Contacts of the helix formed by residues 265 - 279 (chain B) in PDB entry 2HJ9
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 SER 265 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B PHE* 3.4 29.3 - - - -
215B ARG* 3.9 2.9 - - - -
239B ALA* 5.2 0.3 + - - -
263B ALA* 3.5 2.0 + - - +
264B CYS* 1.3 79.9 - - - +
266B THR* 1.3 59.8 + - - +
267B ASP* 4.1 3.2 + - - +
268B VAL* 3.4 28.9 + - - +
269B ALA* 3.0 30.9 + - - +
289B TRP* 4.0 6.9 - - - +
502B AI2 3.2 18.6 - - - -
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Residues in contact with THR 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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78B VAL* 4.6 2.0 - - + +
79B SER* 3.9 23.1 + - - +
265B SER* 1.3 73.7 - - - +
267B ASP* 1.3 72.1 + - - +
269B ALA* 3.2 5.9 + - - +
270B LEU* 3.1 35.6 + - + +
289B TRP 3.1 1.4 + - - -
290B GLY* 4.7 0.9 - - - -
292B GLY* 5.4 1.8 + - - -
294B ALA* 5.4 0.9 - - + -
295B GLU* 2.5 46.1 + - + +
310B ARG* 4.7 0.2 + - - -
502B AI2 2.8 29.4 + - - -
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Residues in contact with ASP 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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76B GLN 4.7 1.7 - - - +
77B GLN* 3.7 15.3 - - - +
78B VAL* 3.0 35.6 + - - +
79B SER* 2.9 30.8 + - - -
239B ALA 4.3 12.2 - - - +
240B THR* 4.0 4.6 - - - -
241B LYS* 3.3 34.1 + - + +
265B SER* 3.5 3.4 + - - +
266B THR* 1.3 74.9 - - - +
268B VAL* 1.3 62.6 + - - +
270B LEU* 3.3 3.2 + - - +
271B GLY 3.0 19.9 + - - -
502B AI2 5.3 0.9 + - - +
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Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 3.7 34.3 - - + +
205B TYR 4.2 5.8 - - - +
206B PHE* 5.0 1.1 - - + -
237B THR* 3.4 27.4 - - + +
239B ALA* 4.1 12.6 - - - -
240B THR 4.0 11.7 - - - +
244B GLY* 3.8 19.5 - - - -
263B ALA* 4.5 3.6 - - + -
265B SER* 3.4 24.6 + - - +
266B THR 3.3 0.4 - - - -
267B ASP* 1.3 78.0 - - - +
269B ALA* 1.3 61.8 + - - +
271B GLY 3.5 0.3 + - - -
272B ALA* 3.1 21.8 + - - +
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Residues in contact with ALA 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ALA* 3.8 13.2 - - + +
265B SER 3.0 20.0 + - - +
266B THR* 3.2 6.3 + - - +
268B VAL* 1.3 78.3 - - - +
270B LEU* 1.3 57.6 + - + +
272B ALA* 3.3 6.7 + - - +
273B VAL* 3.0 30.9 + - - +
286B ILE* 4.0 3.6 - - + +
287B ASN 3.4 25.6 - - - +
288B GLY* 4.1 11.0 - - - -
295B GLU* 5.9 0.2 - - - -
304B LEU* 4.2 6.3 - - + -
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Residues in contact with LEU 270 (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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78B VAL* 3.6 30.7 - - + -
241B LYS* 4.1 17.9 - - + +
266B THR* 3.1 23.1 + - + +
267B ASP* 4.0 4.0 - - - +
268B VAL 3.3 0.4 - - - -
269B ALA* 1.3 73.2 - - + +
271B GLY* 1.3 65.6 + - - +
273B VAL* 3.3 17.0 + - + +
274B ASP* 3.4 18.7 + - - +
294B ALA* 4.1 18.8 - - + +
295B GLU* 4.9 1.3 - - + -
298B ALA* 4.0 16.4 - - + -
304B LEU* 3.8 32.3 - - + -
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Residues in contact with GLY 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LYS* 3.3 36.8 - - - +
245B TYR* 3.4 18.0 - - - -
267B ASP 3.0 11.4 + - - -
268B VAL 3.9 0.4 - - - -
270B LEU* 1.3 76.1 - - - +
272B ALA* 1.3 59.2 + - - +
274B ASP* 3.2 9.1 + - - +
