Contacts of the helix formed by residues 253 - 271 (chain F) in PDB entry 3HX0
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 253 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251F ASN* 3.4 8.4 + - - +
252F HIS* 1.3 78.4 - - - +
254F LEU* 1.3 57.2 + - - +
255F HIS* 3.1 10.9 - - - -
256F ILE* 2.9 36.5 + - + +
257F THR* 3.1 13.9 + - - +
286F LEU* 3.3 49.3 + - + +
289F PHE* 4.0 4.6 - - - +
291F LYS 3.5 16.0 + - - -
292F PRO* 3.0 8.6 - - - +
293F VAL 2.7 28.8 + - - +
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Residues in contact with LEU 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251F ASN* 2.8 37.3 - - + +
252F HIS 3.3 4.2 + - - -
253F ASN* 1.3 77.0 - - - +
255F HIS* 1.3 58.0 + - - +
256F ILE 3.1 0.2 - - - -
257F THR* 3.8 5.4 - - - +
258F GLU* 2.8 52.5 + - + +
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Residues in contact with HIS 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252F HIS 3.6 20.0 + - - -
253F ASN* 3.7 17.8 - - - -
254F LEU* 1.3 79.0 + - - +
256F ILE* 1.3 70.5 + - + +
258F GLU* 4.0 12.0 - - - +
259F LYS* 4.3 12.8 - - - +
292F PRO* 4.7 8.1 - - + -
293F VAL 4.9 1.4 + - - -
316F ILE* 3.7 19.4 - - + +
317F LEU* 3.4 34.6 - - + +
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Residues in contact with ILE 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253F ASN* 2.9 33.8 + - + +
255F HIS* 1.3 95.5 - - + +
257F THR* 1.3 68.4 + - - +
258F GLU 2.9 1.1 - - - -
259F LYS* 2.8 18.4 + - - +
260F LEU* 3.2 22.1 + - + +
286F LEU* 3.9 18.4 - - + -
293F VAL* 4.5 7.2 - - + +
313F ILE* 3.8 35.2 - - + -
316F ILE* 4.3 16.3 - - + +
317F LEU* 3.9 17.5 - - + -
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Residues in contact with THR 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251F ASN* 3.5 16.1 + - - +
253F ASN 3.1 14.7 + - - +
254F LEU* 3.8 4.3 + - - +
256F ILE* 1.3 78.0 - - - +
258F GLU* 1.3 65.3 + - - +
260F LEU* 3.8 11.2 - - - -
261F GLU* 2.9 32.0 + - - +
283F ILE* 3.6 41.1 - - + +
286F LEU* 3.7 22.0 - - + -
287F LYS* 3.9 11.2 - - + +
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Residues in contact with GLU 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254F LEU* 2.8 36.0 + - + +
255F HIS* 4.0 14.8 - - - +
257F THR* 1.3 83.5 + - - +
259F LYS* 1.3 63.2 + - + +
261F GLU* 4.2 8.5 + - - +
262F VAL* 3.5 13.7 - - - +
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Residues in contact with LYS 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255F HIS 4.3 9.6 - - - +
256F ILE 2.8 14.1 + - - +
258F GLU* 1.3 76.2 - - + +
260F LEU* 1.3 59.4 + - - +
261F GLU 3.1 2.2 - - - -
262F VAL* 2.8 33.8 + - + +
263F LEU* 3.6 2.9 + - - +
316F ILE* 3.7 37.7 - - + -
320F GLY* 3.3 32.0 + - - -
321F HIS* 4.1 12.4 + - - +
322F LEU* 4.4 14.1 - - + +
325F LEU* 4.2 22.5 - - + +
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Residues in contact with LEU 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F ILE* 3.2 29.5 + - + +
257F THR* 3.9 5.8 - - - +
259F LYS* 1.3 76.2 - - - +
261F GLU* 1.3 58.3 + - - +
263F LEU* 2.9 24.0 + - + +
264F ALA* 2.9 12.5 + - - +
279F TYR* 3.7 14.7 - - + -
282F ALA* 5.3 0.7 - - + -
283F ILE* 4.1 23.1 - - + +
286F LEU* 4.0 17.3 - - + -
309F MET* 4.1 34.1 - - + -
312F LYS* 4.5 19.1 - - + -
313F ILE* 5.0 3.8 - - + -
316F ILE* 4.6 12.1 - - + -
322F LEU* 5.1 4.7 - - + -
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Residues in contact with GLU 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257F THR* 2.9 17.5 + - - +
258F GLU* 4.2 7.4 - - - +
259F LYS 3.1 0.2 - - - -
260F LEU* 1.3 76.5 - - - +
262F VAL* 1.3 62.3 + - - +
263F LEU 3.4 0.2 - - - -
264F ALA* 3.8 7.4 - - + +
265F LYS* 3.2 23.7 + - - +
283F ILE* 3.6 33.7 - - + +
287F LYS* 4.6 11.4 + - - +
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Residues in contact with VAL 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258F GLU 3.5 15.7 - - - +
259F LYS* 2.8 23.1 + - + +
261F GLU* 1.3 79.2 - - - +
