Contacts of the helix formed by residues 236 - 253 (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 HIS 236 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A GLN* 5.7 7.7 + - - -
237B PRO* 1.4 74.8 - - - +
238B ASP* 3.3 4.0 - - - +
239B VAL* 3.4 33.9 - - + +
269B ILE* 3.4 37.5 - - + +
272B LYS* 6.2 2.7 - - + +
273B THR* 4.0 22.3 - - + +
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Residues in contact with PRO 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B HIS* 1.4 88.9 - - - +
238B ASP* 1.3 70.4 + - - +
239B VAL 3.3 0.7 - - - -
240B ALA* 3.4 8.1 - - + +
241B THR* 3.3 20.3 + - - -
269B ILE* 4.0 9.8 - - + -
270B ARG* 4.5 2.9 + - + -
273B THR* 3.7 24.2 - - + +
274B LEU* 4.5 26.2 - - + -
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Residues in contact with ASP 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B HIS* 3.3 2.3 - - - -
237B PRO* 1.3 84.7 - - - +
239B VAL* 1.4 56.4 + - + +
241B THR* 3.1 12.4 + - + +
242B MET* 2.9 50.7 + - + +
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Residues in contact with VAL 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 4.7 0.6 - - + +
249A VAL* 3.6 34.3 - - + -
236B HIS* 3.4 33.4 - - + +
238B ASP* 1.4 78.2 - - + +
240B ALA* 1.4 55.7 + - - +
242B MET* 3.2 17.5 + - + +
243B LEU* 3.0 36.3 + - + +
269B ILE* 4.0 17.5 - - + -
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Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B HIS 4.0 0.8 + - - -
237B PRO 3.4 11.8 + - - +
239B VAL* 1.4 78.4 - - - +
241B THR* 1.4 50.6 + - - +
243B LEU* 3.2 16.3 + - - +
244B ASN* 2.8 34.0 + - - +
266B ALA* 3.5 22.7 - - - +
269B ILE* 3.8 18.1 - - + +
270B ARG* 3.6 24.2 - - + +
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Residues in contact with THR 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B PRO 3.3 9.6 + - - -
238B ASP* 3.1 16.3 + - + +
240B ALA* 1.4 75.0 - - - +
242B MET* 1.3 59.5 + - + +
244B ASN* 3.2 4.8 + - - +
245B ILE* 2.9 48.1 + - + +
270B ARG* 2.9 21.8 + - - +
211Y ALA 3.8 11.4 + - - +
212Y ILE* 5.1 10.9 - - + +
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Residues in contact with MET 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ILE* 5.2 12.6 - - + -
246A LEU* 4.1 14.1 - - + +
249A VAL* 4.8 17.5 - - - -
238B ASP* 2.9 31.6 + - + +
239B VAL* 3.2 17.0 + - + +
241B THR* 1.3 75.2 - - + +
243B LEU* 1.4 60.7 + - - +
245B ILE* 3.3 15.4 + - + +
246B LEU* 3.1 23.4 + - - +
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 3.6 30.7 - - + +
249A VAL* 5.4 1.6 - - + -
250A TYR* 3.4 32.1 - - + +
239B VAL* 3.0 24.8 + - + +
240B ALA* 3.3 13.9 - - - +
242B MET* 1.4 74.4 - - - +
244B ASN* 1.3 52.9 + - - +
246B LEU* 3.3 3.6 + - - +
247B ALA* 2.9 33.5 + - - +
262B LEU* 3.8 23.2 - - + +
265B ASP* 4.0 6.7 - - + -
266B ALA* 3.7 24.7 - - + +
269B ILE* 3.8 16.6 - - + -
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Residues in contact with ASN 244 (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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240B ALA 2.8 13.3 + - - +
241B THR* 3.2 14.4 - - + +
243B LEU* 1.3 73.1 - - - +
245B ILE* 1.3 64.7 + - + +
247B ALA* 3.3 16.1 + - - +
248B LEU* 3.3 20.3 + - - +
263B LEU* 3.5 23.2 - - - +
266B ALA* 4.7 1.3 - - + +
270B ARG* 3.2 25.3 - - - +
284B THR* 4.4 2.8 + - - +
287B ASN* 5.1 4.5 + - - +
207Y TRP* 5.5 5.9 + - - -
211Y ALA* 3.5 25.2 - - - +
212Y ILE* 4.1 16.0 - - + +
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Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A MET* 4.9 17.0 - - - -
241B THR* 2.9 39.5 + - + +
242B MET* 3.3 13.2 + - + +
244B ASN* 1.3 73.3 - - - +
246B LEU* 1.4 63.3 + - + +
