Contacts of the helix formed by residues 231 - 248 (chain C) in PDB entry 4X4R
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 231 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ARG* 3.1 30.3 + - - +
229C ASN 3.1 6.6 + - - -
230C LEU* 1.3 75.6 - - - +
232C LEU* 1.3 60.7 + - - +
233C ASP* 3.8 9.2 + - - +
234C ASN* 3.1 33.4 + - - +
235C LEU* 2.9 27.9 + - - +
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Residues in contact with LEU 232 (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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349A PHE* 4.0 13.7 - - + -
371A ASN* 3.6 13.0 - - - +
372A GLY* 3.5 28.5 - - - -
197C ARG* 3.6 44.4 - - + +
214C PHE* 6.3 0.2 - - + -
230C LEU 3.7 1.2 + - - -
231C SER* 1.3 73.2 - - - +
233C ASP* 1.3 60.0 + - - +
235C LEU* 3.4 15.8 + - + +
236C ALA* 2.9 27.4 + - - +
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Residues in contact with ASP 233 (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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369A ILE* 4.0 10.1 - - + +
370A GLU* 3.5 7.9 - - - -
371A ASN* 2.8 37.9 + - - +
372A GLY 3.1 10.6 + - - -
231C SER* 3.2 9.2 + - - +
232C LEU* 1.3 74.7 - - - +
234C ASN* 1.3 53.7 + - - +
236C ALA* 3.3 7.5 + - - +
237C ARG* 2.7 61.4 + - - +
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Residues in contact with ASN 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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160C ILE* 3.1 32.5 - - + +
167C VAL 2.5 30.9 + - - -
168C ARG* 2.8 19.8 + - - +
169C GLY* 4.1 0.8 - - - +
170C PHE* 4.4 0.7 - - - -
230C LEU* 3.8 9.6 - - + -
231C SER* 3.1 18.4 + - - +
233C ASP* 1.3 74.2 - - - +
235C LEU* 1.3 65.7 + - - +
237C ARG* 3.7 20.8 + - - +
238C PHE* 3.0 24.1 + - - +
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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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349A PHE* 4.5 9.6 - - + -
170C PHE* 4.8 2.0 - - + -
195C TRP* 3.7 31.6 - - + -
196C THR 4.1 9.4 - - - +
197C ARG* 4.4 2.5 - - - -
214C PHE* 3.6 41.3 - - + -
230C LEU* 3.8 23.2 - - + +
231C SER 2.9 14.2 + - - +
232C LEU* 3.5 26.7 - - + +
233C ASP 3.3 0.2 - - - -
234C ASN* 1.3 76.7 - - - +
236C ALA* 1.3 62.0 + - - +
238C PHE* 3.2 5.2 + - - +
239C VAL* 3.1 27.7 + - + +
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Residues in contact with ALA 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A PHE* 3.6 44.5 - - + +
369A ILE* 4.0 21.7 - - + +
372A GLY* 5.4 0.7 - - - -
232C LEU 2.9 14.3 + - - +
233C ASP 3.4 8.1 - - - +
235C LEU* 1.3 75.3 - - - +
237C ARG* 1.3 66.0 + - - +
238C PHE 3.1 0.3 + - - -
239C VAL* 3.2 2.1 + - - +
240C HIS* 2.9 26.2 + - - +
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Residues in contact with ARG 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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368A PHE* 5.8 0.8 - - - +
369A ILE* 3.8 42.0 + - + +
158C ASN 6.0 0.2 - - - -
160C ILE* 4.9 11.0 - - + -
233C ASP* 2.7 54.6 + - - +
234C ASN* 3.3 26.4 + - - +
236C ALA* 1.3 72.7 - - - +
238C PHE* 1.3 59.0 + - - +
240C HIS* 4.1 4.0 - - - +
241C LEU* 3.1 33.5 + - + +
317C ARG* 4.6 12.1 - - - +
431C GLU* 5.5 4.8 + - - -
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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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151C LEU* 4.5 15.9 - - + -
154C PHE* 3.8 23.3 - + - -
155C LEU* 3.7 24.7 - - + -
160C ILE* 4.0 7.8 - - + +
170C PHE* 3.6 26.9 - + + -
178C LEU* 5.6 2.5 - - + -
188C THR* 5.2 7.0 - - + -
189C VAL* 5.3 3.1 - - + -
192C ALA* 3.5 16.4 - - + -
195C TRP* 3.4 32.8 - + - -
234C ASN 3.0 13.1 + - - +
235C LEU 3.5 7.2 - - - +
236C ALA 3.1 0.2 - - - -
237C ARG* 1.3 75.6 - - - +
239C VAL* 1.3 67.3 + - - +
241C LEU* 3.0 16.5 + - + +
242C CYS* 3.0 33.3 + - - -
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Residues in contact with VAL 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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349A PHE* 4.1 26.9 - - + -
192C ALA 3.6 19.3 - - - +
193C ARG* 3.6 24.9 - - - +
195C TRP* 4.1 17.7 - - + +
235C LEU* 3.1 21.9 + - + +
236C ALA 3.7 5.6 - - - +
238C PHE* 1.3 78.8 - - + +
240C HIS* 1.3 63.9 + - - +
242C CYS* 3.2 8.1 + - - +
243C ARG* 3.1 39.3 + - - +
505C PEG 5.4 0.2 - - - -
