Contacts of the helix formed by residues 293 - 310 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B ASP* 3.6 6.6 - - - +
292B GLN* 1.3 83.0 - - + +
294B SER* 1.3 64.3 + - - +
295B ALA* 3.0 33.5 + - - +
296B VAL* 3.2 29.7 + - - +
297B VAL* 3.3 13.5 + - - +
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Residues in contact with SER 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B SER* 4.5 3.9 + - - -
292B GLN 3.8 3.0 + - - -
293B ASP* 1.3 71.5 - - - +
295B ALA* 1.3 55.8 + - - +
296B VAL 3.4 0.2 - - - -
297B VAL* 3.7 6.3 - - - -
298B SER* 3.0 35.0 + - - -
358B ASP* 2.8 34.4 + - - +
361B ASN* 3.3 33.5 + - - +
362B LEU* 3.5 15.9 - - - +
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ASP* 3.0 18.0 + - + +
294B SER* 1.3 79.7 + - - +
296B VAL* 1.3 60.5 + - + +
298B SER* 3.9 3.9 - - - -
299B SER* 3.3 25.8 + - - -
361B ASN* 5.4 3.9 + - - +
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B VAL* 5.0 0.2 - - - +
291B ASP* 3.7 23.4 - - + +
293B ASP* 3.2 23.3 + - - +
295B ALA* 1.3 75.5 - - + +
297B VAL* 1.3 61.0 + - - +
299B SER* 4.7 3.4 - - - -
300B ASN* 3.1 42.1 + - - +
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B SER* 3.5 22.9 - - - +
238B VAL* 4.2 0.9 - - - -
239B ALA* 3.8 21.8 - - + +
289B VAL* 3.4 33.8 - - + +
291B ASP* 3.5 21.8 - - + +
292B GLN 4.3 0.9 - - - +
293B ASP 3.3 19.3 - - - +
294B SER* 3.8 10.3 - - - +
295B ALA 3.2 0.6 - - - -
296B VAL* 1.3 78.2 - - - +
298B SER* 1.3 67.4 + - - +
300B ASN 3.4 1.4 + - - -
301B ILE* 3.3 16.1 + - - +
362B LEU* 4.3 9.4 - - + -
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Residues in contact with SER 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B SER 3.0 21.4 + - - -
295B ALA* 3.9 4.9 - - - -
297B VAL* 1.3 75.3 - - - +
299B SER* 1.3 65.1 + - - +
301B ILE* 2.8 18.2 + - - +
302B LYS* 2.9 20.9 + - - +
361B ASN 3.4 10.7 + - - -
362B LEU* 3.7 0.9 - - - +
363B PRO* 3.1 38.5 - - - +
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Residues in contact with SER 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 5.1 1.0 - - - +
295B ALA 3.3 15.7 + - - -
296B VAL* 4.5 3.1 - - - -
298B SER* 1.3 79.0 - - - +
300B ASN* 1.3 68.7 + - - +
302B LYS* 4.1 7.5 - - - +
303B LYS* 3.4 24.4 + - - +
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Residues in contact with ASN 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B GLY 4.3 3.4 + - - -
270B LEU* 3.2 59.7 + - - +
289B VAL* 3.8 11.2 - - + +
296B VAL* 3.1 35.5 + - - +
298B SER 3.1 1.4 - - - -
299B SER* 1.3 81.2 - - - +
301B ILE* 1.3 58.7 + - - +
303B LYS* 4.3 1.6 - - - -
304B ILE* 2.8 27.3 + - - +
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Residues in contact with ILE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B ALA* 3.6 44.2 - - + +
240B ALA* 4.0 8.7 - - - +
241B ILE* 4.8 4.9 - - + -
287B LEU* 4.5 8.7 - - + -
289B VAL* 4.2 15.3 - - + -
297B VAL 3.3 10.6 + - - +
298B SER* 2.8 19.0 + - - +
300B ASN* 1.3 72.0 - - - +
302B LYS* 1.3 64.9 + - - +
303B LYS 3.1 1.8 - - - -
304B ILE* 3.7 6.7 - - + -
305B VAL* 3.0 47.3 + - + +
353B TYR* 4.1 13.2 - - + +
363B PRO* 4.6 7.0 - - + -
368B LEU* 3.8 15.0 - - + -
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Residues in contact with LYS 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B SER* 2.9 19.0 + - - +
299B SER* 4.1 6.7 - - - +
301B ILE* 1.3 78.4 - - - +
