Contacts of the helix formed by residues 241 - 255 (chain C) in PDB entry 2OFJ
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 SER 241 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C LEU* 4.1 17.2 - - - +
84C ALA* 3.6 20.8 - - - +
88C SER* 3.5 9.0 - - - -
240C GLY* 1.3 75.2 - - - +
242C LEU* 1.3 59.8 + - - +
243C GLU* 3.4 16.4 + - - +
244C LYS* 3.0 27.7 + - - +
245C VAL* 2.9 26.0 + - - +
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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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85C PHE* 4.0 9.9 - - + -
88C SER* 3.2 26.1 + - - +
89C CYS* 3.9 15.0 - - - -
92C ALA* 3.4 33.0 - - + -
98C LEU* 4.9 5.2 - - + -
241C SER* 1.3 73.2 - - - +
243C GLU* 1.3 69.2 + - - +
245C VAL* 3.5 9.4 + - + +
246C ARG* 3.0 28.4 + - - +
277C ILE* 3.4 37.2 - - + -
280C TRP* 4.1 25.9 - - + -
281C LEU* 4.7 3.3 - - + +
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Residues in contact with GLU 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 4.5 8.5 - - + +
88C SER* 4.3 6.1 - - - -
241C SER* 3.2 15.4 + - - +
242C LEU* 1.3 85.7 + - - +
244C LYS* 1.3 64.8 + - - +
246C ARG* 3.4 30.4 + - - +
247C GLU* 3.1 34.0 + - - +
280C TRP* 5.8 1.4 - - - -
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Residues in contact with LYS 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PRO* 6.3 0.2 - - - +
239C THR* 3.5 38.4 + - + +
240C GLY* 4.8 0.4 - - - -
241C SER* 3.0 24.2 + - - +
243C GLU* 1.3 76.9 - - - +
245C VAL* 1.3 64.4 + - - +
246C ARG 3.3 0.2 + - - -
247C GLU* 3.3 18.0 + - - +
248C GLN* 3.2 40.0 + - + +
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Residues in contact with VAL 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C ILE* 4.0 10.3 - - + -
236C PRO* 3.8 32.1 - - + -
239C THR* 4.4 6.1 - - + -
240C GLY 4.1 5.4 - - - +
241C SER 2.9 18.5 + - - +
242C LEU* 3.7 14.4 - - + +
243C GLU 3.4 0.2 - - - -
244C LYS* 1.3 74.9 - - - +
246C ARG* 1.3 61.6 + - - +
248C GLN* 3.5 9.7 + - - +
249C VAL* 3.1 28.6 + - + +
261C ILE* 3.7 30.3 - - + -
277C ILE* 4.5 7.4 - - + -
281C LEU* 3.7 13.9 - - + -
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Residues in contact with ARG 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C LEU 3.0 17.0 + - - +
243C GLU* 3.6 31.8 + - - +
244C LYS 3.2 0.4 - - - -
245C VAL* 1.3 75.8 - - - +
247C GLU* 1.3 64.0 + - - +
249C VAL* 3.4 2.4 + - + +
250C GLN* 2.9 48.4 + - + +
280C TRP* 3.5 37.5 - - + -
281C LEU* 3.9 26.1 - - + +
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Residues in contact with GLU 247 (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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243C GLU* 3.1 21.1 + - - +
244C LYS* 3.5 19.2 - - - +
246C ARG* 1.3 77.4 - - + +
248C GLN* 1.3 55.0 + - + +
250C GLN* 3.2 7.7 + - - +
251C ALA* 2.8 37.2 + - - +
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Residues in contact with GLN 248 (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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216C LEU* 3.6 39.3 - - + +
217C ARG* 6.4 0.2 - - - +
223C PHE* 3.5 34.5 - - + -
234C ILE* 3.9 22.9 - - + +
239C THR* 3.4 33.3 + - - +
244C LYS* 3.2 25.7 + - + +
245C VAL* 3.8 4.0 - - - +
247C GLU* 1.3 80.6 - - + +
249C VAL* 1.3 57.7 + - - +
251C ALA 3.5 0.2 + - - -
252C ALA* 3.0 25.8 + - - +
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Residues in contact with VAL 249 (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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234C ILE* 3.5 23.1 - - + -
245C VAL* 3.1 27.4 + - + +
246C ARG* 3.6 6.1 - - - +
247C GLU 3.2 0.2 - - - -
248C GLN* 1.3 72.1 - - - +
250C GLN* 1.3 70.4 + - + +
252C ALA* 2.8 17.5 + - - +
253C HIS* 3.0 43.7 + - + +
259C ALA* 4.6 2.0 - - + -
261C ILE* 4.4 7.9 - - + -
281C LEU* 3.5 25.8 - - + +
282C THR* 4.1 7.9 - - + -
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Residues in contact with GLN 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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246C ARG* 2.9 41.6 + - + +
247C GLU* 3.8 6.4 - - - +
249C VAL* 1.3 80.8 - - + +
251C ALA* 1.3 60.0 + - - +
253C HIS* 3.7 8.5 + - - +
254C ALA* 3.1 23.9 + - - +
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Residues in contact with ALA 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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223C PHE* 3.6 32.5 - - + +
247C GLU 2.8 21.6 + - - +
248C GLN* 3.6 5.8 - - - +
250C GLN* 1.3 75.0 - - - +
252C ALA* 1.3 61.3 + - - +
254C ALA* 3.4 18.5 + - - +
255C LEU* 3.4 15.2 + - - +
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Residues in contact with ALA 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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223C PHE* 4.0 5.1 - - + -
232C VAL* 3.8 27.4 - - + -
248C GLN 3.0 12.9 + - - +
249C VAL 2.8 14.3 + - - +
251C ALA* 1.3 69.6 - - - +
253C HIS* 1.3 62.3 + - - +
255C LEU 3.1 7.6 + - - -
257C LEU* 2.9 46.1 + - + +
259C ALA* 4.2 13.0 - - + -
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Residues in contact with HIS 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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249C VAL* 3.0 40.1 + - + +
250C GLN* 4.0 7.5 - - - +
252C ALA* 1.3 74.4 - - - +
254C ALA* 1.3 65.7 + - - +
256C GLY* 3.1 13.3 + - - +
257C LEU 3.5 18.4 - - - +
258C THR* 5.1 0.9 - - - -
259C ALA* 4.1 16.4 + - + +
281C LEU 3.5 14.4 - - - -
282C THR* 4.3 3.6 - - + +
284C ASP* 4.1 24.2 + - - -
285C THR* 5.2 0.6 + - - -
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Residues in contact with ALA 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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250C GLN 3.1 18.7 + - - +
251C ALA* 3.4 11.0 - - - +
252C ALA 3.2 0.4 - - - -
253C HIS* 1.3 79.4 - - - +
255C LEU* 1.3 59.8 + - + +
256C GLY 3.5 2.3 + - - -
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Residues in contact with LEU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C PHE* 3.6 43.3 - - + +
224C VAL* 3.9 2.5 - - - +
225C ALA* 3.9 37.1 - - + +
226C GLU* 5.7 1.1 - - - +
230C ARG* 4.9 4.5 + - - -
251C ALA 3.5 9.2 - - - +
252C ALA 3.1 7.8 + - - +
254C ALA* 1.3 79.1 - - + +
256C GLY* 1.3 60.0 + - - +
257C LEU* 3.3 32.8 + - + +
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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