Contacts of the helix formed by residues 250 - 268 (chain F) in PDB entry 1NU9
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 HIS 250 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242F SER 3.4 17.7 + - - -
243F SER* 2.8 32.1 + - - -
244F LYS* 3.3 18.1 - - - +
246F HIS* 2.7 20.2 + - + +
249F ASN* 1.3 98.0 + - + +
251F SER* 1.3 53.8 + - - +
252F GLU* 3.3 3.1 - - - -
253F GLY* 3.0 5.0 + - - +
254F PHE 2.7 30.3 + - - -
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Residues in contact with SER 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246F HIS 3.6 0.8 + - - -
247F TYR 3.4 21.3 + - - -
248F LYS* 4.1 9.7 + - - +
249F ASN 3.9 0.4 - - - -
250F HIS* 1.3 73.0 - - - +
252F GLU* 1.3 68.0 + - - +
254F PHE* 3.0 5.3 + - - +
255F GLU* 2.8 32.1 + - - +
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Residues in contact with GLU 252 (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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250F HIS 3.3 0.6 - - - -
251F SER* 1.3 81.4 - - - +
253F GLY* 1.3 64.4 + - - +
255F GLU* 3.1 6.4 + - - +
256F ALA* 2.9 24.4 + - - +
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Residues in contact with GLY 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F LYS 3.6 18.8 - - - -
245F HIS* 3.6 8.1 + - - -
250F HIS* 3.0 9.1 + - - +
252F GLU* 1.3 79.2 - - - +
254F PHE* 1.3 66.6 + - - +
256F ALA* 3.3 7.7 + - - +
257F LEU* 3.0 21.0 + - - +
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Residues in contact with PHE 254 (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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173F PHE* 3.7 47.8 - + + -
177F ARG* 3.7 30.5 - - - -
240F TYR* 5.2 0.9 - + - -
245F HIS* 3.2 30.7 + - + +
247F TYR* 3.3 39.5 - + + -
250F HIS 2.7 14.0 + - - +
251F SER* 3.2 9.4 - - - +
253F GLY* 1.3 71.5 - - - +
255F GLU* 1.3 72.1 + - + +
257F LEU* 2.8 23.8 + - + +
258F VAL* 3.0 25.5 + - + +
2002F IMD 4.6 10.1 - + - -
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Residues in contact with GLU 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177F ARG* 2.6 45.4 + - - -
251F SER* 2.8 22.2 + - - +
252F GLU* 3.6 8.5 - - - +
254F PHE* 1.3 81.0 - - + +
256F ALA* 1.3 58.5 + - - +
258F VAL* 3.3 7.6 + - - +
259F LYS* 2.8 32.3 + - - +
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Residues in contact with ALA 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252F GLU 2.9 16.5 + - - +
253F GLY* 3.7 8.7 - - - +
254F PHE 3.2 0.2 - - - -
255F GLU* 1.3 76.5 - - - +
257F LEU* 1.3 57.2 + - - +
259F LYS* 3.9 6.5 - - - +
260F GLU* 3.0 30.7 + - - +
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Residues in contact with LEU 257 (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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170F SER* 3.5 34.3 - - - +
173F PHE* 5.1 7.6 - - + -
238F THR* 4.0 20.2 - - + +
240F TYR* 3.9 12.6 - - + -
245F HIS* 3.8 42.4 - - + +
253F GLY 3.0 11.0 + - - +
254F PHE* 2.8 12.4 + - + +
256F ALA* 1.3 76.0 - - - +
258F VAL* 1.3 58.1 + - + +
260F GLU* 3.5 6.0 + - - +
261F THR* 2.6 52.2 + - - +
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Residues in contact with VAL 258 (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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170F SER 5.8 0.2 - - - -
173F PHE* 3.8 22.0 - - + +
174F ALA* 3.8 22.0 - - - +
177F ARG* 4.3 13.7 - - - +
254F PHE* 3.0 37.3 + - + +
255F GLU* 3.7 11.2 - - - +
257F LEU* 1.3 75.8 - - + +
259F LYS* 1.3 62.1 + - - +
261F THR* 3.1 2.9 + - - -
262F ARG* 2.8 54.0 + - - +
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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 GLU 2.8 18.1 + - - +
256F ALA* 3.9 7.0 - - - +
258F VAL* 1.3 78.3 - - - +
