Contacts of the helix formed by residues 239 - 250 (chain B) in PDB entry 4NH1
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 239 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203B LEU 5.2 1.6 - - - -
237B ASP* 2.9 14.0 + - - +
238B ASN* 1.3 84.9 - - + +
240B ASP* 1.3 66.0 + - - +
241B GLN 3.1 2.4 + - - -
242B LEU 3.3 2.9 + - - -
243B VAL* 3.2 24.8 + - - +
266B ASP* 3.1 16.9 + - + -
268B ARG* 2.9 57.9 + - + -
269B PHE* 3.4 44.1 - + + -
272B ILE* 4.4 15.5 - - + -
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Residues in contact with ASP 240 (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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235B GLY* 3.3 19.9 - - - -
236B HIS* 3.4 21.1 + - + +
237B ASP* 2.4 28.7 + - - +
239B TYR* 1.3 70.6 - - - +
241B GLN* 1.3 58.1 + - - +
243B VAL* 3.3 14.0 + - - +
244B ARG* 2.8 54.1 + - - +
272B ILE* 5.8 1.1 - - - -
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Residues in contact with GLN 241 (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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195B ARG* 3.1 39.0 + - + +
196B TYR* 3.4 11.6 + - - +
198B LYS* 5.1 2.1 + - + +
203B LEU* 3.9 20.9 - - + -
216B TRP* 6.2 0.2 - - - +
233B PHE* 2.9 45.8 + - - +
235B GLY* 3.2 16.5 + - - -
237B ASP 3.2 20.5 + - - +
238B ASN* 4.4 4.7 - - - -
239B TYR 3.1 0.2 - - - -
240B ASP* 1.3 78.6 - - - +
242B LEU* 1.3 62.7 + - - +
244B ARG* 3.1 6.0 + - - +
245B ILE* 3.1 31.6 + - + +
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Residues in contact with LEU 242 (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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200B PRO* 4.6 14.1 - - + +
203B LEU* 3.7 26.8 - - + +
204B VAL* 4.0 18.2 - - + -
238B ASN 4.4 0.6 + - - +
239B TYR 3.3 9.6 + - - +
241B GLN* 1.3 78.4 - - - +
243B VAL* 1.3 53.0 + - - +
245B ILE* 3.2 12.2 + - + +
246B ALA* 2.7 35.7 + - - +
254B LEU* 4.4 32.3 - - + -
265B LEU* 5.3 1.8 - - + -
269B PHE* 3.6 39.9 - - + -
273B LEU* 4.7 3.6 - - + -
307B TYR* 4.6 7.2 - - + -
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Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TYR 3.2 17.2 + - - +
240B ASP* 3.4 19.7 - - - +
241B GLN 3.2 0.6 - - - -
242B LEU* 1.3 74.7 - - - +
244B ARG* 1.3 67.7 + - - +
246B ALA* 3.2 7.3 + - - +
247B LYS* 3.0 44.6 + - + +
269B PHE* 5.1 1.1 - - + -
272B ILE* 4.2 36.1 - - + +
273B LEU* 4.4 13.7 - - + +
276B HIS* 4.6 9.0 - - + +
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Residues in contact with ARG 244 (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 PHE* 4.1 19.8 - - + +
234B HIS* 2.7 39.9 + - - +
235B GLY* 4.1 1.1 - - - -
236B HIS* 4.0 17.2 + - - -
240B ASP* 2.8 46.0 + - - +
241B GLN* 3.3 9.9 - - - +
243B VAL* 1.3 79.9 - - - +
245B ILE* 1.3 61.5 + - - +
247B LYS* 3.6 27.7 + - - +
248B VAL* 3.7 17.7 - - - +
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Residues in contact with ILE 245 (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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198B LYS 4.4 6.3 - - - +
200B PRO* 5.0 3.1 - - + -
203B LEU* 4.1 22.0 - - + -
216B TRP* 3.6 41.7 - - + -
233B PHE* 3.6 33.2 - - + -
241B GLN* 3.1 21.7 + - - +
242B LEU* 3.5 11.0 - - + +
244B ARG* 1.3 73.0 - - - +
246B ALA* 1.3 61.3 + - - +
247B LYS 3.1 0.4 - - - -
248B VAL* 3.0 4.5 + - - +
249B LEU* 2.8 41.7 + - + +
307B TYR* 4.4 10.3 - - + +
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Residues in contact with ALA 246 (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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242B LEU* 2.7 20.6 + - + +
243B VAL* 3.2 10.5 + - - +
245B ILE* 1.3 73.7 - - - +
247B LYS* 1.3 57.4 + - - +
248B VAL 3.1 0.7 - - - -
250B GLY* 3.1 31.4 + - - +
251B THR* 4.9 2.7 - - - -
254B LEU* 4.3 10.1 - - + -
273B LEU* 4.3 16.4 - - + -
276B HIS* 3.3 18.2 - - + +
307B TYR* 3.4 15.7 + - + +
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Residues in contact with LYS 247 (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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243B VAL* 3.0 29.7 + - + +
244B ARG* 3.8 24.7 - - - +
245B ILE 3.1 0.2 - - - -
246B ALA* 1.3 76.9 - - - +
248B VAL* 1.3 61.9 + - + +
250B GLY 4.5 0.4 - - - -
276B HIS* 3.5 41.4 - - + +
277B SER 4.1 3.7 - - - +
279B LYS* 3.3 24.4 - - - +
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Residues in contact with VAL 248 (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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232B PHE* 4.8 1.8 - - + -
233B PHE* 4.0 19.7 - - + -
244B ARG 3.7 14.1 - - - +
245B ILE 3.0 5.5 + - - +
247B LYS* 1.3 83.8 - - + +
249B LEU* 1.3 61.1 + - + +
250B GLY 3.1 4.0 - - - -
278B ARG* 3.6 0.7 - - - +
279B LYS* 2.9 39.7 + - + +
281B TRP* 4.1 25.4 - - + -
284B PHE* 3.7 40.8 - - + -
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Residues in contact with LEU 249 (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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216B TRP* 3.6 36.8 - - + -
233B PHE* 5.0 2.2 - - + -
245B ILE* 2.8 22.2 + - + +
248B VAL* 1.3 77.0 - - + +
250B GLY* 1.3 62.7 + - - +
253B ASP* 3.5 13.2 - - - +
278B ARG* 3.2 33.6 + - - +
281B TRP* 3.6 36.3 - - + -
305B LEU* 3.8 16.8 - - + +
306B ARG* 4.7 1.1 - - - +
307B TYR* 3.3 33.5 - - + +
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Residues in contact with GLY 250 (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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246B ALA* 3.1 18.0 + - - +
248B VAL 3.1 4.4 + - - -
249B LEU* 1.3 80.6 - - - +
251B THR* 1.3 60.6 + - - -
252B GLU* 3.2 7.4 - - - -
254B LEU 4.2 0.3 + - - -
276B HIS 3.2 10.5 - - - -
277B SER 3.7 1.3 - - - -
278B ARG* 3.6 16.8 - - - -
307B TYR* 2.7 30.3 + - - -
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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