Contacts of the helix formed by residues 233 - 245 (chain C) in PDB entry 4XQ2
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 GLY 233 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231C VAL 3.9 0.8 + - - -
232C PRO* 1.3 74.0 - - - +
234C ALA* 1.3 60.7 + - - -
236C ASP* 3.3 21.5 + - - +
237C CYS* 3.0 31.3 + - - -
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Residues in contact with ALA 234 (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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28C ILE* 3.9 11.4 - - + +
29C HIS 3.2 32.8 - - - +
30C VAL* 4.2 9.0 - - + -
51C ASN* 4.1 10.4 - - - +
53C THR* 3.7 9.7 - - - +
233C GLY* 1.3 68.3 - - - -
235C LEU* 1.3 61.0 + - - +
237C CYS* 3.2 9.9 + - - +
238C PHE* 2.9 28.4 + - - +
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Residues in contact with LEU 235 (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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28A ILE* 4.8 7.9 - - + -
235A LEU* 4.7 14.1 - - + -
238A PHE* 6.3 2.9 - - + -
28C ILE* 4.1 27.6 - - + -
30C VAL* 4.7 12.6 - - + -
233C GLY 3.4 0.4 - - - -
234C ALA* 1.3 78.0 - - - +
236C ASP* 1.3 62.6 + - - +
238C PHE* 3.3 10.8 + - + +
239C LEU* 3.0 32.4 + - + +
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Residues in contact with ASP 236 (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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205C VAL* 3.5 27.1 - - + +
206C LEU 4.6 5.6 - - - +
232C PRO* 4.9 4.9 - - + -
233C GLY* 3.3 31.9 + - - +
234C ALA 3.1 0.2 - - - -
235C LEU* 1.3 80.8 + - - +
237C CYS* 1.3 59.8 + - - +
239C LEU* 3.1 5.9 + - - +
240C VAL* 2.9 33.3 + - - +
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Residues in contact with CYS 237 (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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53C THR* 3.9 17.7 - - + +
54C ARG* 4.0 26.7 - - - -
57C LEU* 4.0 23.9 - - + +
72C VAL* 4.4 0.2 - - - -
232C PRO* 3.6 29.6 - - - -
233C GLY 3.0 21.6 + - - +
234C ALA* 3.6 7.2 - - - +
236C ASP* 1.3 74.8 - - - +
238C PHE* 1.3 57.2 + - - +
240C VAL* 3.8 1.9 - - - +
241C ARG* 2.9 32.3 + - - +
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Residues in contact with PHE 238 (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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30A VAL* 4.3 13.7 - - + -
235A LEU* 6.1 1.8 - - + -
204B ASP* 3.1 30.7 - - + -
239B LEU* 4.2 17.5 - - + -
25C VAL* 4.4 14.1 - - + -
26C PRO 5.4 1.8 - - - -
28C ILE* 3.7 42.2 - - + -
53C THR* 4.2 6.9 - - + +
234C ALA 2.9 13.1 + - - +
235C LEU* 3.3 15.3 - - + +
236C ASP 3.1 0.2 - - - -
237C CYS* 1.3 77.4 - - - +
239C LEU* 1.3 77.1 + - + +
241C ARG* 3.3 7.0 + - + +
242C ARG* 2.8 37.4 + - + +
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Residues in contact with LEU 239 (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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238B PHE* 4.0 27.1 - - + -
239B LEU* 4.8 1.3 - - + -
242B ARG* 3.0 50.1 + - - +
200C ALA 4.8 0.2 - - - +
204C ASP* 3.8 24.7 - - - +
205C VAL* 4.1 12.3 - - + -
235C LEU* 3.0 18.4 + - + +
236C ASP* 3.1 8.5 + - - +
238C PHE* 1.3 92.4 - - + +
240C VAL* 1.3 66.3 + - - +
242C ARG* 4.3 1.3 - - - -
243C GLY* 3.1 12.3 + - - -
30D VAL* 5.6 5.4 - - + -
