Contacts of the helix formed by residues 239 - 256 (chain C) in PDB entry 4DAJ
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 PHE 239 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ALA 2.7 12.5 + - - +
237C ALA 3.4 0.4 - - - -
238C ALA* 1.3 79.3 - - - +
240C TYR* 1.3 92.1 + + - +
241C MET 3.2 2.2 - - - -
242C PRO* 2.9 13.1 - - - +
243C VAL* 2.9 32.3 + - + +
499C PHE* 3.8 15.9 - + - -
500C ILE 4.7 0.4 - - - -
503C TRP* 3.4 40.6 - + + -
504C THR* 3.1 42.2 - - + -
507C ASN* 3.2 39.3 - - + +
2000C 0HK 3.0 16.8 - - - +
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Residues in contact with TYR 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C PHE* 4.9 4.7 - + - -
235C ALA* 2.9 52.6 + - + +
236C ILE* 3.3 21.8 - - + +
239C PHE* 1.3 89.1 - + - +
241C MET* 1.3 56.4 + - - +
243C VAL* 3.3 4.0 + - - +
244C THR* 2.9 40.0 + - + +
504C THR* 6.3 0.4 - - + -
507C ASN* 2.5 48.2 + - + -
508C ILE* 3.6 5.2 + - + -
511C LEU* 3.6 23.1 + - + +
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Residues in contact with MET 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C LEU* 6.2 0.7 - - - -
236C ILE* 2.8 17.7 + - - +
237C ALA* 4.0 15.3 - - - +
240C TYR* 1.3 70.0 - - - +
242C PRO* 1.3 78.4 - - + +
244C THR* 2.9 21.2 + - - -
245C ILE* 2.9 20.5 + - + +
233D GLY* 3.4 36.8 - - - +
234D THR* 5.4 0.2 - - - -
236D ILE* 3.7 40.2 - - + -
237D ALA* 3.7 16.6 - - + -
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Residues in contact with PRO 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C VAL* 5.3 9.4 - - + -
159C LEU* 3.6 34.4 - - + +
237C ALA 3.3 19.7 - - - +
238C ALA* 4.0 12.1 - - - +
239C PHE* 2.9 20.4 - - - +
241C MET* 1.3 100.8 - - + +
243C VAL* 1.3 54.6 + - + +
245C ILE* 4.6 1.1 - - + -
246C MET* 2.9 42.7 + - + +
499C PHE* 6.3 0.9 - - + -
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Residues in contact with VAL 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 41.4 + - + +
240C TYR* 3.3 10.1 - - - +
242C PRO* 1.3 76.1 - - + +
244C THR* 1.3 67.9 + - + +
246C MET* 3.2 11.8 + - - +
247C THR* 2.9 26.6 + - - +
496C LEU* 5.3 3.3 - - + +
499C PHE* 3.5 30.3 - - + -
500C ILE* 4.4 27.8 - - + -
504C THR* 5.3 1.1 - - + -
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Residues in contact with THR 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C TYR* 2.9 24.3 + - + +
241C MET* 2.9 14.8 + - - -
243C VAL* 1.3 75.9 - - + +
245C ILE* 1.3 73.3 + - - +
247C THR* 3.0 7.7 + - - -
248C ILE* 2.9 38.1 + - - +
232D PHE* 5.3 2.7 - - - -
236D ILE* 4.5 12.4 - - + +
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Residues in contact with ILE 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C LEU* 4.5 9.9 - - + -
163C PHE* 3.9 26.9 - - + -
241C MET* 2.9 23.8 + - + +
242C PRO* 3.9 4.7 - - + +
244C THR* 1.3 83.6 + - - +
246C MET* 1.3 62.3 + - + +
247C THR 3.1 0.5 + - - -
248C ILE* 3.1 6.9 + - - +
249C LEU* 2.9 38.4 + - + +
229D THR* 3.6 24.2 - - + +
230D ILE* 4.7 4.7 - - - -
232D PHE* 4.9 9.9 - - + -
233D GLY* 3.5 31.0 - - - +
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Residues in contact with MET 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C VAL* 4.9 2.9 - - + +
158C LEU* 3.4 33.9 - - + +
159C LEU* 3.4 29.6 - - + -
162C SER* 3.9 19.0 + - - +
163C PHE* 6.4 0.2 - - + -
242C PRO* 2.9 33.3 + - + +
243C VAL* 3.2 10.7 + - - +
245C ILE* 1.3 78.9 - - + +
247C THR* 1.3 56.2 - - - +
249C LEU* 3.9 5.6 - - + +
250C TYR* 2.9 30.2 + - - +
496C LEU* 3.7 28.5 - - + +
499C PHE* 4.1 19.7 - - + -
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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
----------------------------------------------------------
243C VAL* 2.9 19.0 + - - +
244C THR* 3.0 10.9 + - - +
246C MET* 1.3 74.1 - - - +
248C ILE* 1.3 72.5 + - + +
249C LEU 3.1 1.8 - - - -
250C TYR* 3.0 5.4 + - - -