260F GLU* 1.3 62.3 + - - +
262F ARG* 3.4 7.9 + - - +
263F GLU* 2.9 59.2 + - + +
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Residues in contact with GLU 260 (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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238F THR* 2.4 40.4 + - - +
256F ALA 3.0 19.9 + - - +
257F LEU* 3.8 9.3 - - - +
259F LYS* 1.3 77.6 - - - +
261F THR* 1.3 57.0 + - - +
263F GLU* 3.5 9.3 + - - +
264F ALA* 3.0 28.1 + - + +
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Residues in contact with THR 261 (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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170F SER* 4.3 3.7 + - - +
171F VAL* 4.2 25.4 - - + +
174F ALA* 3.6 23.1 - - + -
175F PHE* 4.8 0.9 - - + -
234F PRO* 5.8 0.4 - - + -
237F ILE* 4.6 15.3 - - + +
238F THR 5.3 1.0 + - - -
257F LEU* 2.6 39.8 + - - +
258F VAL 3.5 3.1 - - - -
260F GLU* 1.3 77.5 + - - +
262F ARG* 1.3 66.1 + - - +
264F ALA* 3.1 8.6 + - + +
265F VAL* 2.9 33.9 + - + +
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Residues in contact with ARG 262 (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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174F ALA* 3.1 26.5 + - + +
175F PHE* 3.8 20.0 - - + -
177F ARG 5.5 0.2 - - - -
178F ASP* 2.6 46.1 + - - +
258F VAL* 2.8 37.3 + - + +
259F LYS* 3.7 7.9 - - - +
261F THR* 1.3 71.6 - - - +
263F GLU* 1.3 63.8 + - + +
265F VAL* 3.1 8.8 + - - +
266F THR* 3.0 26.4 + - - -
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Residues in contact with GLU 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* 2.9 57.3 + - + +
260F GLU* 3.8 8.0 - - - +
262F ARG* 1.3 78.1 - - + +
264F ALA* 1.3 63.8 + - - +
266F THR* 3.3 7.7 + - - -
267F ASN* 2.9 38.0 + - - +
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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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234F PRO* 3.6 23.5 - - + +
236F ASN* 3.9 13.2 - - + +
260F GLU* 3.0 17.1 + - + +
261F THR* 3.1 12.1 + - - +
263F GLU* 1.3 77.5 - - - +
265F VAL* 1.3 62.4 + - - +
267F ASN* 3.3 7.2 + - - +
268F ALA* 3.0 23.4 + - - +
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Residues in contact with VAL 265 (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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171F VAL* 6.0 0.2 - - + -
175F PHE* 3.9 28.5 - - + -
226F PHE* 3.9 20.4 - - + -
231F LEU* 3.9 30.5 - - + -
232F ASN* 3.6 20.4 + - - +
234F PRO* 4.0 11.2 - - + -
261F THR* 2.9 22.1 + - + +
262F ARG 3.1 7.2 + - - +
264F ALA* 1.3 75.9 - - - +
266F THR* 1.3 65.8 + - - +
268F ALA* 2.9 20.0 + - - +
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Residues in contact with THR 266 (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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262F ARG* 3.0 15.4 + - - -
263F GLU* 3.6 11.2 - - - -
265F VAL* 1.3 77.7 - - - +
267F ASN* 1.3 69.1 + - - +
268F ALA 3.4 4.9 + - - +
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Residues in contact with ASN 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 GLU* 2.9 30.7 + - - +
264F ALA* 3.6 6.8 - - - +
266F THR* 1.3 83.1 - - - +
268F ALA* 1.3 61.7 + - - +
269F ASN* 3.9 1.4 + - - +
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Residues in contact with ALA 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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232F ASN* 3.3 30.8 - - + +
233F LYS 3.8 4.7 - - - +
234F PRO* 3.7 24.7 - - + -
264F ALA 3.0 11.6 + - - +
265F VAL 2.9 16.2 + - - +
266F THR 4.1 4.5 - - - +
267F ASN* 1.3 80.3 - - - +
269F ASN* 1.3 59.9 + - - +
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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