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Residues in contact with VAL 240 (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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57C LEU* 3.7 29.6 - - + -
195C THR* 4.0 23.1 - - + +
199C ILE* 4.0 25.6 - - + +
200C ALA* 4.1 11.4 - - + +
205C VAL* 3.9 21.3 - - + -
206C LEU 4.8 4.7 - - - +
207C GLY* 5.1 1.8 - - - -
236C ASP 2.9 21.3 + - - +
237C CYS* 3.8 4.0 - - - +
239C LEU* 1.3 75.1 - - - +
241C ARG* 1.3 64.6 + - - +
243C GLY* 3.3 2.4 + - - -
244C LEU* 3.1 21.7 + - - +
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Residues in contact with ARG 241 (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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10C LEU 2.9 29.6 + - - -
11C VAL 3.2 19.2 + - - -
13C GLY 2.7 29.7 + - - +
14C GLY 5.0 3.6 + - - -
15C ARG* 5.2 2.8 - - - +
53C THR* 6.1 0.9 - - + +
56C GLU* 4.7 3.9 + - + -
57C LEU* 4.0 34.8 - - + +
60C CYS* 3.5 18.9 - - - +
237C CYS 2.9 19.5 + - - +
238C PHE* 3.6 7.9 - - + +
240C VAL* 1.3 78.6 - - - +
242C ARG* 1.3 61.7 + - - +
244C LEU* 3.6 14.0 + - - +
245C HIS* 3.7 17.3 + - - +
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Residues in contact with ARG 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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200B ALA 3.9 13.5 + - - -
202B HIS* 3.6 33.6 + - + +
204B ASP* 2.7 43.9 + - - +
205B VAL* 4.3 3.8 - - - +
239B LEU* 3.1 32.5 + - - +
242B ARG* 3.3 49.9 - - - +
243B GLY* 3.5 9.9 - - - +
238C PHE* 2.8 36.6 + - + +
239C LEU* 3.7 2.9 - - - +
240C VAL 3.2 0.2 - - - -
241C ARG* 1.3 75.5 - - - +
243C GLY* 1.3 62.9 + - - +
244C LEU 3.4 0.2 + - - -
245C HIS* 3.5 25.7 + - + +
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Residues in contact with GLY 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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202B HIS* 5.6 0.7 - - - -
242B ARG* 3.5 4.6 - - - +
199C ILE 3.7 0.7 - - - -
200C ALA 3.4 20.0 - - - -
202C HIS* 3.7 15.0 - - - -
239C LEU 3.1 11.3 + - - -
240C VAL 3.3 1.1 + - - -
242C ARG* 1.3 76.1 - - - +
244C LEU* 1.3 62.2 + - - +
246C THR* 3.0 17.7 + - - -
250C ARG* 2.9 21.8 + - - -
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Residues in contact with LEU 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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10C LEU* 3.5 29.9 - - + +
57C LEU* 4.1 16.2 - - + -
60C CYS* 3.3 27.8 - - - -
61C LEU* 4.1 18.8 - - + -
64C LEU* 3.7 9.2 - - + -
199C ILE* 3.5 21.8 + - + +
240C VAL 3.1 14.3 + - - +
241C ARG* 3.7 13.7 - - - +
242C ARG 3.3 0.2 - - - -
243C GLY* 1.3 74.9 - - - +
245C HIS* 1.3 65.3 + - - +
247C LEU* 3.0 36.0 + - + +
250C ARG* 4.2 2.2 - - - +
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Residues in contact with HIS 245 (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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202B HIS* 4.1 21.3 - + + +
327B VAL* 3.8 16.1 - - + +
328B HIS* 3.8 18.5 + + - -
363B ILE* 3.2 17.3 - - + +
10C LEU* 3.5 22.8 + - - +
11C VAL* 2.9 52.7 - - + +
15C ARG* 5.5 1.1 - - - -
25C VAL* 6.1 0.8 - - - +
241C ARG* 3.7 30.2 + - + +
242C ARG* 3.5 18.7 + - + +
243C GLY 3.2 0.2 - - - -
244C LEU* 1.3 78.1 - - - +
246C THR* 1.3 61.2 + - + +
247C LEU 3.7 0.2 + - - -
249C LEU* 5.4 0.3 - - - +
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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