Contacts of the helix formed by residues 257 - 277 (chain B) in PDB entry 3KMU
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 ALA 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252B THR* 3.5 9.8 + - + +
253B LEU* 3.5 15.1 + - + +
254B PHE 4.8 0.4 - - - -
255B ASP 3.8 0.6 - - - +
256B HIS* 1.3 81.4 - - - +
258B PRO* 1.4 58.2 - - - +
259B ASP* 3.2 9.6 - - - +
260B LYS* 3.0 28.0 + - + -
261B LEU* 2.7 34.9 + - - +
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Residues in contact with PRO 258 (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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254B PHE 5.5 1.1 - - - +
255B ASP 5.3 3.4 - - - +
256B HIS* 3.8 6.1 - - - +
257B ALA* 1.4 88.3 - - - +
259B ASP* 1.3 63.8 + - - +
261B LEU* 4.0 12.8 - - + -
262B ASN* 2.7 43.6 + - - +
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Residues in contact with ASP 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B HIS 4.8 0.5 - - - +
257B ALA* 3.5 16.7 - - - +
258B PRO* 1.3 84.8 - - - +
260B LYS* 1.3 85.0 + - - +
262B ASN* 4.4 3.3 + - - +
263B VAL* 3.6 21.7 + - - +
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Residues in contact with LYS 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 4.9 15.9 - - + +
257B ALA* 3.0 27.7 + - + +
259B ASP* 1.3 91.6 + - - +
261B LEU* 1.3 51.3 + - - +
262B ASN 2.9 7.3 + - - -
263B VAL* 3.0 8.2 + - - +
264B VAL* 2.8 40.7 + - + +
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Residues in contact with LEU 261 (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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253B LEU 3.8 10.7 + - - +
254B PHE* 3.0 50.0 - - + +
257B ALA 2.7 18.6 + - - +
258B PRO* 3.9 12.8 - - + +
260B LYS* 1.3 70.4 - - - +
262B ASN* 1.3 62.0 + - - +
264B VAL* 3.4 11.5 - - + +
265B LYS* 3.0 49.5 + - + +
354B LEU* 5.4 0.7 - - + -
358B LEU* 3.9 15.9 - - + -
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Residues in contact with ASN 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B PRO* 2.7 30.3 + - - +
259B ASP* 4.8 4.1 - - - +
260B LYS 2.9 1.4 + - - -
261B LEU* 1.3 85.3 - - - +
263B VAL* 1.3 62.2 + - + +
264B VAL 3.2 0.9 - - - -
265B LYS* 4.3 8.8 - - - +
266B LYS* 3.1 27.9 + - - +
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ASP 3.6 17.3 - - - +
260B LYS* 3.0 7.4 + - - +
262B ASN* 1.3 76.9 - - + +
264B VAL* 1.3 57.5 + - - +
266B LYS* 3.6 9.2 + - + +
267B THR* 2.7 45.8 + - - +
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Residues in contact with VAL 264 (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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250B PHE* 5.4 12.1 - - + -
253B LEU* 5.9 8.1 - - + -
260B LYS* 2.8 22.8 + - + +
261B LEU* 3.4 17.3 - - + +
263B VAL* 1.3 73.1 - - + +
265B LYS* 1.3 61.4 + - + +
267B THR* 3.0 7.1 + - - -
268B LEU* 2.7 53.6 + - + +
358B LEU* 4.8 7.4 - - + -
362B TYR* 5.4 16.6 - - + -
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Residues in contact with LYS 265 (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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261B LEU* 3.0 36.1 + - - +
262B ASN* 4.4 9.9 - - - +
263B VAL 3.5 0.2 - - - -
264B VAL* 1.3 69.8 - - + +
266B LYS* 1.3 61.2 - - - +
268B LEU* 3.8 1.0 - - - +
269B ILE* 2.8 41.7 + - + +
286B LEU* 3.9 24.0 - - + -
287B GLU* 3.8 20.0 + - - +
354B LEU* 3.4 25.6 - - + +
358B LEU* 3.7 28.3 - - + -
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Residues in contact with LYS 266 (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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262B ASN 3.1 20.4 + - - +
263B VAL* 3.6 9.2 - - + +
265B LYS* 1.3 75.9 - - - +
267B THR* 1.3 64.8 + - - +
269B ILE* 3.5 9.4 + - - +
270B THR* 3.0 53.9 + - - +
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Residues in contact with THR 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B VAL* 2.7 31.6 + - - +
264B VAL* 3.5 5.2 - - - -
266B LYS* 1.3 80.6 - - - +
268B LEU* 1.3 55.7 + - - +
270B THR* 3.2 13.1 + - + +
271B PHE* 2.8 32.6 + - - +
365B PHE* 3.8 32.8 - - + -
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Residues in contact with LEU 268 (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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264B VAL* 2.7 35.6 + - + +
265B LYS* 3.8 4.0 - - - +
267B THR* 1.3 71.2 - - - +
269B ILE* 1.3 58.6 + - - +
271B PHE* 3.7 7.3 - - + +
