Contacts of the helix formed by residues 262 - 268 (chain B) in PDB entry 1ZJA
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 GLN 262 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B THR 4.6 4.2 + - - -
228B GLN* 2.9 42.3 + - - +
233B HIS* 5.8 1.0 + - - +
258B ALA* 4.5 6.9 - - + +
259B PRO* 3.0 30.5 + - + +
261B ASN* 1.3 90.7 + - - +
263B VAL* 1.3 65.3 + - - +
264B PRO* 3.3 3.8 - - - -
265B LEU* 3.0 39.7 + - + +
266B PHE* 3.4 16.4 - - + -
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Residues in contact with VAL 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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255B ILE* 3.8 32.3 - - + -
258B ALA* 5.3 2.0 - - + +
259B PRO 4.2 2.9 - - - +
260B LEU* 3.0 28.3 + - + +
262B GLN* 1.3 77.6 - - - +
264B PRO* 1.4 65.4 - - + +
266B PHE* 2.9 21.3 + - - +
267B ILE* 3.3 28.4 + - + +
277B ALA* 3.9 8.1 - - + -
279B THR* 3.8 24.0 - - + -
312B ILE* 3.7 10.3 - - + -
319B ASN* 5.1 1.6 - - - +
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Residues in contact with PRO 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 LEU 3.8 1.1 - - - +
261B ASN 3.4 14.4 - - - +
262B GLN 3.3 5.2 - - - -
263B VAL* 1.4 90.7 - - - +
265B LEU* 1.3 63.0 + - + +
267B ILE* 4.2 9.2 - - + -
268B ASP* 3.0 35.1 + - + +
271B ARG* 3.9 1.1 - - - -
312B ILE* 3.2 42.0 - - + +
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Residues in contact with LEU 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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233B HIS* 3.4 33.7 - - + +
261B ASN 5.5 1.1 - - - +
262B GLN* 3.0 34.0 + - + +
264B PRO* 1.3 80.2 - - + +
266B PHE* 1.3 59.1 + - - +
271B ARG* 2.7 48.6 + - - +
273B GLU* 3.1 15.2 - - - +
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Residues in contact with PHE 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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202B VAL* 4.2 11.9 - - + -
203B ALA* 3.8 24.9 - - + -
227B THR* 5.7 0.4 - - - -
232B LEU* 3.5 27.8 - - + -
233B HIS* 3.6 12.8 - + - -
236B LEU* 3.6 29.6 - - + -
255B ILE* 3.7 32.1 - - + -
258B ALA* 4.8 4.0 - - + -
262B GLN* 3.4 29.6 - - + -
263B VAL* 2.9 13.2 + - - +
265B LEU* 1.3 79.9 - - - +
267B ILE* 1.3 61.3 + - + +
268B ASP 3.9 0.8 - - - +
273B GLU* 3.5 7.8 - - - +
274B LEU* 2.8 39.4 + - + +
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Residues in contact with ILE 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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255B ILE* 4.9 0.7 - - + -
263B VAL* 3.3 29.1 + - + +
264B PRO* 4.2 4.9 - - + -
266B PHE* 1.3 87.1 - - + +
268B ASP* 1.3 69.3 + - - +
269B SER* 3.0 4.9 + - - -
274B LEU* 3.5 12.6 - - + +
275B ASP* 4.2 7.4 - - - +
276B MET* 3.5 35.4 - - - +
277B ALA* 3.6 12.1 - - + -
312B ILE* 4.8 3.1 - - + +
313B ALA* 4.4 11.2 - - - -
316B TYR 3.4 0.7 - - - +
317B GLY* 3.3 18.0 - - - -
318B TRP 3.5 30.5 - - - +
319B ASN* 4.3 5.4 - - - +
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Residues in contact with ASP 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 PRO* 3.0 24.7 + - + +
265B LEU 4.8 0.4 - - - -
266B PHE 3.9 0.9 - - - +
267B ILE* 1.3 75.5 - - - +
269B SER* 1.3 58.7 + - - +
270B ARG* 2.8 56.5 + - - +
271B ARG* 2.9 40.9 + - - +
272B LYS 4.0 1.7 + - - -
273B GLU 4.9 2.8 + - - -
274B LEU 5.0 0.3 - - - +
316B TYR* 3.3 18.7 - - - +
317B GLY* 4.2 2.0 - - - +
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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