275B ALA 3.2 17.3 + - - -
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Residues in contact with ALA 272 (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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204B LEU* 3.6 22.2 - - + -
244B GLY 3.7 7.6 + - - -
248B ALA* 4.0 11.7 - - + +
261B ILE* 5.4 1.1 - - + -
268B VAL 3.1 13.7 + - - +
269B ALA* 3.3 9.8 + - - +
271B GLY* 1.3 72.1 - - - +
273B VAL* 1.3 58.4 + - - +
275B ALA* 3.8 2.1 - - - +
276B LEU* 3.0 37.0 + - + +
286B ILE* 3.5 21.1 - - + -
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Residues in contact with VAL 273 (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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269B ALA 3.0 19.4 + - - +
270B LEU* 3.4 16.8 - - + +
271B GLY 3.2 0.4 - - - -
272B ALA* 1.3 73.8 - - - +
274B ASP* 1.3 71.0 + - - +
276B LEU* 3.2 11.6 + - - +
277B ALA* 3.0 22.4 + - + +
286B ILE* 4.3 5.8 - - + -
298B ALA* 6.0 0.4 - - + -
303B ASP* 3.5 48.9 - - + +
304B LEU* 3.5 26.0 - - + -
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Residues in contact with ASP 274 (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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241B LYS* 3.3 27.9 + - - -
245B TYR* 3.9 15.6 - - + +
270B LEU 3.4 11.6 + - - +
271B GLY* 3.2 8.4 + - - +
273B VAL* 1.3 79.6 - - - +
275B ALA* 1.3 58.3 + - - +
277B ALA* 3.0 9.2 + - - +
278B GLU* 2.9 30.2 + - - +
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Residues in contact with ALA 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B TYR* 3.6 37.5 - - + +
248B ALA* 3.8 19.1 - - + -
249B LYS* 3.8 17.9 - - + +
252B LEU* 5.5 0.2 - - + -
271B GLY 3.2 5.6 + - - +
272B ALA 3.9 2.5 - - - +
273B VAL 3.4 0.2 - - - -
274B ASP* 1.3 77.1 - - - +
276B LEU* 1.3 58.7 + - - +
278B GLU* 3.5 2.9 + - - +
279B LEU* 3.0 37.7 + - + +
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ALA* 5.8 0.2 - - + -
252B LEU* 3.7 27.8 - - + -
261B ILE* 4.4 6.7 - - + -
272B ALA 3.0 26.6 + - - +
273B VAL* 3.5 6.7 - - - +
274B ASP 3.2 0.2 - - - -
275B ALA* 1.3 75.2 - - - +
277B ALA* 1.3 59.2 + - - +
279B LEU* 5.0 1.1 - - - -
280B GLY* 2.9 7.1 + - - -
281B ARG* 2.8 52.8 + - + +
282B GLU* 4.2 6.5 + - + +
284B ILE* 4.0 32.3 - - + +
286B ILE* 3.9 35.4 - - + -
303B ASP 5.6 0.9 - - - +
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Residues in contact with ALA 277 (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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273B VAL* 3.0 12.9 + - + +
274B ASP* 3.0 13.1 + - - +
276B LEU* 1.3 74.3 - - - +
278B GLU* 1.3 57.7 + - - +
280B GLY* 2.8 24.8 + - - -
282B GLU* 4.2 18.4 - - + +
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Residues in contact with GLU 278 (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 TYR* 2.7 36.3 + - - -
249B LYS* 3.2 18.7 + - - -
274B ASP 2.9 14.6 + - - +
275B ALA* 3.7 4.5 - - - +
277B ALA* 1.3 77.7 - - - +
279B LEU* 1.3 68.5 + - + +
280B GLY 3.4 0.3 + - - -
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LYS* 4.0 37.0 - - + +
252B LEU* 3.9 37.2 - - + -
253B ALA 5.5 0.2 - - - +
275B ALA 3.0 18.5 + - - +
276B LEU 4.4 1.1 - - - +
278B GLU* 1.3 82.5 - - + +
280B GLY* 1.3 65.3 + - - +
281B ARG* 3.3 18.5 + - + +
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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