Contacts of the helix formed by residues 255 - 274 (chain B) in PDB entry 3ZFW
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 LYS 255 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ASP* 3.2 22.5 + - - +
269A ILE* 6.0 3.4 - - - +
250B TYR* 2.9 40.7 + - + +
253B GLN* 3.4 40.6 + - + +
254B ASN* 1.4 73.9 - - - +
256B TYR* 1.4 57.1 + - - +
257B LYS 3.5 2.5 - - - -
258B ASP* 3.4 16.0 + - + +
259B ALA* 2.9 28.3 + - - +
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Residues in contact with TYR 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ARG* 4.0 11.9 - - + -
254B ASN* 2.8 56.0 + - + -
255B LYS* 1.4 67.7 - - - +
257B LYS* 1.4 56.6 + - - +
259B ALA* 3.0 6.7 + - - +
260B ALA* 2.8 36.2 + - - +
291B LEU* 3.8 30.5 - - + +
294B LYS* 3.6 60.2 + - + +
295B ARG* 3.9 21.8 - - + -
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Residues in contact with LYS 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LYS 3.5 0.6 - - - -
256B TYR* 1.4 76.0 - - - +
258B ASP* 1.4 59.4 + - - +
260B ALA* 3.7 6.3 + - - +
261B HIS* 3.2 48.5 + - + -
295B ARG* 3.9 44.7 - - - +
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Residues in contact with ASP 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A HIS* 3.0 36.2 + - + -
265A ASP* 5.3 0.7 - - - +
250B TYR* 3.5 30.2 - - + -
255B LYS* 3.4 19.1 + - + +
256B TYR 3.2 0.4 - - - -
257B LYS* 1.4 77.8 - - - +
259B ALA* 1.3 63.2 + - - +
261B HIS* 3.9 11.1 + - - +
262B LEU* 3.6 25.6 + - - +
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Residues in contact with ALA 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ALA* 3.6 28.1 - - - +
250B TYR* 3.8 6.3 - - + +
251B ARG* 3.8 14.4 - - + +
255B LYS 2.9 16.6 + - - +
256B TYR* 3.0 4.9 + - - +
258B ASP* 1.3 74.1 - - - +
260B ALA* 1.4 58.2 + - - +
262B LEU* 3.5 5.4 + - - +
263B LEU* 3.1 30.5 + - - +
291B LEU* 3.8 18.6 - - + -
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Residues in contact with ALA 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B TYR 2.8 16.9 + - - +
257B LYS* 3.7 8.3 - - - +
259B ALA* 1.4 74.2 - - - +
261B HIS* 1.4 65.6 + - - +
263B LEU 3.1 1.9 + - - -
264B ASN* 3.0 30.9 + - - +
288B LEU* 3.5 15.2 - - + +
291B LEU* 3.7 20.6 - - + +
292B TYR* 5.5 11.4 - - + -
295B ARG* 6.0 4.0 - - - +
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Residues in contact with HIS 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ASP* 5.5 7.2 - - - -
257B LYS* 3.2 37.9 + - + +
258B ASP* 4.1 13.2 - - - +
259B ALA 3.5 0.2 - - - -
260B ALA* 1.4 78.6 - - - +
262B LEU* 1.4 62.3 + - + +
264B ASN* 3.3 19.7 + - - +
265B ASP* 3.3 20.8 + - - +
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 3.9 12.8 - - + -
250A TYR* 3.7 24.5 - - + +
262A LEU* 4.9 8.1 - - + -
243B LEU* 3.8 30.9 - - + +
246B LEU* 3.7 25.1 - - + -
247B ALA* 3.8 5.4 - - + +
250B TYR* 3.6 35.9 - - + -
258B ASP 3.6 9.3 + - - +
259B ALA 3.5 8.9 + - - +
260B ALA 3.3 0.2 - - - -
261B HIS* 1.4 79.3 - - + +
263B LEU* 1.4 62.5 + - - +
265B ASP* 3.5 5.9 + - - +
266B ALA* 3.2 20.6 + - - +
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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
----------------------------------------------------------
244B ASN* 3.5 33.0 - - + +
247B ALA* 3.7 18.8 - - + -
259B ALA 3.1 15.1 + - - +
260B ALA 3.1 6.9 + - - +
262B LEU* 1.4 72.8 - - - +
264B ASN* 1.4 55.0 + - - +
266B ALA* 3.4 4.0 + - + -
267B LEU* 2.7 34.6 + - - +
284B THR* 3.4 13.9 - - + +
287B ASN* 3.7 34.5 - - + -
288B LEU* 3.8 14.6 - - + +
291B LEU* 3.8 13.2 - - + -
207Y TRP* 3.8 18.8 - - + -
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Residues in contact with ASN 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ALA* 3.0 26.7 + - - +
261B HIS* 3.3 14.9 + - - +
263B LEU* 1.4 74.8 - - - +
265B ASP* 1.4 53.3 + - - +
267B LEU* 3.1 14.3 + - + +
268B ALA* 2.7 34.9 + - - +
288B LEU* 3.4 24.3 - - - +
292B TYR* 5.1 11.6 + - - -
304B LEU* 5.8 1.4 - - - +
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Residues in contact with ASP 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A TYR* 3.3 27.4 + - - +
