Contacts of the helix formed by residues 253 - 270 (chain B) in PDB entry 5DKW
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 ASN 253 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251B ASN* 3.3 6.4 + - - +
252B HIS* 1.3 81.7 - - - +
254B LEU* 1.3 57.3 + - - +
255B HIS* 3.3 7.4 + - - +
256B ILE* 3.1 22.7 + - + +
257B THR* 2.9 30.1 + - - +
286B LEU* 3.0 47.8 + - + +
289B PHE* 4.0 5.1 - - - +
291B LYS 3.5 19.0 + - - -
292B PRO* 3.5 4.9 - - - +
293B VAL* 2.9 29.4 + - - +
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Residues in contact with LEU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ASN* 3.2 37.9 - - + +
252B HIS 3.5 2.8 + - - -
253B ASN* 1.3 77.4 - - - +
255B HIS* 1.3 60.6 + - + +
257B THR* 5.1 0.2 - - - +
258B GLU* 3.0 65.5 + - + +
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Residues in contact with HIS 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B HIS 4.2 14.4 + - - -
253B ASN* 4.6 2.5 + - - -
254B LEU* 1.3 87.0 - - + +
256B ILE* 1.3 96.0 + - + +
258B GLU* 4.4 8.7 - - - +
259B LYS* 4.2 18.9 + - - +
292B PRO* 5.4 4.6 - - - +
293B VAL 6.0 0.2 - - - -
316B ILE* 3.3 23.3 + - + +
317B LEU* 3.9 24.2 - - + +
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Residues in contact with ILE 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ASN* 3.1 26.5 + - + +
255B HIS* 1.3 111.9 - - + +
257B THR* 1.3 63.5 + - - +
258B GLU 3.3 0.2 - - - -
259B LYS* 3.3 7.1 + - - +
260B LEU* 3.2 28.6 + - + +
286B LEU* 3.6 25.6 - - + -
293B VAL* 5.9 1.6 - - + +
313B ILE* 3.7 38.6 - - + +
316B ILE* 3.7 20.6 - - + +
317B LEU* 3.8 10.1 - - + +
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Residues in contact with THR 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ASN* 3.3 14.7 + - - -
253B ASN* 2.9 21.6 + - + +
254B LEU* 3.3 5.0 + - - +
256B ILE* 1.3 74.4 - - - +
258B GLU* 1.3 67.0 + - - +
260B LEU* 3.7 8.3 - - - +
261B GLU* 3.0 29.8 + - - +
283B ILE* 4.0 22.4 - - + +
286B LEU* 3.7 35.2 - - + -
287B LYS* 4.0 16.5 - - + +
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Residues in contact with GLU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LEU* 3.0 54.4 + - + +
255B HIS* 4.4 6.5 - - - +
257B THR* 1.3 80.9 + - - +
259B LYS* 1.3 68.3 + - + +
261B GLU* 3.5 11.9 + - - +
262B VAL* 3.5 23.6 + - - +
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Residues in contact with LYS 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B HIS* 4.2 13.4 + - - +
256B ILE 3.3 8.5 + - - +
257B THR 3.3 0.4 - - - -
258B GLU* 1.3 84.1 + - + +
260B LEU* 1.3 65.1 + - - +
262B VAL* 3.6 8.4 + - + +
263B LEU* 3.5 15.2 + - - +
316B ILE* 3.8 30.9 - - + +
320B GLY 3.2 24.3 + - - +
321B HIS* 4.4 7.9 - - - +
322B LEU* 4.4 15.0 - - + +
325B LEU* 3.9 28.9 - - + +
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ILE* 3.2 20.7 + - + +
257B THR* 3.8 2.7 - - - +
258B GLU 3.3 0.2 - - - -
259B LYS* 1.3 76.7 - - - +
261B GLU* 1.3 59.8 + - - +
263B LEU* 3.2 5.9 + - + +
264B ALA* 2.9 28.1 + - - +
279B TYR* 4.1 26.2 - - + -
282B ALA* 5.4 0.7 - - + -
283B ILE* 3.6 25.7 - - + +
286B LEU* 3.9 28.3 - - + -
309B MET* 4.8 13.0 - - + -
312B LYS* 4.8 12.1 - - + -
313B ILE* 4.3 10.1 - - + -
316B ILE* 4.4 14.6 - - + -
322B LEU* 4.5 10.8 - - + -
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Residues in contact with GLU 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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257B THR* 3.0 21.1 + - - +
258B GLU* 3.8 12.9 - - - +
259B LYS 3.3 0.2 - - - -
260B LEU* 1.3 74.4 - - - +
262B VAL* 1.3 66.0 + - + +
264B ALA* 3.3 3.2 + - + +
265B LYS* 3.0 25.5 + - - +
283B ILE* 3.6 26.4 - - + +
287B LYS* 3.0 31.0 + - - -
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Residues in contact with VAL 262 (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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258B GLU 3.5 15.4 + - - +
