Contacts of the helix formed by residues 249 - 261 (chain C) in PDB entry 4OIR
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 LYS 249 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239C PHE* 4.8 0.4 - - - -
247C PRO* 3.0 14.3 + - + +
248C PRO* 1.3 75.3 - - - +
250C ARG* 1.3 69.3 + - + +
251C ASP* 3.2 31.9 - - - +
252C LYS* 3.8 15.8 - - + +
253C ALA* 3.0 23.1 + - - +
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Residues in contact with ARG 250 (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* 4.6 29.1 + - + +
235C LEU* 5.0 2.6 - - + +
236C ILE* 4.8 19.0 - - + +
248C PRO 3.7 1.8 + - - -
249C LYS* 1.3 74.4 - - - +
251C ASP* 1.3 69.1 + - - +
253C ALA* 3.0 8.1 + - - +
254C VAL* 2.9 55.0 + - + +
293C PHE* 5.5 2.4 - - - -
296C GLY* 4.2 17.2 + - - -
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Residues in contact with ASP 251 (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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249C LYS* 3.2 33.6 - - - +
250C ARG* 1.3 93.9 - - - +
252C LYS* 1.3 67.2 + - - +
254C VAL* 3.9 6.0 - - - +
255C ALA* 2.9 30.0 + - - +
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Residues in contact with LYS 252 (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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239C PHE* 3.9 11.9 - - + -
243C ARG* 5.4 1.8 - - - +
246C ASP* 2.5 41.8 + - - +
247C PRO* 4.1 16.4 - - + +
249C LYS* 3.8 21.5 - - + +
250C ARG 3.2 0.8 - - - -
251C ASP* 1.3 82.6 + - - +
253C ALA* 1.3 60.2 + - - +
255C ALA* 3.7 6.0 - - + +
256C TYR* 2.9 29.3 + - + +
7H G 6.4 0.4 - - - +
8H G 5.4 7.9 + - - -
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Residues in contact with ALA 253 (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* 4.2 18.2 - - + +
236C ILE* 4.8 7.4 - - + -
239C PHE* 3.5 37.8 - - + -
248C PRO 5.4 0.4 - - - -
249C LYS 3.0 18.6 + - - +
250C ARG* 3.4 6.1 - - - +
252C LYS* 1.3 74.3 - - - +
254C VAL* 1.3 66.0 + - - +
256C TYR* 3.3 1.0 + - - +
257C VAL* 2.9 28.2 + - - +
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Residues in contact with VAL 254 (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* 3.6 22.6 - - + +
250C ARG* 2.9 49.4 + - + +
251C ASP* 3.9 6.1 - - - +
253C ALA* 1.3 73.8 - - - +
255C ALA* 1.3 58.7 + - - +
257C VAL* 4.7 0.2 - - - -
258C TYR* 2.9 35.5 + - + +
293C PHE* 3.8 22.7 - - + -
298C PHE* 3.6 23.8 - - + -
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Residues in contact with ALA 255 (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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251C ASP 2.9 19.0 + - - +
252C LYS* 3.7 7.9 - - + +
253C ALA 3.2 0.2 - - - -
254C VAL* 1.3 77.4 - - - +
256C TYR* 1.3 57.2 + - - +
258C TYR* 3.8 9.1 - - - +
259C GLY* 2.9 25.6 + - - -
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Residues in contact with TYR 256 (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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187C ASN* 4.3 5.4 + - - -
239C PHE* 3.6 26.7 - + + -
242C LEU* 4.3 27.6 + - + +
243C ARG* 4.0 40.2 - - + -
252C LYS* 2.9 18.9 + - + +
253C ALA 3.9 0.7 - - - +
255C ALA* 1.3 73.6 - - - +
257C VAL* 1.3 66.1 + - + +
259C GLY* 3.2 3.1 + - - -
260C LEU* 2.9 52.0 + - + +
266C ARG* 6.1 2.0 - - - -
10H A 4.7 7.2 - - - -
11H G 3.7 30.5 + - - -
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Residues in contact with VAL 257 (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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196C LEU* 5.1 5.8 - - + -
199C VAL* 5.0 3.8 - - + -
235C LEU* 3.8 26.2 - - + -
238C LEU* 4.2 23.1 - - + -
239C PHE* 6.3 0.4 - - + -
242C LEU* 5.4 4.9 - - + -
253C ALA 2.9 13.1 + - - +
254C VAL 3.9 2.0 - - - +
256C TYR* 1.3 84.7 - - + +
258C TYR* 1.3 61.0 + - - +
260C LEU* 3.3 6.2 + - + -
261C ILE* 2.9 42.4 + - + +
298C PHE* 3.5 30.9 - - + -
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Residues in contact with TYR 258 (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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254C VAL* 2.9 22.9 + - + +
255C ALA* 3.8 8.3 - - - +
257C VAL* 1.3 75.9 - - - +
259C GLY* 1.3 59.7 + - - +
262C ALA* 3.0 41.2 + - + +
263C ASP* 2.8 66.6 + - - +
264C PRO* 3.9 8.3 - - - +
265C ARG* 5.6 1.7 - - - -
293C PHE* 3.9 26.9 - + + -
298C PHE* 3.9 13.5 - - + -
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Residues in contact with GLY 259 (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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255C ALA 2.9 15.4 + - - -
256C TYR* 3.2 5.1 + - - -
258C TYR* 1.3 76.7 - - - +
260C LEU* 1.3 60.3 + - - +
263C ASP* 3.7 19.1 - - - +
266C ARG* 3.5 38.2 + - - +
267C TYR* 4.3 4.2 + - - +
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Residues in contact with LEU 260 (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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170C PRO* 4.2 20.8 - - + +
184C MET* 6.2 0.7 - - + -
186C VAL* 3.7 25.1 - - + -
187C ASN* 4.0 17.0 - - - +
242C LEU* 4.7 12.6 - - + -
256C TYR* 2.9 45.3 + - + +
257C VAL* 3.7 9.4 - - + +
258C TYR 3.2 0.2 - - - -
259C GLY* 1.3 77.9 - - - +
261C ILE* 1.3 78.0 + - + +
267C TYR* 3.6 23.1 - - - -
11H G 5.1 11.2 - - + +
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Residues in contact with ILE 261 (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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172C ILE* 4.4 14.4 - - + -
184C MET* 5.0 5.4 - - + -
196C LEU* 5.4 9.2 - - + -
200C LEU* 6.2 1.8 - - + -
257C VAL* 2.9 24.6 + - + +
258C TYR* 5.3 0.2 - - - -
260C LEU* 1.3 103.6 - - + +
262C ALA* 1.3 62.7 + - + +
263C ASP 3.4 3.1 + - - -
267C TYR* 3.9 10.7 - - + +
289C THR* 3.4 19.1 - - - +
290C LEU* 3.9 15.6 + - + -
291C ALA* 3.5 33.2 - - + +
298C PHE* 6.4 1.6 - - + -
303C PHE* 4.3 23.8 - - + -
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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