255A LYS* 3.1 28.8 + - - +
258A ASP* 5.2 2.8 - - - +
243B LEU* 4.0 11.0 - - + -
261B HIS* 3.3 17.8 + - - +
262B LEU 3.5 9.2 - - - +
263B LEU 3.3 0.2 - - - -
264B ASN* 1.4 75.9 - - - +
266B ALA* 1.3 57.5 + - - +
268B ALA* 3.3 9.2 + - - +
269B ILE* 3.0 33.7 + - + +
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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
----------------------------------------------------------
240B ALA* 3.5 39.3 - - + +
243B LEU* 3.7 8.2 - - + +
244B ASN 4.7 2.5 - - - +
262B LEU 3.2 10.9 + - - +
263B LEU* 3.7 15.3 - - + +
265B ASP* 1.3 75.1 - - - +
267B LEU* 1.4 60.5 + - - +
269B ILE 3.6 0.2 + - - -
270B ARG* 3.0 44.9 + - - +
284B THR* 4.6 0.9 - - + -
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Residues in contact with LEU 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 2.7 19.0 + - - +
264B ASN* 3.1 17.0 + - + +
266B ALA* 1.4 69.3 - - - +
268B ALA* 1.3 58.1 + - - +
270B ARG* 3.1 5.7 + - - +
271B GLU* 2.9 46.6 + - - +
281B VAL* 3.8 25.1 - - + +
284B THR* 3.8 16.6 - - + +
285B LEU* 3.8 36.3 - - + +
288B LEU* 3.7 18.6 - - + -
304B LEU* 5.3 1.3 - - + -
307B ARG* 5.4 1.3 - - - +
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Residues in contact with ALA 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ASN 2.7 15.9 + - - +
265B ASP* 3.4 12.6 - - - +
267B LEU* 1.3 72.9 - - - +
269B ILE* 1.4 61.5 + - + +
271B GLU* 3.5 16.3 + - - +
272B LYS* 3.3 27.2 + - - +
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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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253A GLN* 5.6 5.8 - - - +
255A LYS* 6.1 2.7 - - - +
236B HIS* 3.4 47.3 - - + +
237B PRO* 4.0 2.2 - - + -
239B VAL* 4.0 18.6 - - + -
240B ALA* 3.8 15.0 - - + +
243B LEU* 3.8 23.8 - - + -
265B ASP* 3.0 21.3 + - + +
266B ALA 3.9 4.0 - - - +
267B LEU 3.3 0.2 - - - -
268B ALA* 1.4 73.5 - - + +
270B ARG* 1.3 57.3 + - - +
272B LYS* 3.2 4.1 + - - +
273B THR* 2.8 46.5 + - + +
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Residues in contact with ARG 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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237B PRO* 4.5 3.3 + - + -
240B ALA* 3.6 19.5 + - + +
241B THR* 2.9 43.6 + - - +
244B ASN* 3.2 22.2 - - - +
266B ALA* 3.0 21.1 + - - +
267B LEU* 3.1 5.8 + - - +
269B ILE* 1.3 73.7 - - + +
271B GLU* 1.3 56.0 + - - +
273B THR* 4.1 4.7 - - - +
274B LEU* 3.1 33.0 + - + +
275B GLY 3.1 24.9 + - - +
280B ALA* 4.2 15.3 + - + +
281B VAL* 4.0 18.6 - - + +
284B THR* 3.0 30.1 + - - +
211Y ALA* 3.7 20.1 + - - +
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Residues in contact with GLU 271 (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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267B LEU* 2.9 28.2 + - + +
268B ALA* 3.5 20.6 - - - +
270B ARG* 1.3 75.4 - - - +
272B LYS* 1.3 60.8 + - + +
275B GLY* 3.3 24.9 - - - -
276B LYS* 3.4 29.7 + - + +
281B VAL* 4.3 9.2 - - + -
307B ARG* 3.2 34.3 + - - +
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Residues in contact with LYS 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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236B HIS* 6.2 2.9 - - + -
268B ALA 3.3 15.8 + - - +
269B ILE* 3.2 6.0 + - - +
271B GLU* 1.3 81.6 - - + +
273B THR* 1.4 67.4 + - + +
275B GLY* 4.0 4.0 + - - -
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Residues in contact with THR 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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236B HIS* 4.0 42.4 - - + +
237B PRO* 3.7 26.4 - - - +
269B ILE* 2.8 35.1 + - + +
270B ARG* 4.1 0.2 - - - -
272B LYS* 1.4 76.6 - - + +
274B LEU* 1.3 67.9 + - - +
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B PRO* 4.5 21.3 - - + -
270B ARG* 3.1 36.5 + - + +
273B THR* 1.3 85.1 + - - +
275B GLY* 1.3 61.7 + - - +
276B LYS 5.0 0.3 - - - +
278B HIS* 3.9 40.6 - - + +
280B ALA* 4.0 18.6 - - + -
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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