Contacts of the helix formed by residues 293 - 310 (chain M) 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 ASP 293 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237M SER* 5.0 0.2 - - - -
291M ASP* 3.5 4.8 + - - +
292M GLN* 1.3 80.7 - - + +
294M SER* 1.3 65.1 + - - +
295M ALA* 3.0 21.9 + - - +
296M VAL* 3.3 32.5 + - - +
297M VAL* 3.5 13.7 + - - +
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Residues in contact with SER 294 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237M SER* 4.5 5.1 + - - -
292M GLN 4.0 1.6 + - - -
293M ASP* 1.3 72.2 - - - +
295M ALA* 1.3 56.4 + - - +
297M VAL* 3.5 4.7 + - - -
298M SER* 2.9 33.5 + - - -
358M ASP* 3.0 39.1 + - - +
361M ASN* 3.4 26.8 + - - +
362M LEU* 3.4 15.5 - - - +
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Residues in contact with ALA 295 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293M ASP* 3.0 17.5 + - - +
294M SER* 1.3 76.8 + - - +
296M VAL* 1.3 62.0 + - + +
298M SER* 2.9 10.4 + - - -
299M SER* 2.9 30.5 + - - -
361M ASN 5.3 0.4 - - - -
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Residues in contact with VAL 296 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289M VAL* 6.2 0.4 - - + -
291M ASP* 3.6 26.9 - - + +
293M ASP* 3.3 24.9 + - - +
295M ALA* 1.3 76.7 - - + +
297M VAL* 1.3 61.3 + - - +
299M SER* 4.5 4.0 - - - +
300M ASN* 2.7 48.4 + - - +
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Residues in contact with VAL 297 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237M SER* 3.6 21.5 - - - +
239M ALA* 3.5 25.6 - - + +
289M VAL* 3.4 28.2 - - - +
291M ASP* 3.7 23.1 - - + +
293M ASP 3.5 14.4 - - - +
294M SER* 3.5 10.3 - - - +
295M ALA 3.1 0.4 - - - -
296M VAL* 1.3 77.8 - - - +
298M SER* 1.3 62.9 + - - +
301M ILE* 3.1 24.3 + - - +
362M LEU* 3.6 16.4 - - + -
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Residues in contact with SER 298 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294M SER 2.9 18.7 + - - -
295M ALA* 2.9 12.6 + - - -
297M VAL* 1.3 78.6 - - - +
299M SER* 1.3 61.6 + - - +
301M ILE* 3.4 2.2 - - - +
302M LYS* 3.1 35.4 + - - +
361M ASN 3.2 12.0 + - - -
362M LEU* 3.8 0.2 - - - +
363M PRO* 3.1 35.6 - - - +
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Residues in contact with SER 299 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295M ALA 2.9 16.0 + - - -
296M VAL* 3.9 3.5 - - - -
298M SER* 1.3 76.9 - - - +
300M ASN* 1.3 74.2 + - - +
301M ILE 3.1 0.3 + - - -
302M LYS* 3.8 4.3 - - - +
303M LYS* 3.1 26.4 + - - +
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Residues in contact with ASN 300 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269M GLY 4.4 2.8 + - - -
270M LEU* 3.3 59.7 + - + +
289M VAL* 3.9 10.1 - - + +
296M VAL* 2.7 35.1 + - - +
299M SER* 1.3 82.5 - - - +
301M ILE* 1.3 50.4 + - - +
303M LYS* 4.1 1.7 - - - +
304M ILE* 2.7 38.6 + - - +
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Residues in contact with ILE 301 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239M ALA* 4.2 28.5 - - + +
240M ALA* 5.2 0.2 - - - -
241M ILE* 4.4 15.7 - - + -
287M LEU* 4.2 17.3 - - + -
289M VAL* 3.9 21.1 - - + -
297M VAL 3.1 20.4 + - - +
298M SER* 3.4 11.0 - - - +
300M ASN* 1.3 73.9 - - - +
302M LYS* 1.3 77.1 + - - +
303M LYS 2.9 5.3 + - - -
304M ILE* 3.1 3.6 + - + -
305M VAL* 3.1 30.0 + - + +
353M TYR* 4.4 8.5 - - + +
363M PRO* 4.5 9.9 - - + -
368M LEU* 4.2 19.7 - - + -
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Residues in contact with LYS 302 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298M SER* 3.1 17.6 - - - +
299M SER* 3.8 4.5 - - - +
301M ILE* 1.3 83.3 - - + +
303M LYS* 1.3 59.6 + - - +