272B VAL* 3.1 35.4 + - - +
286B LEU* 3.9 12.1 - - + -
358B LEU* 3.9 42.0 - - + +
361B LEU* 3.4 41.7 - - + +
362B TYR* 3.9 7.2 - - + +
365B PHE* 4.0 17.7 - - + -
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Residues in contact with ILE 269 (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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265B LYS* 2.8 32.6 + - + +
266B LYS* 3.9 7.2 - - - +
268B LEU* 1.3 73.7 - - - +
270B THR* 1.3 65.0 + - - +
272B VAL* 3.9 4.7 - - - -
273B ASN* 2.7 42.6 + - - +
283B VAL* 3.1 36.1 - - + +
284B THR* 4.5 15.5 - - - +
286B LEU* 3.7 23.8 - - + +
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Residues in contact with THR 270 (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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266B LYS* 3.0 37.1 + - - -
267B THR* 3.2 18.1 + - + +
269B ILE* 1.3 76.4 - - - +
271B PHE* 1.3 59.5 + - - +
273B ASN* 3.9 3.0 - - - +
274B LYS* 3.0 31.4 + - + +
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Residues in contact with PHE 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B THR 2.8 18.1 + - - +
268B LEU* 3.7 10.5 - - + +
269B ILE 3.3 0.2 - - - -
270B THR* 1.3 75.9 - - - +
272B VAL* 1.3 78.2 + - + +
274B LYS* 3.2 15.8 - - + +
275B HIS* 3.1 40.9 - + - -
299B LEU* 5.1 2.5 - - + -
303B LEU* 4.0 25.1 - - + -
361B LEU* 4.1 2.9 - - - -
364B LEU* 4.0 13.2 - - + -
365B PHE* 3.9 52.0 - + + -
368B TYR* 3.8 34.5 - - + -
369B ARG* 5.2 3.6 - - - -
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Residues in contact with VAL 272 (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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268B LEU 3.1 19.5 + - - +
269B ILE* 3.5 13.0 - - - +
271B PHE* 1.3 89.6 - - + +
273B ASN* 1.3 60.0 + - - +
275B HIS* 3.4 2.1 + - - +
276B LEU* 2.8 37.2 + - + +
283B VAL* 3.9 26.2 - - + -
286B LEU* 4.5 1.1 - - + -
290B PHE* 3.8 27.4 - - + -
299B LEU* 4.0 18.8 - - + +
361B LEU* 4.2 13.9 - - + -
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Residues in contact with ASN 273 (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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269B ILE* 2.7 37.5 + - - +
270B THR* 4.0 3.8 - - - +
272B VAL* 1.3 75.2 - - - +
274B LYS* 1.3 64.9 + - - +
275B HIS 3.1 2.2 - - - -
276B LEU* 4.3 2.2 - - - +
277B ASN* 3.0 58.0 + - - +
281B LEU 4.1 0.3 - - - +
282B GLU* 3.4 11.3 + - - +
283B VAL* 2.8 50.8 + - - +
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Residues in contact with LYS 274 (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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270B THR* 3.0 18.4 + - + +
271B PHE* 3.2 18.8 - - + +
273B ASN* 1.3 78.2 - - - +
275B HIS* 1.3 76.1 + - + +
277B ASN* 4.6 2.5 + - - +
278B LYS* 3.8 19.8 + - - +
369B ARG 5.1 5.6 - - - +
371B VAL 3.6 17.5 - - - +
372B GLU* 3.2 39.8 + - - +
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Residues in contact with HIS 275 (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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271B PHE* 3.1 41.5 - + - -
272B VAL 3.4 1.5 + - - +
273B ASN 3.1 0.2 - - - -
274B LYS* 1.3 90.7 - - + +
276B LEU* 1.3 63.5 + - - +
277B ASN 3.4 0.4 - - - -
278B LYS* 3.2 30.8 + - - +
279B LEU 4.3 0.2 + - - -
299B LEU* 3.9 19.1 - - + -
302B LEU* 3.6 26.8 + - + +
303B LEU* 3.4 29.5 - - + +
368B TYR 4.7 0.6 + - - -
371B VAL* 3.6 28.3 + - + -
372B GLU* 3.9 23.5 + - - -
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Residues in contact with LEU 276 (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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272B VAL* 2.8 24.8 + - + +
273B ASN* 4.7 1.8 - - - -
275B HIS* 1.3 69.0 - - - +
277B ASN* 1.3 59.4 + - - +
278B LYS 3.2 0.2 - - - -
279B LEU* 3.0 19.6 + - + +
281B LEU* 3.1 47.0 + - + +
283B VAL* 3.7 26.5 - - + -
290B PHE* 4.1 18.2 - - + -
295B TYR* 4.0 27.6 - - + +
298B LEU* 4.2 12.3 - - + -
299B LEU* 4.2 13.2 - - + +
302B LEU* 4.1 17.9 - - + -
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Residues in contact with ASN 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ASN* 3.0 48.4 + - - +
274B LYS* 4.8 2.7 - - - +
276B LEU* 1.3 76.1 - - - +
278B LYS* 1.3 55.7 + - + +
280B ASN* 2.7 32.6 + - - +
281B LEU 2.9 20.4 + - - +
282B GLU* 3.7 12.0 - - - +
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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