Contacts of the helix formed by residues 249 - 262 (chain B) in PDB entry 2ZOQ
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 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B PTR 5.2 1.3 - - - +
208B ARG* 2.8 18.1 - - - +
247B GLY 3.1 1.0 - - - -
248B LYS* 1.3 89.9 - - + +
250B TYR* 1.3 69.0 + - + +
251B LEU* 3.5 17.2 - - + +
252B ASP* 3.3 42.5 + - + +
253B GLN* 2.8 22.7 + - - +
255B ASN* 5.8 0.2 + - - -
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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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201B LEU* 3.0 50.9 - - + -
202B THR 3.0 22.3 + - - -
203B GLU* 4.1 11.4 - - - -
204B PTR 3.1 44.2 + + + +
208B ARG* 4.2 0.2 - - - +
211B ARG* 3.9 15.9 - - - +
215B ILE* 3.7 2.6 + - + -
216B MET* 3.1 41.3 - - + +
249B HIS* 1.3 79.7 - - + +
251B LEU* 1.4 69.6 + - + +
253B GLN* 3.6 12.0 + - - +
254B LEU 3.8 1.6 + - - -
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B LEU* 4.6 21.8 - - + -
249B HIS* 3.5 14.3 - - + +
250B TYR* 1.4 84.8 - - + +
252B ASP* 1.5 54.4 + - - +
254B LEU* 2.6 44.2 + - + +
255B ASN* 3.1 14.6 + - - +
280B TYR* 3.0 44.9 - - + +
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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
----------------------------------------------------------
247B GLY* 2.7 7.1 - - - -
248B LYS* 3.1 29.9 + - - +
249B HIS* 3.3 39.0 + - + +
251B LEU* 1.5 74.7 - - - +
253B GLN* 1.3 62.3 + - - +
255B ASN* 2.9 14.8 + - - +
256B HIS* 2.5 58.0 + - - -
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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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208B ARG* 2.9 40.4 + - + +
209B TRP* 3.5 10.2 + - - -
211B ARG* 4.5 3.0 + - + +
216B MET* 4.0 18.8 - - + -
245B PHE* 2.9 45.4 + - - +
247B GLY* 3.0 18.5 + - - -
249B HIS 2.8 19.3 + - - +
250B TYR* 3.6 8.5 - - - +
251B LEU 2.9 0.2 + - - -
252B ASP* 1.3 74.1 - - - +
254B LEU* 1.3 63.7 + - - +
256B HIS* 3.1 9.8 + - - +
257B ILE* 3.1 29.0 + - + +
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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
----------------------------------------------------------
201B LEU* 5.1 4.0 - - + -
213B PRO* 4.2 26.7 - - + +
216B MET* 3.9 36.0 - - + +
217B LEU* 4.2 24.0 - - + -
250B TYR 3.8 0.8 + - - -
251B LEU* 2.6 24.4 + - + +
253B GLN* 1.3 75.8 - - - +
255B ASN* 1.3 55.4 + - - +
257B ILE* 3.4 5.1 + - + +
258B LEU* 3.0 45.7 + - + +
280B TYR* 4.1 24.7 - - + -
281B LEU* 4.9 3.4 - - + -
313B PHE* 5.2 0.4 - - + -
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Residues in contact with ASN 255 (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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249B HIS* 5.8 0.2 + - - -
251B LEU* 3.1 33.3 + - - +
252B ASP* 2.9 13.1 + - - +
254B LEU* 1.3 75.3 - - - +
256B HIS* 1.3 66.3 + - + +
258B LEU* 3.9 7.1 - - - +
259B GLY* 2.9 21.3 + - - -
280B TYR* 2.9 21.5 + - - -
284B LEU* 4.2 14.9 - - - +
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Residues in contact with HIS 256 (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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245B PHE* 3.8 17.0 - - - -