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Residues in contact with HIS 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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349A PHE* 6.1 0.7 - - + -
359A LEU* 3.8 19.6 - - + +
369A ILE* 5.1 0.7 - - + -
374A TRP* 3.6 30.8 - + + +
236C ALA 2.9 15.9 + - - +
237C ARG* 4.1 7.0 - - - +
239C VAL* 1.3 78.1 - - - +
241C LEU* 1.3 52.7 + - + +
243C ARG* 3.3 2.3 + - - +
244C GLU* 2.6 73.5 + - + +
505C PEG 3.1 59.1 + - - -
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Residues in contact with LEU 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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154C PHE* 4.0 17.9 - - + -
158C ASN* 3.3 48.0 - - + +
160C ILE* 4.5 6.1 - - + -
237C ARG* 3.1 22.8 + - + +
238C PHE* 3.0 13.9 + - - +
240C HIS* 1.3 79.0 - - + +
242C CYS* 1.3 53.5 + - - +
244C GLU* 3.2 20.5 + - - +
245C PHE* 2.6 37.9 + - - +
253C PHE* 3.7 19.9 - - + -
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Residues in contact with CYS 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C PHE* 4.7 3.8 - - - -
189C VAL* 3.5 45.8 - - + +
192C ALA* 4.0 3.4 - - - -
193C ARG* 3.6 9.2 - - + +
238C PHE* 3.0 52.0 + - - -
239C VAL* 3.2 8.5 + - - +
241C LEU* 1.3 77.8 - - - +
243C ARG* 1.3 56.3 + - - +
245C PHE* 3.7 2.3 - - - +
246C MET* 2.8 36.0 + - - +
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Residues in contact with ARG 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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349A PHE 2.6 26.4 + - - -
350A GLU* 2.6 27.2 + - - +
352A GLU* 3.4 36.5 + - - +
193C ARG* 2.5 51.6 + - + +
194C ARG* 4.5 4.8 - - - +
195C TRP 4.6 3.2 + - - -
239C VAL* 3.1 21.6 + - - +
240C HIS 3.7 6.1 - - - +
242C CYS* 1.3 72.6 - - - +
244C GLU* 1.3 65.6 + - - +
246C MET* 4.3 0.2 - - - +
247C GLU* 3.1 33.9 + - - +
505C PEG 3.1 39.4 + - - +
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Residues in contact with GLU 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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240C HIS* 2.6 62.7 + - + +
241C LEU* 3.5 27.9 - - - +
243C ARG* 1.3 72.4 - - - +
245C PHE* 1.3 61.2 + - - +
247C GLU* 4.1 6.5 - - - +
248C ALA* 3.3 25.1 + - - +
253C PHE* 4.0 12.6 - - + -
505C PEG 4.4 4.9 - - - +
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Residues in contact with PHE 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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3C VAL 5.6 2.0 - - - -
6C ILE* 5.8 2.5 - - + -
7C LEU* 4.2 22.0 - - + -
154C PHE* 4.6 6.5 - + + -
185C PHE* 4.3 19.1 - + - -
186C LEU* 4.6 6.5 - - + -
189C VAL* 4.1 11.0 - - + -
241C LEU 2.6 22.9 + - - +
242C CYS* 3.7 4.9 - - - +
244C GLU* 1.3 72.5 - - - +
246C MET* 1.3 85.8 + - + +
248C ALA 4.3 0.2 - - - -
249C PRO* 2.8 49.6 - - + +
250C SER 3.8 27.1 - - - -
253C PHE* 3.7 37.5 - + + -
254C PHE* 4.6 6.1 - + - -
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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
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186C LEU* 3.7 26.2 - - + -
189C VAL* 3.8 12.8 - - + -
190C LYS* 3.4 34.8 - - - -
193C ARG* 3.0 38.4 - - - +
242C CYS 2.8 23.9 + - - +
243C ARG 4.3 0.9 - - - +
245C PHE* 1.3 96.8 - - + +
247C GLU* 1.3 62.3 + - - +
248C ALA 3.4 0.3 + - - -
249C PRO* 3.8 12.3 - - + +
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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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352A GLU* 3.3 22.2 - - - +
356A LYS* 3.2 36.6 + - - +
193C ARG* 5.8 2.0 - - - +
243C ARG* 3.1 27.1 + - - +
244C GLU* 4.2 4.8 - - - +
246C MET* 1.3 77.4 - - + +
248C ALA* 1.3 64.4 + - + +
249C PRO* 4.1 0.7 - - - +
505C PEG 3.8 19.0 + - - +
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Residues in contact with ALA 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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244C GLU 3.3 15.5 + - - +
245C PHE 3.1 3.7 + - - -
246C MET 3.2 0.4 - - - -
247C GLU* 1.3 82.4 - - + +
249C PRO* 1.3 72.5 - - - +
250C SER* 3.8 2.4 + - - -
253C PHE* 4.0 9.5 - - - -
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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
------------------------------------------------------------
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