Contacts of the helix formed by residues 242 - 258 (chain C) in PDB entry 5DQZ
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 GLU 242 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240C PRO* 4.2 6.8 - - - +
241C GLY* 1.3 79.0 - - - +
243C PRO* 1.3 69.7 - - - +
244C ASP* 3.3 6.2 + - + +
245C ARG* 3.8 20.8 + - + +
246C GLU* 4.4 5.4 + - - +
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Residues in contact with PRO 243 (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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175C THR* 5.0 4.9 - - + -
178C GLN* 3.8 25.6 - - + +
179C CYS* 3.8 29.4 - - - -
235C ILE* 4.5 0.2 - - - +
240C PRO* 3.8 23.3 - - + +
241C GLY 3.4 12.8 - - - +
242C GLU* 1.3 82.4 - - - +
244C ASP* 1.3 71.7 + - - +
246C GLU* 3.2 7.4 + - - +
247C VAL* 2.9 31.0 + - + +
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Residues in contact with ASP 244 (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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80C GLU* 4.8 7.8 - - - +
81C ALA* 3.9 33.4 + - - -
82C GLY* 4.7 3.1 - - - +
178C GLN* 5.0 4.5 - - - +
182C ALA* 4.2 14.4 - - + +
242C GLU* 3.3 4.5 + - + +
243C PRO* 1.3 87.0 - - - +
245C ARG* 1.3 57.6 + - - +
247C VAL* 3.3 8.5 + - - +
248C ARG* 2.9 51.3 + - - +
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Residues in contact with ARG 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C GLU* 3.8 17.3 + - + +
243C PRO 3.2 1.0 + - - -
244C ASP* 1.3 77.7 - - - +
246C GLU* 1.3 60.2 + - + +
248C ARG* 3.0 26.2 + - + +
249C LEU* 2.9 27.5 + - + +
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Residues in contact with GLU 246 (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 ILE* 3.2 28.3 - - + +
238C ARG* 2.4 49.0 + - - +
240C PRO* 3.8 21.5 - - + +
242C GLU 4.4 4.4 + - - +
243C PRO 3.2 8.8 + - - +
245C ARG* 1.3 78.5 - - + +
247C VAL* 1.3 60.9 + - - +
249C LEU* 3.8 11.3 - - + +
250C ALA* 2.9 24.7 + - + +
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Residues in contact with VAL 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C CYS* 4.1 22.9 - - + +
182C ALA* 4.0 7.0 - - + +
183C ALA* 3.6 42.2 - - + +
186C CYS* 5.2 1.8 - - - -
232C ALA* 5.5 2.7 - - - -
235C ILE* 3.4 26.2 - - + -
243C PRO 2.9 25.0 + - - +
244C ASP* 3.5 10.5 - - - +
246C GLU* 1.3 75.7 - - - +
248C ARG* 1.3 58.8 + - + +
250C ALA* 3.4 0.9 + - + +
251C CYS* 2.9 32.0 + - - -
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Residues in contact with ARG 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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17C MET* 3.9 8.0 - - + +
19C PHE* 3.3 60.2 - - + +
55C GLU* 2.9 43.4 + - - +
78C VAL* 5.7 0.6 - - - +
80C GLU* 5.2 5.7 - - - +
82C GLY* 5.4 7.1 - - - +
182C ALA* 6.5 0.7 - - + -
186C CYS* 4.6 4.5 - - - -
244C ASP* 2.9 39.1 + - - +
245C ARG* 3.0 20.9 + - - +
247C VAL* 1.3 77.6 - - + +
249C LEU* 1.3 57.7 + - - +
251C CYS* 3.2 2.9 + - - +
252C ARG* 2.9 41.3 + - - +
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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
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245C ARG* 2.9 14.4 + - + +
246C GLU* 3.8 13.9 - - + +
247C VAL 3.4 0.2 - - - -
248C ARG* 1.3 74.5 - - - +
250C ALA* 1.3 59.1 + - - +
252C ARG* 3.3 32.4 + - - +
253C ASP* 3.0 47.6 + - - +
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Residues in contact with ALA 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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231C LYS* 3.5 31.9 - - + +
234C GLU* 6.3 0.2 - - - -
235C ILE* 3.5 17.3 - - + -
238C ARG* 5.6 4.7 - - - +
