Contacts of the helix formed by residues 246 - 260 (chain C) in PDB entry 4QYJ
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 246 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243C PHE* 3.3 11.3 - - - -
245C GLY* 1.3 71.2 - - - -
247C THR* 1.3 63.9 + - - +
248C GLU* 3.1 21.1 + - - +
249C VAL* 3.2 24.5 + - - +
250C GLY 3.3 14.9 + - - -
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Residues in contact with THR 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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245C GLY 3.4 3.8 + - - -
246C SER* 1.3 72.5 + - - +
248C GLU* 1.3 67.4 + - + +
250C GLY* 3.4 7.3 + - - -
251C ARG* 3.4 24.2 + - - +
268C LEU* 3.4 38.4 - - - +
269C GLY* 3.7 10.9 - - - +
400C GLU* 5.5 1.9 + - - +
426C TYR* 3.4 34.5 - - + +
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Residues in contact with GLU 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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246C SER* 3.1 10.0 + - - +
247C THR* 1.3 80.6 - - + +
249C VAL* 1.3 60.6 + - + +
250C GLY 2.9 4.0 - - - -
251C ARG* 2.8 34.9 + - - +
252C ILE* 3.4 6.5 + - - +
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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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243C PHE* 4.0 12.8 - - + -
246C SER* 3.2 25.8 + - - +
248C GLU* 1.3 76.4 - - + +
250C GLY* 1.3 56.4 + - - +
252C ILE* 3.1 17.0 + - + +
253C ILE* 3.0 44.0 + - + +
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Residues in contact with GLY 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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243C PHE* 3.8 23.1 - - - -
246C SER 3.3 6.9 + - - -
247C THR 3.6 7.0 - - - -
248C GLU 2.9 1.6 + - - -
249C VAL* 1.3 78.9 - - - +
251C ARG* 1.3 55.3 + - - +
253C ILE* 3.4 2.7 + - - +
254C GLY* 2.8 25.6 + - - -
266C LEU* 3.7 15.6 - - - +
268C LEU* 3.8 10.5 - - - -
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Residues in contact with ARG 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C THR* 3.4 23.1 + - - +
248C GLU* 2.8 19.7 + - - +
250C GLY* 1.3 70.4 - - - -
252C ILE* 1.3 61.4 + - + +
254C GLY* 4.3 2.5 - - - +
255C SER* 3.2 26.0 + - - -
266C LEU* 5.8 0.2 - - - -
268C LEU* 5.3 1.5 - - + +
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Residues in contact with ILE 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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230C ASP* 5.3 9.2 - - - +
248C GLU 4.1 3.4 - - - +
249C VAL* 3.1 26.2 + - + +
251C ARG* 1.3 77.2 - - + +
253C ILE* 1.3 66.5 + - + +
255C SER* 3.6 5.1 + - - -
256C ALA* 3.1 25.3 + - + +
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Residues in contact with ILE 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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165C ILE* 4.4 12.3 - - + -
233C VAL* 3.9 19.3 - - + -
241C VAL* 3.5 28.3 - - + -
243C PHE* 3.5 38.4 - - + -
249C VAL* 3.0 28.2 + - + +
250C GLY 3.8 5.6 - - - +
252C ILE* 1.3 75.0 - - + +
254C GLY* 1.3 54.6 + - - +
256C ALA* 3.3 6.3 + - - +
257C CYS* 2.7 47.9 + - - +
264C VAL* 4.2 7.4 - - + -
266C LEU* 4.3 5.8 - - + -
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Residues in contact with GLY 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 GLY 2.8 20.3 + - - -
251C ARG* 4.0 3.4 - - - -
252C ILE 3.4 0.2 - - - -
253C ILE* 1.3 72.6 - - - +
255C SER* 1.3 64.7 + - - +
257C CYS* 2.9 4.2 + - - +
258C GLY* 2.9 22.2 + - - -
264C VAL* 5.1 6.1 - - - -
266C LEU* 4.7 10.5 - - - +
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Residues in contact with SER 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 ARG 3.2 15.4 + - - -
252C ILE* 3.7 9.2 - - - -
253C ILE 3.5 0.2 - - - -
254C GLY* 1.3 72.4 - - - +
256C ALA* 1.3 64.9 + - - +
258C GLY* 3.2 8.1 + - - -
259C ARG* 3.2 16.0 + - - +
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Residues in contact with ALA 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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233C VAL* 3.8 23.3 - - + -
234C ARG* 5.9 4.0 - - + -
252C ILE* 3.1 18.5 + - + +
253C ILE* 3.6 3.8 - - - +
255C SER* 1.3 79.6 - - - +
257C CYS* 1.3 56.9 + - - +
259C ARG* 3.8 4.0 + - - +
260C SER* 3.1 32.6 + - - -
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Residues in contact with CYS 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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233C VAL* 4.7 4.3 - - - -
241C VAL* 3.4 40.2 - - - -
253C ILE* 2.7 26.7 + - - +
254C GLY 3.6 3.4 - - - +
256C ALA* 1.3 74.2 - - - +
258C GLY* 1.3 58.2 + - - +
260C SER 3.4 1.4 + - - -
261C LEU 3.0 6.8 + - - -
262C LYS* 2.9 56.5 + - + +
264C VAL* 3.8 22.2 - - + -
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Residues in contact with GLY 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 GLY 2.9 13.0 + - - -
255C SER 3.7 2.7 - - - -
257C CYS* 1.3 77.9 - - - +
259C ARG* 1.3 61.7 + - - +
260C SER 3.3 0.2 - - - -
261C LEU* 3.5 18.8 + - - +
262C LYS 5.1 1.3 - - - -
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Residues in contact with ARG 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 SER 3.2 14.1 + - - +
256C ALA* 4.3 3.8 - - - +
258C GLY* 1.3 74.7 - - - +
260C SER* 1.3 62.2 + - - +
261C LEU* 3.6 7.0 + - - +
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Residues in contact with SER 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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233C VAL 5.4 0.7 + - - -
234C ARG* 5.5 4.2 - - - -
256C ALA 3.1 21.3 + - - -
257C CYS 3.7 2.9 - - - -
258C GLY 3.3 0.2 - - - -
259C ARG* 1.3 78.2 - - - +
261C LEU* 1.3 70.1 + - - +
262C LYS* 3.2 33.7 + - - +
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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