251C TRP* 2.9 54.8 + - + +
496C LEU* 4.6 9.4 - - - +
500C ILE* 5.4 6.1 - - - +
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Residues in contact with ILE 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C THR* 2.9 27.8 + - - +
245C ILE* 3.9 5.8 - - + +
247C THR* 1.3 82.0 - - + +
249C LEU* 1.3 60.9 + - + +
251C TRP* 4.2 4.7 + - - +
252C ARG* 3.5 36.4 + - - +
229D THR* 5.5 7.4 - - + -
232D PHE* 5.4 13.7 - - + -
514D THR* 5.2 6.7 - - + -
515D PHE* 4.2 35.4 - - + -
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Residues in contact with LEU 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C SER* 4.3 10.3 - - - -
163C PHE* 3.8 55.4 - - + +
166C TYR* 4.2 31.4 - - + -
245C ILE* 2.9 25.8 + - + +
246C MET* 3.9 5.2 - - + +
248C ILE* 1.3 76.4 - - + +
250C TYR* 1.3 57.3 + - - +
251C TRP 3.1 2.0 - - - -
252C ARG* 2.7 28.4 + - - +
253C ILE* 2.9 17.1 + - + +
229D THR* 3.8 29.2 - - + +
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Residues in contact with TYR 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C SER* 5.7 0.7 - - - +
246C MET 2.9 23.0 + - - +
247C THR* 3.0 2.9 + - - +
249C LEU* 1.3 74.5 - - - +
251C TRP* 1.3 106.0 + + - +
253C ILE* 3.4 7.1 + - - +
254C TYR* 2.9 45.0 + - + +
489C ALA* 4.6 5.8 - - + -
492C LEU* 3.8 30.7 - - + -
493C SER* 2.5 47.2 + - - -
496C LEU* 3.5 20.2 - - + -
497C LEU* 5.7 7.0 - - + +
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Residues in contact with TRP 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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247C THR* 2.9 49.3 + - + +
248C ILE* 4.6 5.4 - - - +
250C TYR* 1.3 109.6 - + - +
252C ARG* 1.3 58.7 + - + +
254C TYR* 4.0 32.2 - + - +
255C LYS* 2.9 27.5 + - - +
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Residues in contact with ARG 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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166C TYR* 3.6 42.2 + - + -
169C ILE* 5.8 1.4 - - - +
248C ILE* 3.5 24.8 + - - +
249C LEU* 2.7 17.1 + - - +
251C TRP* 1.3 72.9 - - - +
253C ILE* 1.3 58.0 + - - +
254C TYR 3.3 0.2 - - - -
255C LYS* 3.5 10.7 - - + +
256C GLU* 3.1 28.1 + - - +
228D PRO* 5.2 4.8 - - - +
229D THR* 4.5 13.5 - - - +
514D THR* 3.2 29.0 + - - +
515D PHE* 3.9 25.9 - - - +
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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
----------------------------------------------------------
162C SER* 3.2 30.7 - - - +
165C ARG* 3.7 18.8 - - + -
166C TYR* 3.2 33.2 - - + +
169C ILE* 4.7 14.3 - - + +
249C LEU* 2.9 17.7 + - + +
250C TYR* 3.9 7.4 - - - +
252C ARG* 1.3 74.4 - - - +
254C TYR* 1.3 60.8 + - - +
256C GLU 3.9 8.6 - - - +
257C THR* 3.2 21.0 + - + +
489C ALA* 3.9 24.2 + - - +
492C LEU* 4.2 16.8 - - + -
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Residues in contact with TYR 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C TYR* 2.9 33.3 + - + +
251C TRP* 4.0 33.2 - + + +
253C ILE* 1.3 77.3 - - - +
255C LYS* 1.3 72.3 + - - +
257C THR* 4.2 6.3 + - - -
489C ALA* 3.9 26.7 - - + +
493C SER* 4.9 1.8 - - - -
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Residues in contact with LYS 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 TRP 2.9 21.4 + - - +
252C ARG* 3.5 13.2 - - + +
253C ILE 3.4 0.2 - - - -
254C TYR* 1.3 85.8 - - - +
256C GLU* 1.3 64.7 + - + +
257C THR 3.8 1.6 + - - -
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Residues in contact with GLU 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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169C ILE* 3.6 26.2 - - + +
252C ARG 3.1 10.9 + - - +
253C ILE 3.9 5.7 - - - +
255C LYS* 1.3 84.3 - - + +
257C THR* 1.3 58.0 + - - +
258C GLU* 3.3 26.5 - - + +
259C LYS* 4.7 15.6 + - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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