246C GLU* 2.9 20.1 + - + +
247C VAL* 3.7 2.7 - - - +
249C LEU* 1.3 78.4 - - - +
251C CYS* 1.3 57.2 + - - +
253C ASP* 3.4 8.1 + - - +
254C ILE* 2.9 30.0 + - - +
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Residues in contact with CYS 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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17C MET* 3.8 15.9 - - + -
183C ALA* 3.8 41.3 - - - -
186C CYS* 4.4 2.9 - - + -
228C VAL* 4.3 15.5 - - - -
231C LYS* 5.6 2.9 - - - -
247C VAL* 2.9 26.8 + - - +
248C ARG 3.7 3.6 - - - +
250C ALA* 1.3 74.5 - - - +
252C ARG* 1.3 61.2 + - - +
254C ILE* 3.1 7.3 - - - +
255C PHE* 2.9 44.0 + - + -
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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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15C VAL* 5.0 7.8 - - - +
16C SER* 3.9 19.2 + - - +
17C MET* 3.4 40.7 + - + +
19C PHE* 6.1 2.7 - - + -
248C ARG* 2.9 21.9 + - - +
249C LEU* 3.3 38.5 + - - +
251C CYS* 1.3 76.8 - - - +
253C ASP* 1.3 58.2 + - - +
255C PHE* 3.3 4.3 + - - +
256C ARG* 3.0 30.1 + - - +
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Residues in contact with ASP 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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231C LYS* 5.2 6.7 - - - +
249C LEU* 3.0 41.5 + - - +
250C ALA* 3.7 6.9 - - - +
252C ARG* 1.3 78.2 + - - +
254C ILE* 1.3 57.9 + - - +
256C ARG* 3.2 28.7 + - - +
257C SER* 2.9 32.8 + - - -
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Residues in contact with ILE 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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226C ASP 5.2 3.6 - - - +
227C THR* 3.6 48.7 - - + +
228C VAL* 4.8 3.4 - - + -
231C LYS* 4.1 28.7 - - + +
250C ALA 2.9 18.0 + - - +
251C CYS* 3.1 25.8 - - + +
253C ASP* 1.3 76.8 - - - +
255C PHE* 1.3 62.3 + - + +
257C SER* 3.2 13.3 + - - +
258C SER* 2.8 37.8 + - - +
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Residues in contact with PHE 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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16C SER* 4.1 27.1 - - - +
17C MET* 4.2 17.3 - - + -
186C CYS* 4.4 4.0 - - + -
187C LEU* 4.0 27.8 - - + -
190C VAL* 4.0 20.4 - - + -
227C THR* 3.7 22.0 - - + -
228C VAL* 3.7 21.3 - - + -
251C CYS* 2.9 29.2 + - + +
252C ARG* 3.6 4.3 - - - +
253C ASP 3.2 0.2 - - - -
254C ILE* 1.3 77.8 - - + +
256C ARG* 1.3 61.1 + - - +
259C LYS* 3.1 3.1 + - - -
260C THR* 3.0 53.6 + - + +
261C LEU* 4.7 5.6 + - + +
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Residues in contact with ARG 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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252C ARG 3.0 14.2 + - - +
253C ASP* 3.2 39.7 + - - +
255C PHE* 1.3 77.0 - - - +
257C SER* 1.3 74.0 + - - +
259C LYS* 3.4 16.9 + - - +
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Residues in contact with SER 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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253C ASP 2.9 15.1 + - - -
254C ILE* 3.2 25.5 + - - +
256C ARG* 1.3 90.1 - - - +
258C SER* 1.3 60.9 + - - +
259C LYS* 3.2 6.9 + - - +
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Residues in contact with SER 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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226C ASP 6.1 0.9 - - - -
227C THR* 4.4 10.3 + - - +
254C ILE* 2.8 26.2 + - - +
257C SER* 1.3 79.5 + - - +
259C LYS* 1.3 66.7 + - - +
260C THR* 3.1 15.9 + - - -
263C LYS* 3.2 28.2 + - - +
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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