 13.7 + - - +
282L GLN* 3.4 26.3 - - - +
368L LEU 3.1 20.2 + - - +
369L LEU* 3.4 20.9 - - - +
371L LEU* 1.3 81.5 - - + +
373L LEU* 1.3 67.8 + - - +
375L GLN* 3.7 14.3 + - - +
376L LEU* 3.3 24.5 + - - +
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Residues in contact with LEU 373 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274L TYR* 6.3 0.9 - - + -
275L PHE* 4.2 11.9 - - + -
278L LYS* 5.1 13.2 - - + +
369L LEU* 2.7 33.8 + - + +
370L LYS* 3.6 3.6 - - - +
372L GLN* 1.3 77.6 - - - +
374L GLY* 1.3 63.5 + - - +
376L LEU* 3.2 28.4 + - + +
377L TYR* 3.2 30.8 + - + +
402L LEU* 4.3 13.5 - - + -
405L ALA* 4.2 18.6 - - + -
406L PHE* 4.5 2.2 - - + -
409L ILE* 3.5 30.5 - - + -
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Residues in contact with GLY 374 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370L LYS 2.8 16.1 + - - -
371L LEU 3.6 1.6 - - - -
373L LEU* 1.3 72.7 - - - +
375L GLN* 1.3 54.3 + - - +
376L LEU 2.9 4.6 + - - -
377L TYR 3.1 0.7 + - - -
378L GLU* 2.6 36.4 + - - +
402L LEU* 3.9 20.6 - - - +
406L PHE* 4.8 1.3 - - - -
28M ILE* 3.8 19.1 - - - -
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Residues in contact with GLN 375 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371L LEU* 3.1 30.1 + - - +
372L GLN* 4.0 11.7 - - - +
373L LEU 3.4 0.2 - - - -
374L GLY* 1.3 74.4 - - - +
376L LEU* 1.3 60.5 + - - +
378L GLU 3.8 18.4 - - - +
379L SER* 4.1 7.8 - - - -
28M ILE* 4.0 8.8 - - + +
77M THR* 5.4 2.5 + - - +
92M THR* 3.6 38.2 + - + +
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Residues in contact with LEU 376 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278L LYS* 6.0 4.5 - - - +
372L GLN* 3.3 15.4 + - - +
373L LEU* 3.2 22.0 + - + +
374L GLY 2.9 0.8 + - - -
375L GLN* 1.3 79.6 - - - +
377L TYR* 1.3 77.0 + - + +
379L SER* 4.1 9.0 - - - -
384L ASN* 5.1 5.5 - - + +
385L ASP* 4.8 0.7 - - - +
388L LEU* 3.5 33.1 - - + +
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Residues in contact with TYR 377 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274L TYR* 5.4 6.4 + - - -
275L PHE* 5.9 4.0 - - - -
373L LEU* 3.2 26.2 + - + +
374L GLY 3.1 3.9 + - - +
376L LEU* 1.3 88.6 - - + +
378L GLU* 1.3 59.6 + - + +
379L SER 3.1 2.3 + - - -
385L ASP* 2.6 28.6 - - - +
388L LEU* 3.5 34.1 - - + +
392L GLU* 3.8 16.9 + - - +
399L LYS* 4.2 23.8 + - - +
400L LEU* 4.1 18.4 - - - +
402L LEU* 3.8 38.6 - - + -
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Residues in contact with GLU 378 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374L GLY 2.6 19.6 + - - +
375L GLN* 3.8 12.2 - - - +
377L TYR* 1.3 69.8 - - + +
379L SER* 1.3 59.0 + - - +
402L LEU* 3.1 29.0 - - + +
26M THR* 3.3 21.2 - - + -
27M LYS* 2.9 24.7 + - - +
28M ILE* 2.9 37.7 + - + +
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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
------------------------------------------------------------
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