Contacts of the helix formed by residues 230 - 243 (chain C) in PDB entry 5D4D
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 230 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198C ARG* 4.2 3.8 - - - +
228C ALA 3.9 2.4 + - - +
229C MET* 1.3 75.6 - - - +
231C PRO* 1.3 77.2 - - + +
232C GLU* 3.8 31.1 + - - +
233C GLU* 3.1 38.7 + - + +
234C ALA* 2.9 20.3 + - - +
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Residues in contact with PRO 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C ARG* 3.7 46.4 - - + +
199C VAL* 4.2 14.5 - - - +
201C GLY* 4.7 9.2 - - - +
230C ARG* 1.3 88.0 - - + +
232C GLU* 1.3 66.2 + - - +
234C ALA* 3.8 4.6 - - + +
235C LEU* 2.9 30.5 + - - +
297C GLU* 6.1 0.9 - - - +
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Residues in contact with GLU 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C ARG* 3.1 31.0 + - - +
231C PRO* 1.3 89.7 - - - +
233C GLU* 1.3 58.6 + - + +
235C LEU* 3.1 11.1 + - - +
236C ILE* 3.0 34.9 + - + +
250C ARG* 3.3 40.8 + - - +
297C GLU* 6.1 1.2 - - - +
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Residues in contact with GLU 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C MET* 3.3 29.5 - - + +
230C ARG* 3.1 49.8 + - - +
232C GLU* 1.3 76.5 - - + +
234C ALA* 1.3 57.4 + - - +
236C ILE* 3.4 9.1 + - + +
237C ARG* 2.9 28.6 + - - +
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Residues in contact with ALA 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C LEU* 3.7 23.6 - - + +
198C ARG* 3.8 28.5 - - + -
199C VAL* 3.6 8.6 - - + +
226C VAL 5.0 0.2 - - - +
229C MET* 4.0 11.6 - - + -
230C ARG 2.9 15.0 + - - +
231C PRO 3.9 4.3 - - - +
233C GLU* 1.3 74.4 - - - +
235C LEU* 1.3 59.6 + - - +
237C ARG* 4.2 0.4 - - - -
238C LEU* 2.9 30.1 + - - +
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Residues in contact with LEU 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C VAL* 3.5 27.8 - - + +
231C PRO 2.9 15.6 + - - +
232C GLU* 3.2 11.4 - - - +
234C ALA* 1.3 77.2 - - - +
236C ILE* 1.3 58.0 + - + +
238C LEU* 3.3 3.4 + - + +
239C PHE* 2.9 27.5 + - - +
250C ARG* 4.6 13.7 - - + +
253C ALA* 4.2 10.1 - - + +
254C VAL* 3.5 34.3 - - + +
257C VAL* 3.6 32.8 - - + -
298C PHE* 4.2 11.7 - - + -
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Residues in contact with ILE 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C GLU* 3.0 18.1 + - + +
233C GLU* 3.9 7.2 - - - +
235C LEU* 1.3 75.8 - - + +
237C ARG* 1.3 56.6 + - - +
239C PHE* 3.3 7.3 + - + +
240C THR* 2.9 35.9 + - + +
248C PRO* 3.4 36.8 - - + +
249C LYS 5.2 0.4 - - - +
250C ARG* 3.7 44.0 - - + -
253C ALA* 4.7 3.1 - - + -
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Residues in contact with ARG 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C LEU* 3.7 21.5 - - + +
229C MET* 4.5 15.4 - - + +
233C GLU 2.9 18.5 + - - +
234C ALA* 3.7 7.6 - - - +
236C ILE* 1.3 77.0 - - - +
238C LEU* 1.3 56.7 + - - +
240C THR* 2.5 27.3 + - - -
241C LEU* 3.0 43.1 + - - +
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Residues in contact with LEU 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C PHE* 3.4 41.1 - - + -
195C LEU* 3.6 14.4 - - + -
196C LEU* 4.1 35.7 - - + -
199C VAL* 4.2 9.6 - - + -
234C ALA 2.9 18.1 + - - +
235C LEU* 3.6 5.2 - - + +
237C ARG* 1.3 76.8 - - - +
239C PHE* 1.3 58.0 + - - +
241C LEU* 2.9 7.3 + - + +
242C LEU* 2.9 50.8 + - + +
257C VAL* 4.8 17.3 - - + -
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Residues in contact with PHE 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C LEU 2.9 17.2 + - - +
236C ILE* 3.6 4.7 - - - +
238C LEU* 1.3 75.8 - - - +
240C THR* 1.3 60.3 + - - +
242C LEU* 4.5 5.4 - - - +
243C ARG* 2.9 40.9 + - + +
246C ASP* 3.7 36.1 - - + -
247C PRO 3.8 20.6 - - - -
248C PRO* 4.1 14.8 - - + -
249C LYS 4.7 2.0 - - - -
252C LYS* 4.1 15.0 - - + -
253C ALA* 3.5 32.8 - - + -
256C TYR* 3.8 34.5 - + + -
257C VAL* 5.1 4.2 - - + +
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Residues in contact with THR 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C ILE* 2.9 19.3 + - + +
237C ARG* 2.5 36.0 + - - -
239C PHE* 1.3 77.2 - - + +
241C LEU* 1.3 64.5 + - - +
243C ARG 4.0 7.3 - - - +
244C PRO* 4.0 18.9 - - - +
246C ASP 5.4 1.1 - - - +
248C PRO* 3.5 36.8 - - + -
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Residues in contact with LEU 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C ARG* 3.7 20.1 + - - +
191C PHE* 4.2 23.3 - - + -
192C PRO* 4.8 7.4 - - + -
195C LEU* 3.7 26.0 - - + -
237C ARG* 3.0 43.9 + - - +
238C LEU* 2.9 13.7 + - + +
240C THR* 1.3 83.3 - - - +
242C LEU* 1.3 63.0 + - + +
244C PRO* 4.2 2.8 - - - +
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Residues in contact with LEU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C VAL* 5.0 9.9 - - + +
189C ARG* 3.1 37.6 + - + +
191C PHE* 4.1 30.5 - - + -
238C LEU* 2.9 36.6 + - + +
239C PHE* 4.2 2.9 - - - +
241C LEU* 1.3 79.7 - - + +
243C ARG* 1.3 65.8 + - + +
244C PRO* 3.5 3.4 - - - +
256C TYR* 3.6 39.0 + - + +
257C VAL* 5.2 4.0 - - + -
260C LEU* 4.0 18.4 - - + -
82F ARG* 5.4 0.2 + - - -
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Residues in contact with ARG 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C PHE* 2.9 38.9 + - + +
240C THR* 4.0 7.7 - - - +
242C LEU* 1.3 90.6 - - + +
244C PRO* 1.3 65.9 - - - +
245C GLY 3.5 0.5 + - - -
246C ASP* 2.8 53.0 + - + +
256C TYR* 4.2 22.1 - - + -
82F ARG* 3.1 18.1 - - - +
8H G 4.1 3.4 + - - -
9H G 2.7 38.0 + - - -
10H A 3.0 31.9 + - - +
11H G 5.4 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
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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