259B LYS* 3.6 12.1 - - - +
260B LEU 3.2 0.4 - - - -
261B GLU* 1.3 79.1 - - + +
263B LEU* 1.3 62.8 + - - +
265B LYS* 3.4 5.9 + - - +
266B ALA* 3.3 20.2 + - + +
325B LEU* 3.7 22.0 - - + -
328B ILE* 5.9 4.5 - - + -
332B VAL* 5.9 0.2 - - - +
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Residues in contact with LEU 263 (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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259B LYS 3.5 5.2 + - - +
260B LEU* 3.2 9.7 + - + +
262B VAL* 1.3 77.8 - - - +
264B ALA* 1.3 66.1 + - - +
266B ALA* 3.2 6.2 + - - +
267B TYR* 3.2 41.9 + - + -
279B TYR* 3.5 32.8 - - + +
312B LYS* 4.3 7.4 - - + -
322B LEU* 4.2 19.1 - - + -
324B LYS* 4.3 22.7 - - + -
325B LEU* 4.1 13.2 - - + -
328B ILE* 3.6 31.0 - - + -
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU 2.9 17.0 + - - +
261B GLU* 3.7 9.6 - - + +
262B VAL 3.3 0.2 - - - -
263B LEU* 1.3 76.6 - - - +
265B LYS* 1.3 57.2 + - - +
267B TYR* 3.4 6.6 + - - +
268B SER* 3.0 28.1 + - - -
276B ALA* 4.0 10.2 - - - +
279B TYR* 3.7 30.7 - - + -
280B ALA* 5.0 1.8 - - + +
283B ILE* 4.3 7.0 - - + -
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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 GLU 3.0 17.2 + - - +
262B VAL* 3.7 6.1 - - - +
264B ALA* 1.3 74.6 - - - +
266B ALA* 1.3 65.3 + - - +
268B SER* 3.3 15.9 + - - -
269B VAL* 3.0 48.8 + - + +
332B VAL* 5.2 2.9 - - + -
336B GLU* 4.2 31.9 - - - +
339B SER* 5.5 1.0 + - - -
340B ASN* 5.2 6.2 + - - -
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Residues in contact with ALA 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 VAL* 3.3 10.3 + - + +
263B LEU 3.2 10.7 + - - +
265B LYS* 1.3 79.8 - - - +
267B TYR* 1.3 63.0 + - + +
269B VAL* 3.5 1.2 - - - +
270B GLN* 2.9 37.7 + - - +
328B ILE* 3.8 31.0 - - + -
332B VAL* 4.0 25.4 - - + +
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Residues in contact with TYR 267 (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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263B LEU* 3.2 30.3 + - + -
264B ALA* 3.7 6.1 - - - +
265B LYS 3.3 0.2 - - - -
266B ALA* 1.3 78.6 - - + +
268B SER* 1.3 62.6 + - - +
270B GLN* 3.3 17.2 + - + +
272B ASP* 3.0 43.6 + - + +
275B ARG* 3.5 29.4 - - + -
276B ALA* 4.1 11.7 - - + -
279B TYR* 3.6 37.5 - + - -
324B LYS* 3.0 24.7 + - - -
328B ILE* 5.9 3.4 - - + -
1C G 2.9 20.9 + - - -
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Residues in contact with SER 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 ALA 3.0 14.1 + - - -
265B LYS* 3.4 24.5 + - - -
267B TYR* 1.3 77.1 - - - +
269B VAL* 1.3 58.9 + - - +
271B GLY* 3.1 19.9 + - - -
272B ASP 4.4 1.5 + - - -
273B LYS* 5.7 1.8 - - - +
276B ALA* 3.8 16.2 - - - +
346B THR* 4.7 2.3 - - - -
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LYS* 3.0 33.3 + - + +
266B ALA 3.5 11.2 - - - +
268B SER* 1.3 75.5 - - - +
270B GLN* 1.3 62.7 + - + +
271B GLY 3.3 1.8 - - - -
332B VAL* 4.0 21.5 - - + +
335B LEU* 3.8 29.3 - - + +
336B GLU* 3.7 32.3 - - + +
339B SER* 3.8 15.8 - - - +
346B THR* 3.5 18.3 + - - +
349B ALA* 5.4 0.9 - - - +
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Residues in contact with GLN 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 ALA* 2.9 36.0 + - - +
267B TYR* 4.0 16.1 - - + +
268B SER 3.1 1.6 - - - -
269B VAL* 1.3 81.2 - - + +
271B GLY* 1.3 61.8 + - - +
272B ASP* 3.3 5.1 + - + +
328B ILE* 5.1 5.3 - - - +
329B SER* 4.1 20.8 + - - +
331B SER* 5.0 1.7 + - - -
332B VAL* 4.1 9.9 - - + +
335B LEU* 4.2 14.8 - - + +
346B THR* 3.3 7.0 - - - -
350B GLN* 3.6 18.4 + - - +
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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
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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