Contacts of the helix formed by residues 236 - 248 (chain N) in PDB entry 5U0A
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 ARG 236 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299D ALA 4.5 5.3 + - - -
302D THR* 2.8 47.4 + - + +
304D LEU* 4.9 8.1 - - - +
317D GLU* 2.7 39.8 + - - +
320D ASN* 5.6 0.6 - - - +
324D ARG* 4.7 11.3 - - - +
233N GLY 5.1 0.2 + - - -
234N PRO 4.1 1.4 + - - -
235N GLY* 1.3 72.1 - - - +
237N ASP* 1.3 61.9 + - - +
238N TYR* 3.2 4.1 - - - +
239N GLN* 3.3 31.8 + - - +
240N ASN* 3.2 31.1 + - - +
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Residues in contact with ASP 237 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232N ALA* 3.9 1.1 - - - -
233N GLY* 3.6 35.0 + - - +
234N PRO* 5.5 0.2 - - + -
235N GLY 2.9 8.3 + - - +
236N ARG* 1.3 76.5 - - - +
238N TYR* 1.3 60.7 + - - +
240N ASN* 3.1 15.7 + - - +
241N LYS* 2.8 62.5 + - - +
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Residues in contact with TYR 238 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D GLU* 5.5 11.0 - - + +
7N ARG* 3.7 36.2 + - - -
64N ASP* 3.7 11.6 + - - -
65N ARG* 5.3 9.2 - - - -
112N VAL* 4.1 4.8 - - + +
167N PRO* 4.6 1.7 + - + -
168N LEU* 3.1 25.8 - - - -
169N PRO* 3.0 43.7 - - + +
170N HIS 5.3 2.2 - - - +
232N ALA* 3.6 13.4 - - + +
233N GLY 4.5 3.6 + - - +
236N ARG* 3.2 2.6 - - - +
237N ASP* 1.3 78.4 - - - +
239N GLN* 1.3 64.3 + - + +
241N LYS* 3.5 1.1 + - - +
242N LEU* 3.0 50.4 + - + +
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Residues in contact with GLN 239 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D PRO* 3.7 22.1 + - + +
299D ALA* 4.6 2.5 - - - +
301D GLU* 5.8 2.0 - - - +
302D THR* 5.7 1.4 - - - +
317D GLU* 5.1 2.0 + - - +
321D TYR* 3.1 40.6 - - - -
324D ARG* 3.4 18.0 + - - +
236N ARG* 3.3 35.5 + - - +
237N ASP 3.3 0.2 - - - -
238N TYR* 1.3 82.4 - - + +
240N ASN* 1.3 63.6 + - - +
242N LEU* 3.4 5.5 + - + +
243N PHE* 2.9 45.3 + - + -
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Residues in contact with ASN 240 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D ARG* 2.5 35.0 + - - +
236N ARG* 3.2 20.1 + - - +
237N ASP* 3.1 23.5 + - - +
239N GLN* 1.3 77.4 - - - +
241N LYS* 1.3 63.5 + - + +
243N PHE* 3.1 6.8 + - - +
244N THR* 2.9 27.8 + - - +
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Residues in contact with LYS 241 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167N PRO* 3.6 21.9 - - + +
229N THR* 4.6 10.9 + - - +
230N LEU* 3.8 21.8 - - - +
231N VAL 4.7 0.4 - - - -
232N ALA* 3.5 24.0 - - + +
237N ASP* 2.8 39.4 + - - +
238N TYR 4.2 1.6 - - - +
240N ASN* 1.3 72.8 - - + +
242N LEU* 1.3 58.7 + - - +
244N THR* 3.4 8.6 + - - -
245N TYR* 2.9 28.8 + - - +
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Residues in contact with LEU 242 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7N ARG* 4.4 12.6 - - - +
148N LEU* 3.9 25.6 - - + -
151N LEU* 3.9 23.3 - - + -
166N VAL* 5.4 1.3 - - + -
167N PRO* 3.7 27.6 - - + +
238N TYR* 3.0 61.3 + - + +
239N GLN* 3.6 7.0 - - + +
241N LYS* 1.3 78.7 - - - +
243N PHE* 1.3 56.1 + - - +
245N TYR* 3.1 9.6 - - + +
246N VAL* 2.9 31.0 + - - +
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Residues in contact with PHE 243 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D TYR* 4.0 21.8 - + - -
324D ARG* 3.8 42.2 - - + +
325D LEU* 4.0 16.2 - - + -
328D VAL* 4.1 23.1 - - + +
329D TRP* 5.6 0.2 - + - -
148N LEU* 4.0 26.7 - - + -
239N GLN* 2.9 55.0 + - + +
240N ASN* 3.1 4.7 + - - +
242N LEU* 1.3 73.1 - - + +
244N THR* 1.3 68.1 + - - +
245N TYR 3.0 0.7 - - - -
246N VAL* 3.0 18.3 + - + +
247N LYS* 3.2 21.5 + - - +
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Residues in contact with THR 244 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240N ASN 2.9 15.2 + - - -
241N LYS* 3.5 12.0 - - - +
243N PHE* 1.3 76.7 - - - +
245N TYR* 1.3 61.8 + - - +
247N LYS* 3.6 15.4 + - - +
248N GLN* 3.4 43.5 + - + +
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Residues in contact with TYR 245 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5N LEU* 3.0 9.5 - - - +
151N LEU* 3.8 34.3 - - + -
152N ARG* 2.7 52.2 + - - +
161N GLU* 2.2 36.4 + - - -
165N ALA 2.7 29.4 - - - -
166N VAL* 2.7 19.0 - - + +
167N PRO* 3.5 20.6 - - + -
241N LYS 2.9 14.1 + - - +
242N LEU* 3.1 14.1 - - + +
244N THR* 1.3 75.1 - - - +
246N VAL* 1.3 69.6 + - + +
247N LYS 3.5 0.3 + - - -
248N GLN* 3.5 6.6 + - - -
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Residues in contact with VAL 246 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D VAL* 3.7 13.7 - - + -
329D TRP* 3.4 34.5 - - + -
148N LEU* 3.9 28.5 - - + -
151N LEU* 4.1 28.8 - - + +
152N ARG* 4.2 6.5 + - - +
242N LEU 2.9 15.0 + - - +
243N PHE* 3.0 8.2 + - + +
245N TYR* 1.3 79.4 - - + +
247N LYS* 1.3 64.3 + - - +
248N GLN 4.1 3.6 - - - +
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Residues in contact with LYS 247 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D GLU* 3.4 37.0 - - - +
328D VAL* 3.8 28.5 - - + +
243N PHE* 3.2 21.7 + - - -
244N THR* 4.1 14.7 + - - +
245N TYR 3.4 0.2 - - - -
246N VAL* 1.3 78.7 - - - +
248N GLN* 1.3 66.3 + - + +
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Residues in contact with GLN 248 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152N ARG* 3.4 43.7 + - - +
244N THR* 3.4 34.9 + - + +
245N TYR* 3.5 2.6 + - - -
246N VAL 3.4 2.0 - - - +
247N LYS* 1.3 85.0 - - + +
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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