Contacts of the helix formed by residues 254 - 265 (chain B) in PDB entry 2WZJ
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 254 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252B GLY 3.2 1.8 + - - -
253B GLN* 1.3 85.7 + - - +
255B LEU* 1.3 63.8 + - - +
256B LYS* 3.0 18.2 + - - +
257B GLU* 3.1 25.6 + - - +
258B LEU* 3.1 19.8 + - - +
173C HIS 4.6 3.4 + - - -
174C ARG* 3.9 32.0 - - - +
175C ASP* 4.0 25.8 - - + +
209C PHE* 3.7 13.1 - - - -
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Residues in contact with LEU 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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213B PRO* 3.9 22.2 - - + -
221B PHE* 5.1 5.4 - - + -
254B ASN* 1.3 75.6 - - - +
256B LYS* 1.3 64.4 + - - +
258B LEU* 3.7 11.2 - - + +
259B ARG* 3.0 25.1 + - - +
174C ARG 5.2 3.3 + - - +
175C ASP* 4.7 2.9 + - - +
209C PHE* 3.6 21.9 - - + -
212C SER* 3.8 21.8 - - - +
213C PRO* 3.8 33.0 - - + -
216C ALA* 4.3 4.3 - - + -
220C LEU* 3.9 30.7 - - + +
221C PHE* 6.0 0.4 - - + -
226C TYR* 6.1 2.7 - - + -
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Residues in contact with LYS 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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254B ASN* 3.0 11.5 + - - +
255B LEU* 1.3 79.3 - - - +
257B GLU* 1.3 74.1 + - - +
259B ARG* 3.5 11.7 + - - +
260B GLU* 3.2 37.1 + - - +
174C ARG* 3.6 24.4 + - + +
220C LEU* 4.4 9.3 - - - +
226C TYR* 3.1 48.9 - - + +
227C ASP* 3.6 22.0 - - - -
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Residues in contact with GLU 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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251B ASP 4.2 1.8 - - - -
252B GLY* 3.7 9.7 - - - -
253B GLN* 3.0 33.2 + - - +
254B ASN* 3.1 21.0 + - - +
256B LYS* 1.3 86.7 - - - +
258B LEU* 1.3 65.6 + - - +
260B GLU* 3.2 22.4 + - - +
261B ARG* 3.3 19.3 + - + +
96C LYS* 3.2 32.8 + - - -
200C PHE* 5.5 0.7 - - - -
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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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213B PRO* 3.6 42.4 - - + +
214B PRO* 3.9 8.3 - - + -
221B PHE* 4.6 8.1 - - + -
250B PHE* 3.6 37.9 - - + +
251B ASP* 4.0 10.5 + - - +
252B GLY* 4.2 0.4 - - - -
254B ASN 3.1 16.5 + - - +
255B LEU* 3.7 13.9 - - + +
257B GLU* 1.3 78.4 - - - +
259B ARG* 1.3 62.0 + - - +
260B GLU 3.2 0.2 + - - -
261B ARG* 3.3 3.1 + - - +
262B VAL* 3.0 28.9 + - + +
209C PHE* 3.9 18.4 - - + -
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Residues in contact with ARG 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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221B PHE* 3.7 41.7 - - + -
255B LEU 3.0 17.6 + - - +
256B LYS* 3.6 11.8 + - - +
258B LEU* 1.3 78.0 - - - +
260B GLU* 1.3 63.0 + - - +
262B VAL* 4.5 0.4 - - - -
263B LEU* 3.1 36.9 + - + +
219C GLU 3.2 9.3 + - - -
220C LEU* 3.1 44.7 + - + +
223C GLY* 3.9 4.3 - - - -
224C LYS 2.7 36.1 + - - +
225C LYS* 4.2 1.6 - - - +
226C TYR* 3.8 21.0 - - - +
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Residues in contact with GLU 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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256B LYS* 3.2 30.8 + - - +
257B GLU* 3.2 19.9 + - - +
258B LEU 3.1 0.4 - - - -
259B ARG* 1.3 79.6 - - - +
261B ARG* 1.3 64.1 + - + +
263B LEU* 3.6 5.0 + - - +
264B ARG* 3.2 40.9 + - - +
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Residues in contact with ARG 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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250B PHE* 3.8 25.6 - - + +
251B ASP 3.4 25.8 + - - +
257B GLU* 3.5 8.6 + - - +
258B LEU 3.3 6.4 + - - +
260B GLU* 1.3 74.3 - - + +
262B VAL* 1.3 67.1 + - - +
264B ARG* 3.1 33.2 + - - +
265B GLY* 2.9 20.4 + - - -
266B LYS 4.3 6.1 + - - +
92C SER* 5.8 1.6 + - - -
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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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213B PRO 5.2 1.1 - - - +
214B PRO 4.9 4.9 - - - +
216B ALA 3.5 25.4 - - - +
217B ALA 4.2 0.2 - - - -
218B PRO* 3.7 26.7 - - + -
221B PHE* 4.2 15.9 - - + -
234B TRP* 4.2 7.9 - - + +
250B PHE* 3.9 31.1 - - + -
258B LEU* 3.0 31.9 + - + +
259B ARG 4.1 2.9 - - - +
261B ARG* 1.3 74.2 - - - +
263B LEU* 1.3 64.5 + - - +
265B GLY* 3.0 17.0 + - - -
287B LEU* 3.8 6.9 - - - +
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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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218B PRO* 3.8 25.8 - - + +
221B PHE* 4.1 9.0 - - + +
222B GLN* 3.6 45.4 + - + +
259B ARG* 3.1 46.5 + - + +
260B GLU* 4.1 4.3 - - - +
262B VAL* 1.3 76.6 - - - +
264B ARG* 1.3 60.2 + - - +
287B LEU* 3.4 21.0 - - - +
223C GLY* 5.2 4.7 - - - -
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Residues in contact with ARG 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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260B GLU* 3.2 36.9 + - - +
261B ARG* 3.1 39.9 + - - +
263B LEU* 1.3 75.8 - - - +
265B GLY* 1.3 61.1 - - - +
266B LYS* 3.4 42.7 + - + +
287B LEU* 3.6 14.6 - - - +
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Residues in contact with GLY 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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234B TRP* 4.8 3.1 - - - -
250B PHE* 3.8 12.0 - - - -
261B ARG 2.9 10.7 + - - -
262B VAL 3.0 13.4 + - - -
264B ARG* 1.3 77.7 - - - +
266B LYS* 1.3 61.0 + - - +
267B TYR* 3.4 19.9 - - - -
285B LEU* 5.0 5.5 - - - +
287B LEU* 4.2 13.2 - - - -
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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