Contacts of the helix formed by residues 260 - 270 (chain H) in PDB entry 2POZ
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 TYR 260 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B TRP* 3.8 7.7 + + - -
83B LYS 4.9 2.3 + - - -
84B ASN* 4.1 20.2 - - - +
85B GLY* 5.8 0.2 - - - -
237B PHE* 3.7 6.0 - + + -
85H GLY 4.4 4.5 - - - +
86H GLY* 4.0 11.0 - - - -
87H ALA* 3.3 40.2 - - + +
90H PHE* 4.0 17.3 - - + -
257H GLU 4.2 1.1 - - - -
258H ARG* 3.4 44.3 - - - +
259H VAL* 1.3 88.8 - - - +
261H THR* 1.3 80.1 + - - +
264H GLY* 3.1 13.1 + - - -
283H THR* 3.2 47.6 - - + +
284H ALA* 4.3 1.8 - - - +
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Residues in contact with THR 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B PHE* 3.6 2.7 - - + -
72H TRP* 4.5 9.0 - - + -
90H PHE* 3.5 44.0 - - + -
260H TYR* 1.3 80.9 + - - +
262H ARG* 1.3 65.2 + - - +
263H PHE* 3.1 30.7 + - + +
265H PHE* 2.9 24.1 + - - -
284H ALA* 2.8 29.7 + - - +
289H GLU* 3.6 9.2 - - - -
293H ILE* 3.5 11.3 - - - +
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Residues in contact with ARG 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C ALA* 2.9 38.6 + - - +
298C GLU* 3.0 33.5 + - - +
299C ALA* 4.4 3.9 - - + +
72H TRP* 4.0 19.2 - - - -
261H THR* 1.3 71.8 - - - +
263H PHE* 1.3 77.8 - - + +
265H PHE 3.3 0.4 + - - +
266H ARG* 2.9 30.8 + - - +
289H GLU* 2.7 43.1 + - - +
292H LYS* 3.9 35.8 - - + +
293H ILE* 3.7 5.4 - - + +
296H MSE 3.2 39.1 - - + +
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Residues in contact with PHE 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ARG* 4.6 9.9 - - - -
235B ASP* 5.2 0.2 - - - -
237B PHE* 3.4 50.8 - + + +
298C GLU* 3.8 21.8 - - + -
299C ALA* 3.7 35.9 - - + +
72H TRP* 4.7 7.2 - + - -
76H TYR* 3.6 32.1 - + - -
261H THR* 3.1 13.9 - - - +
262H ARG* 1.3 107.4 - - + +
264H GLY* 1.3 62.0 + - - +
266H ARG* 3.7 16.0 + - - +
267H LYS* 3.6 11.6 - - - +
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Residues in contact with GLY 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B PHE* 3.8 6.2 - - - -
259H VAL* 3.5 17.7 - - - +
260H TYR 3.1 20.5 + - - -
261H THR 3.0 4.2 + - - -
263H PHE* 1.3 78.9 - - - +
265H PHE* 1.3 60.3 + - - +
267H LYS* 3.2 36.2 + - - +
268H ILE* 3.9 2.1 + - - +
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Residues in contact with PHE 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255H VAL 4.7 0.4 - - - -
256H GLY* 3.7 28.5 - - - -
259H VAL* 3.4 40.6 - - + -
260H TYR 4.4 0.2 - - - -
261H THR 2.9 26.8 + - - +
262H ARG 3.3 2.4 + - - +
264H GLY* 1.3 71.8 - - - +
266H ARG* 1.3 65.7 + - - +
267H LYS 3.0 2.0 - - - -
268H ILE* 2.9 21.2 + - + +
269H PHE* 2.9 36.1 + + + -
277H ILE* 4.0 29.4 - - + -
279H PRO* 3.7 19.7 - - + -
284H ALA* 4.6 0.9 - - + -
293H ILE* 3.4 34.3 - - + -
296H MSE 4.5 1.1 - - + -
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Residues in contact with ARG 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B ASP* 2.9 27.8 + - - +
239B ASN 5.8 0.2 - - - -
240B GLY* 3.9 9.3 - - - -
272C GLN* 2.5 34.6 + - - +
299C ALA* 2.9 36.1 + - + -
300C TYR* 3.4 42.1 - - + +
262H ARG 2.9 16.7 + - - +
263H PHE* 3.7 9.9 - - - +
264H GLY 3.2 0.4 - - - -
265H PHE* 1.3 76.3 - - - +
267H LYS* 1.3 65.9 + - + +
269H PHE* 3.7 11.5 - - - +
270H GLU* 3.1 44.9 + - - +
296H MSE 5.5 2.9 - - - -
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Residues in contact with LYS 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ASN* 5.5 6.9 + - - +
237B PHE* 3.9 32.0 + - - +
239B ASN* 5.7 4.7 - - - +
267B LYS* 4.6 26.1 - - + +
84H ASN* 4.4 8.1 + - - -
239H ASN* 3.7 18.3 + - - +
263H PHE 3.6 7.6 - - - +
264H GLY* 3.2 28.4 + - - +
265H PHE 3.0 0.2 - - - -
266H ARG* 1.3 81.8 - - + +
268H ILE* 1.3 57.9 + - + +
270H GLU* 4.2 5.9 + - - +
271H LEU* 3.2 27.2 + - - +
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Residues in contact with ILE 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236H PRO 5.9 0.4 - - - +
239H ASN* 3.8 25.8 - - - +
242H LEU* 4.1 15.5 - - + -
255H VAL* 3.9 25.1 - - + -
259H VAL* 4.2 34.1 - - + -
264H GLY 4.3 1.3 - - - +
265H PHE* 2.9 15.5 + - + +
267H LYS* 1.3 75.2 - - - +
269H PHE* 1.3 69.7 + - + +
271H LEU* 3.1 21.1 + - - +
272H GLN* 3.6 3.5 + - - -
273H ALA 4.8 1.7 + - - -
274H CYS* 4.2 17.5 + - + -
277H ILE* 4.6 13.9 - - + -
302H MSE 4.9 2.0 - - + +
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Residues in contact with PHE 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265H PHE* 2.9 37.0 + + + +
266H ARG* 3.7 9.4 - - - +
268H ILE* 1.3 78.1 - - + +
270H GLU* 1.3 61.7 + - + +
271H LEU 3.1 1.3 + - - -
272H GLN* 3.1 13.4 + - - +
277H ILE* 4.2 11.2 - - + -
293H ILE* 3.6 13.0 - - + -
296H MSE 3.5 42.2 - - + -
297H ALA* 3.6 33.9 - - + -
300H TYR* 3.2 52.2 - + + +
302H MSE 3.8 24.0 - - - -
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Residues in contact with GLU 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C GLU* 4.6 17.7 - - - +
300C TYR* 2.9 35.1 + - - +
243H LYS* 5.3 3.3 + - - -
266H ARG* 3.1 42.2 + - + +
267H LYS* 4.6 6.2 - - - +
269H PHE* 1.3 73.7 - - - +
271H LEU* 1.3 60.6 + - - +
272H GLN* 4.6 7.5 + - - +
300H TYR* 4.4 11.7 - - - +
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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