248B LEU* 3.2 26.8 + - + +
249B VAL* 3.5 9.1 + - + +
212Y ILE* 3.7 29.6 - - + -
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Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A VAL 4.7 0.4 - - - +
242A MET* 3.9 27.8 - - + +
243A LEU* 3.8 43.3 - - + +
246A LEU* 3.6 28.9 - - + -
262A LEU* 4.1 10.8 - - + -
242B MET 3.1 16.2 + - - +
243B LEU 3.3 4.5 + - - +
245B ILE* 1.4 73.4 - - + +
247B ALA* 1.4 61.9 + - - +
248B LEU 3.3 0.2 - - - -
249B VAL* 3.3 24.2 + - + +
250B TYR* 3.3 29.5 + - + -
262B LEU* 3.7 4.9 - - + -
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Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU 2.9 13.5 + - - +
244B ASN 3.4 11.2 - - - +
245B ILE 3.3 0.6 - - - -
246B LEU* 1.4 74.6 - - - +
248B LEU* 1.3 58.8 + - + +
250B TYR 3.3 0.7 + - - -
251B ARG* 2.9 29.9 + - - +
259B ALA* 3.6 23.8 - - + +
262B LEU* 3.8 11.6 - - + +
263B LEU* 3.7 27.4 - - + -
207Y TRP* 5.4 4.5 - - + -
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Residues in contact with LEU 248 (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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244B ASN* 3.4 24.7 - - - +
245B ILE* 3.2 12.3 + - + +
247B ALA* 1.3 75.6 - - - +
249B VAL* 1.3 58.8 + - - +
251B ARG* 3.5 37.0 - - - +
252B ASP* 3.0 38.0 + - - +
207Y TRP* 3.5 26.2 - - + +
209Y ASP* 5.4 3.1 - - - +
212Y ILE* 3.8 34.8 - - + -
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A VAL* 3.6 29.8 - - + -
242A MET* 4.5 19.3 - - + -
243A LEU* 5.6 1.3 - - + -
245B ILE* 3.5 12.8 + - + +
246B LEU* 3.3 28.9 + - + +
247B ALA 3.3 0.4 - - - -
248B LEU* 1.3 78.8 - - + +
250B TYR* 1.4 66.5 + - + +
252B ASP* 3.5 5.5 + - - +
253B GLN* 3.3 25.3 + - + +
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Residues in contact with TYR 250 (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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243A LEU* 3.3 28.1 - - + +
261A HIS* 4.3 4.5 + + - -
262A LEU* 3.4 16.6 - - + +
265A ASP* 3.2 36.2 + - - -
246B LEU* 3.3 25.0 + - + -
247B ALA 3.7 6.1 - - - +
249B VAL* 1.4 80.0 - - + +
251B ARG* 1.4 61.4 + - - +
253B GLN* 3.1 9.7 + - - -
255B LYS* 2.9 62.7 + - + +
258B ASP* 3.5 32.3 - - + -
259B ALA* 3.8 8.3 - - + -
262B LEU* 3.6 21.3 - - + -
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Residues in contact with ARG 251 (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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247B ALA 2.9 18.0 + - - +
248B LEU* 3.5 25.6 + - - +
250B TYR* 1.4 73.4 - - - +
252B ASP* 1.3 86.0 + - - +
254B ASN* 2.9 26.5 + - - +
255B LYS 4.8 1.6 - - - +
256B TYR* 4.0 9.0 - - + -
259B ALA* 3.8 11.6 - - + +
290B VAL* 6.0 0.4 - - + -
291B LEU* 4.1 17.3 - - + -
294B LYS* 6.1 3.1 - - - -
207Y TRP* 3.3 61.4 - - + +
209Y ASP* 5.2 1.2 + - - -
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Residues in contact with ASP 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU* 3.0 15.7 + - - +
249B VAL* 3.9 6.1 - - - +
250B TYR 3.3 0.2 - - - -
251B ARG* 1.3 115.7 + - - +
253B GLN* 1.3 58.6 + - + +
254B ASN* 3.2 8.7 + - - +
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Residues in contact with GLN 253 (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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269A ILE* 5.7 4.9 - - - +
249B VAL* 3.3 15.4 + - + +
250B TYR* 3.1 9.8 + - - +
252B ASP* 1.3 75.7 - - - +
254B ASN* 1.4 69.6 + - - +
255B LYS* 3.2 41.6 + - + +
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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
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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