263F LEU* 1.3 57.4 + - - +
265F LYS* 3.9 3.8 - - - +
266F ALA* 3.0 25.1 + - - +
325F LEU* 3.4 28.5 - - + -
328F ILE* 4.4 7.9 - - + -
336F GLU* 5.5 0.7 - - - +
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Residues in contact with LEU 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259F LYS 3.6 1.5 + - - +
260F LEU* 2.9 7.2 + - + +
262F VAL* 1.3 78.5 - - - +
264F ALA* 1.3 56.6 + - - +
266F ALA* 2.9 7.0 + - + +
267F TYR* 2.8 53.7 + - + +
279F TYR* 3.5 37.7 - - + +
312F LYS* 4.2 13.5 - - + -
322F LEU* 4.1 20.4 - - + -
324F LYS* 4.2 15.3 - - + -
325F LEU* 4.0 12.6 - - + -
328F ILE* 3.9 27.8 - - + -
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Residues in contact with ALA 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260F LEU 2.9 15.2 + - - +
261F GLU* 3.8 13.7 - - + +
262F VAL 3.4 0.2 - - - -
263F LEU* 1.3 77.3 - - - +
265F LYS* 1.3 58.7 + - - +
267F TYR* 5.0 0.4 - - - -
268F SER* 2.9 31.7 + - - -
276F ALA* 3.7 15.6 - - + +
279F TYR* 3.9 25.5 - - + -
280F ALA* 5.1 2.2 - - - +
283F ILE* 4.4 6.3 - - + -
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Residues in contact with LYS 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F GLU 3.2 16.9 + - - +
262F VAL* 4.1 4.0 - - - +
264F ALA* 1.3 77.0 - - - +
266F ALA* 1.3 64.0 + - - +
268F SER* 3.9 7.4 - - - -
269F VAL* 3.2 32.9 + - + +
336F GLU* 3.3 25.7 - - + +
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Residues in contact with ALA 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262F VAL 3.0 16.5 + - - +
263F LEU* 2.9 24.9 + - + +
265F LYS* 1.3 74.8 - - - +
267F TYR* 1.3 67.6 + - + +
269F VAL* 3.0 19.6 - - - +
270F GLN* 3.2 15.0 - - - +
328F ILE* 4.5 14.6 - - + -
332F VAL* 3.9 21.2 - - + +
336F GLU* 5.1 0.7 - - - -
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Residues in contact with TYR 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263F LEU* 2.8 40.4 + - + +
264F ALA* 4.1 2.5 - - - +
266F ALA* 1.3 74.1 - - + +
268F SER* 1.3 65.3 + - - +
270F GLN* 2.9 31.1 + - - +
271F GLY 3.1 8.3 + - - -
272F ASP* 3.4 23.2 + - + -
275F ARG* 3.2 51.0 + - + -
276F ALA* 4.3 11.2 - - + +
279F TYR* 3.4 30.0 + + - -
1I G 2.7 17.0 + - - -
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Residues in contact with SER 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264F ALA 2.9 21.3 + - - -
265F LYS* 3.7 9.6 - - - -
267F TYR* 1.3 75.5 - - - +
269F VAL* 1.3 65.6 + - - +
271F GLY* 2.9 17.7 + - - -
272F ASP 5.0 2.5 - - - +
273F LYS* 5.3 1.9 + - - +
276F ALA* 3.7 15.6 - - - +
346F THR* 3.9 6.5 + - - -
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Residues in contact with VAL 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265F LYS* 3.2 16.2 - - + +
266F ALA 3.0 19.5 - - - +
268F SER* 1.3 77.6 - - - +
270F GLN* 1.3 60.9 + - + +
332F VAL* 3.9 26.2 - - + +
335F LEU* 4.8 14.1 - - + +
336F GLU* 4.0 33.9 - - + +
339F SER* 4.7 12.8 - - - +
346F THR* 3.0 31.6 + - - +
349F ALA* 6.0 1.0 - - - +
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Residues in contact with GLN 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266F ALA* 3.2 19.6 - - - +
267F TYR* 2.9 28.9 + - - +
269F VAL* 1.3 81.5 - - + +
271F GLY* 1.3 58.2 + - - +
272F ASP* 3.6 4.4 - - + +
329F SER* 4.5 11.7 - - - -
331F SER* 4.8 3.6 + - - -
332F VAL* 4.0 21.9 - - + +
335F LEU* 5.0 11.6 - - + +
346F THR* 4.1 6.0 - - - +
350F GLN* 4.2 9.0 - - - +
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Residues in contact with GLY 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267F TYR 3.1 0.2 + - - -
268F SER 2.9 13.5 + - - -
269F VAL 3.2 0.4 - - - -
270F GLN* 1.3 80.1 - - - +
272F ASP* 1.3 52.2 + - - +
273F LYS* 2.5 26.4 + - - +
346F THR* 4.3 10.5 - - - -
347F LYS* 6.1 1.6 - - - -
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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
------------------------------------------------------------
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