246B PRO* 3.2 39.8 + - + +
247B GLY* 3.6 8.7 - - - +
248B LYS* 4.7 4.6 + - - +
252B ASP* 2.5 47.8 + - - -
253B GLN 3.1 8.5 + - - +
255B ASN* 1.3 73.6 - - + +
257B ILE* 1.3 61.0 - - - +
259B GLY* 3.2 4.4 + - - -
260B ILE* 2.6 38.0 - - - +
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Residues in contact with ILE 257 (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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211B ARG 3.5 24.2 - - - +
213B PRO* 4.0 17.9 - - + -
216B MET* 4.0 14.4 - - + -
229B TRP* 3.6 35.0 - - + +
245B PHE* 3.8 20.2 - - + -
253B GLN* 3.1 29.4 + - - +
254B LEU* 3.5 8.1 - - + +
256B HIS* 1.3 77.0 - - - +
258B LEU* 1.3 58.9 + - + +
260B ILE* 3.5 0.7 + - - +
261B LEU* 2.9 39.0 + - + +
313B PHE* 5.5 2.2 - - + -
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Residues in contact with LEU 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 LEU* 3.0 39.4 + - + +
255B ASN* 3.9 9.2 - - - +
257B ILE* 1.3 73.3 - - + +
259B GLY* 1.3 61.4 + - - +
260B ILE 3.0 2.0 - - - -
261B LEU* 4.7 1.3 - - + -
262B GLY* 2.5 52.6 + - - +
263B SER* 4.9 1.3 - - - -
264B PRO* 3.8 20.4 - - + -
281B LEU* 4.2 8.7 - - + -
284B LEU* 3.4 32.8 - - + -
287B LYS* 4.0 11.3 - - + +
313B PHE* 4.4 21.1 - - + -
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Residues in contact with GLY 259 (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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255B ASN 2.9 15.1 + - - -
256B HIS* 3.2 4.9 + - - -
258B LEU* 1.3 76.9 - - - +
260B ILE* 1.3 64.4 + - - +
262B GLY 4.4 1.2 + - - -
287B LYS* 3.2 27.4 - - - +
288B THR 4.7 4.2 - - - +
290B VAL* 4.3 11.8 - - - +
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Residues in contact with ILE 260 (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 ILE* 4.6 7.6 - - + -
245B PHE* 3.9 28.3 - - + +
256B HIS* 2.6 38.1 + - + +
257B ILE 4.0 0.2 - - - +
258B LEU 3.0 0.4 - - - -
259B GLY* 1.3 82.3 - - - +
261B LEU* 1.3 64.4 + - + +
262B GLY 3.2 1.5 + - - -
289B LYS* 3.9 3.3 - - - +
290B VAL* 3.0 48.3 + - + +
292B TRP* 4.2 17.7 - - + -
295B LEU* 3.7 17.0 - - + -
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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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229B TRP* 4.1 13.7 - - + -
245B PHE* 3.9 24.5 - - + -
257B ILE* 2.9 24.9 + - + +
258B LEU* 4.7 2.2 - - + -
260B ILE* 1.3 81.9 - - + +
262B GLY* 1.3 65.1 + - - +
263B SER 4.7 1.9 - - - +
289B LYS* 3.7 32.1 - - - +
292B TRP* 4.6 9.2 - - + -
311B LEU* 3.4 27.1 - - + +
313B PHE* 3.6 35.4 - - + +
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Residues in contact with GLY 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 LEU* 2.5 39.7 + - - +
259B GLY 4.9 0.2 - - - -
260B ILE 3.2 3.8 + - - -
261B LEU* 1.3 79.4 - - - +
263B SER* 1.3 65.9 + - - -
264B PRO* 3.6 2.3 - - - +
287B LYS* 3.5 17.0 - - - -
288B THR 3.8 14.8 - - - -
289B LYS 4.3 0.4 - - - -
313B PHE* 6.0 0.2 - - - -
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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