303B LYS* 1.3 57.9 + - - +
305B VAL* 4.5 0.9 - - - +
306B ALA* 3.1 25.1 + - - +
363B PRO* 3.8 26.0 - - - +
367B GLU* 3.5 24.9 + - + +
368B LEU* 4.1 30.5 - - + +
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Residues in contact with LYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B GLU* 5.5 7.4 + - - +
267B LEU* 4.3 13.4 - - + +
270B LEU* 3.9 24.2 - - + +
299B SER 3.4 15.9 + - - +
301B ILE 3.1 0.4 - - - -
302B LYS* 1.3 76.9 - - - +
304B ILE* 1.3 60.1 + - - +
305B VAL 3.2 1.6 - - - -
306B ALA* 2.8 5.5 + - - -
307B ASP* 2.7 59.3 + - - +
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Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ILE* 5.1 1.6 - - + -
260B LEU* 5.3 0.9 - - + -
267B LEU* 3.5 50.5 - - + +
270B LEU* 4.3 4.7 - - + -
271B ILE* 3.7 21.8 - - + -
287B LEU* 3.8 33.2 - - + -
289B VAL* 4.7 0.4 - - + -
300B ASN 2.8 26.9 + - - +
301B ILE* 3.4 9.3 + - + +
303B LYS* 1.3 80.3 - - - +
305B VAL* 1.3 65.6 + - + +
307B ASP* 4.2 0.5 - - - +
308B LEU* 3.1 40.3 + - + +
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ILE* 4.1 21.8 - - + -
301B ILE* 3.0 29.1 + - + +
302B LYS 4.5 0.4 - - - +
304B ILE* 1.3 75.0 - - - +
306B ALA* 1.3 65.4 + - - +
308B LEU* 3.5 4.1 + - - +
309B LYS* 3.1 28.9 + - + +
348B LEU* 4.3 7.6 - - + +
351B PHE* 3.9 31.2 - - + -
368B LEU* 3.3 40.4 - - + +
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Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B LYS 3.1 20.1 + - - +
303B LYS* 2.8 8.8 + - + +
305B VAL* 1.3 78.9 - - - +
307B ASP* 1.3 66.6 + - - +
309B LYS* 3.2 22.7 + - - +
310B LYS* 3.4 7.6 + - - +
368B LEU 4.5 6.9 + - - +
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Residues in contact with ASP 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 4.0 17.5 - - + +
303B LYS* 2.7 50.9 + - - +
306B ALA* 1.3 78.8 - - - +
308B LEU* 1.3 59.1 + - + +
309B LYS 3.3 0.2 - - - -
310B LYS* 2.9 36.8 + - + +
312B LYS* 4.6 18.9 + - + +
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B ILE* 6.0 2.0 - - + -
256B LEU* 4.8 17.9 - - + -
259B TYR* 5.3 3.4 - - + -
260B LEU* 4.5 27.8 - - + -
267B LEU* 5.3 4.5 - - + -
285B PHE* 6.1 2.0 - - + -
287B LEU* 4.7 3.6 - - + -
304B ILE* 3.1 37.8 + - + +
305B VAL* 4.2 1.8 - - - +
307B ASP* 1.3 76.6 - - + +
309B LYS* 1.3 63.8 + - - +
310B LYS 3.1 3.1 - - - -
311B GLY* 3.5 10.3 + - - -
312B LYS* 4.7 22.4 - - + +
346B PHE* 4.7 8.9 - - + +
347B LYS 3.7 7.8 - - - +
348B LEU* 3.2 39.4 - - + +
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Residues in contact with LYS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B VAL* 3.1 17.0 + - + +
306B ALA* 3.2 14.3 + - - +
308B LEU* 1.3 77.3 - - - +
310B LYS* 1.3 57.8 + - - +
311B GLY 3.1 5.4 + - - -
347B LYS* 5.4 1.6 - - - +
348B LEU* 4.2 34.0 + - + +
349B GLY 4.8 3.8 + - - -
351B PHE* 4.7 11.3 - - - -
368B LEU* 4.5 22.1 + - - +
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Residues in contact with LYS 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ALA 3.4 7.7 + - - +
307B ASP* 2.9 28.9 - - + +
308B LEU 3.1 0.2 - - - -
309B LYS* 1.3 75.5 - - - +
311B GLY* 1.3 74.6 + - - +
312B LYS* 3.5 11.3 + - + +
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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
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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