305M VAL* 4.5 0.7 - - - +
306M ALA* 3.4 23.2 + - - +
363M PRO* 3.9 25.7 - - - +
367M GLU* 4.2 25.1 + - + +
368M LEU* 4.2 27.4 - - - +
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Residues in contact with LYS 303 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266M GLU 5.7 2.9 - - - -
267M LEU* 4.9 5.2 - - + -
270M LEU* 3.7 25.8 - - + -
299M SER 3.1 17.8 + - - +
300M ASN* 4.1 4.3 - - - +
302M LYS* 1.3 75.9 - - - +
304M ILE* 1.3 59.1 + - + +
306M ALA* 3.2 3.0 + - - +
307M ASP* 2.7 65.3 + - + +
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Residues in contact with ILE 304 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241M ILE* 6.2 1.1 - - + -
260M LEU* 5.5 0.2 - - + -
267M LEU* 3.8 33.2 - - + +
270M LEU* 3.8 26.9 - - + -
271M ILE* 4.2 14.1 - - + -
287M LEU* 4.2 24.9 - - + -
289M VAL* 4.6 2.9 - - + -
300M ASN 2.7 26.5 - - - +
301M ILE* 3.1 9.5 + - + +
303M LYS* 1.3 74.9 - - - +
305M VAL* 1.3 58.7 + - + +
307M ASP* 4.3 4.0 - - - -
308M LEU* 2.9 58.9 + - + +
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Residues in contact with VAL 305 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241M ILE* 4.6 17.5 - - + -
301M ILE* 3.1 21.6 + - + +
302M LYS 4.5 1.8 - - - +
304M ILE* 1.3 77.0 - - + +
306M ALA* 1.3 56.9 + - - +
308M LEU* 5.4 0.7 - - + -
309M LYS* 3.1 44.1 + - + +
348M LEU* 3.6 11.8 - - + +
351M PHE* 3.8 29.6 - - + -
368M LEU* 3.4 42.4 - - + +
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Residues in contact with ALA 306 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302M LYS 3.4 17.2 + - - +
303M LYS* 3.2 4.5 + - - +
305M VAL* 1.3 77.9 - - - +
307M ASP* 1.3 62.6 + - - +
308M LEU 3.5 0.3 + - - -
309M LYS* 3.5 18.4 + - + +
310M LYS* 3.6 13.5 + - - +
368M LEU 4.4 9.4 - - - +
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Residues in contact with ASP 307 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267M LEU* 3.6 20.0 - - + +
303M LYS* 2.7 51.6 + - + +
304M ILE 3.9 2.9 - - - +
306M ALA* 1.3 74.5 - - - +
308M LEU* 1.3 58.9 + - - +
310M LYS* 3.5 18.7 - - - +
312M LYS* 3.1 34.6 + - - +
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Residues in contact with LEU 308 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241M ILE* 5.7 6.3 - - + -
256M LEU* 5.0 9.2 - - + -
259M TYR* 5.8 1.8 - - + -
260M LEU* 4.4 30.1 - - + -
267M LEU* 5.1 4.0 - - + -
285M PHE* 6.3 1.8 - - + -
287M LEU* 5.2 2.5 - - + -
304M ILE* 2.9 42.8 + - + +
305M VAL* 6.4 0.2 - - + -
307M ASP* 1.3 76.8 - - + +
309M LYS* 1.3 66.4 + - - +
310M LYS 3.0 1.8 - - - -
311M GLY* 2.8 19.4 + - - -
312M LYS* 4.5 20.4 - - + +
346M PHE* 4.8 11.9 - - + -
347M LYS 3.4 13.1 - - - +
348M LEU* 3.9 29.4 - - + -
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Residues in contact with LYS 309 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305M VAL* 3.1 42.9 + - + +
306M ALA* 3.7 11.7 - - - +
307M ASP 3.5 0.4 - - - -
308M LEU* 1.3 75.6 - - - +
310M LYS* 1.3 57.0 + - - +
311M GLY 3.0 6.1 + - - -
347M LYS* 4.5 8.8 - - - +
348M LEU* 3.9 24.7 + - + +
349M GLY 4.7 7.4 + - - -
351M PHE* 3.9 14.1 - - - -
368M LEU* 3.8 14.3 + - - +
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Residues in contact with LYS 310 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306M ALA 3.6 11.9 + - - +
307M ASP* 3.5 13.6 - - - +
308M LEU 3.0 1.9 - - - -
309M LYS* 1.3 74.2 - - - +
311M GLY* 1.3 68.8 + - - +
312M LYS* 4.6 2.4 - - - +
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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
------------------------------------------------------------
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