Contacts of the helix formed by residues 226 - 241 (chain C) in PDB entry 3IFS
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 ASN 226 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64C GLN* 5.7 0.3 + - - -
224C GLY 4.1 0.6 + - - -
225C LEU* 1.3 69.3 - - - +
227C ILE* 1.3 61.4 + - - +
228C GLU* 2.9 23.4 + - - +
229C GLU* 3.0 30.0 + - + +
230C MSE 3.3 15.2 + - - +
391C GLU* 2.9 30.6 + - - +
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Residues in contact with ILE 227 (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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60C PHE* 3.4 31.9 - - + -
63C ILE* 3.9 28.3 - - + -
64C GLN* 4.0 22.4 - - + +
217C LEU* 3.7 37.5 - - + +
220C ILE* 4.0 20.4 - - + -
221C ALA* 4.1 14.4 - - + +
225C LEU 3.5 2.0 + - - +
226C ASN* 1.3 69.9 + - - +
228C GLU* 1.3 66.0 + - - +
230C MSE 3.6 7.8 - - - +
231C MSE 3.0 27.9 + - - +
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Residues in contact with GLU 228 (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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55C TYR* 5.6 5.6 - - - +
60C PHE* 3.9 18.6 - - + -
64C GLN* 4.7 10.2 + - - +
226C ASN* 2.9 10.7 + - - +
227C ILE* 1.3 80.7 - - - +
229C GLU* 1.3 66.0 + - - +
231C MSE 3.3 4.9 + - + +
232C LYS* 3.0 50.1 + - + +
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Residues in contact with GLU 229 (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 ASN* 3.0 34.1 + - + +
228C GLU* 1.3 79.8 - - - +
230C MSE 1.3 61.2 + - - +
232C LYS* 3.3 35.5 + - - +
233C GLY 3.0 18.4 + - - -
391C GLU* 4.2 10.8 - - + +
392C TYR* 3.3 31.1 - - + +
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Residues in contact with MSE 230 (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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92C ALA* 4.3 1.3 - - + -
96C LEU* 4.1 21.1 - - + -
212C LEU* 4.1 17.7 - - + -
217C LEU* 4.3 11.2 - - + -
220C ILE* 3.7 44.9 - - + -
226C ASN 3.3 9.1 + - - +
227C ILE* 3.6 10.3 - - + +
228C GLU 3.2 0.6 - - - -
229C GLU* 1.3 79.5 - - - +
231C MSE 1.3 62.2 + - - +
233C GLY 3.5 0.7 + - - -
234C ALA* 3.1 18.9 + - - +
391C GLU* 3.4 28.2 - - + +
394C PHE* 3.6 27.8 - - + -
395C GLY* 3.4 18.6 - - - -
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Residues in contact with MSE 231 (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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51C LEU 4.0 3.1 - - - +
52C PRO* 3.2 39.4 - - + +
55C TYR* 3.6 34.1 - - + +
60C PHE* 3.7 21.3 - - + -
212C LEU* 4.1 40.6 - - + +
217C LEU* 4.4 9.9 - - + -
227C ILE 3.0 19.9 + - - +
228C GLU* 3.3 5.4 + - + +
230C MSE 1.3 75.1 - - - +
232C LYS* 1.3 59.9 + - + +
234C ALA* 3.2 6.5 + - + +
235C ALA* 2.8 29.5 + - - +
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Residues in contact with LYS 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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228C GLU* 3.0 44.5 + - + +
229C GLU* 3.3 34.8 + - - +
231C MSE 1.3 76.2 - - + +
233C GLY* 1.3 57.5 + - - +
235C ALA* 3.2 8.3 + - - +
236C ALA* 2.9 27.9 + - - +
392C TYR* 3.8 13.6 - - + -
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Residues in contact with GLY 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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229C GLU 3.0 10.1 + - - -
230C MSE 3.8 1.3 - - - -
232C LYS* 1.3 77.4 - - - +
234C ALA* 1.3 60.7 + - - +
236C ALA* 3.3 4.5 + - - +
237C GLY 3.0 17.2 + - - -
392C TYR* 3.3 41.6 - - - -
396C TYR* 3.4 16.9 - - - -
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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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52C PRO* 3.7 14.2 - - + +
212C LEU* 3.5 32.5 - - + -
230C MSE 3.1 13.3 + - - +
231C MSE 3.2 10.5 + - + +
233C GLY* 1.3 75.2 - - - +
235C ALA* 1.3 57.8 + - - +
237C GLY* 3.2 2.6 + - - -
238C ARG* 2.9 26.9 + - - +
395C GLY 3.5 17.4 - - - +
396C TYR* 4.4 0.9 - - - +
399C TYR* 3.9 7.0 - - + -
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Residues in contact with ALA 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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52C PRO* 3.7 24.4 - - + +
53C LEU* 5.4 6.3 - - + -
231C MSE 2.8 16.1 + - - +
232C LYS* 3.2 9.8 + - - +
234C ALA* 1.3 74.9 - - - +
236C ALA* 1.3 64.9 + - - +
238C ARG* 3.2 6.9 + - - +
239C ASP* 3.1 28.3 + - - +
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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
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4C HIS* 6.2 0.2 - - - +
232C LYS 2.9 10.0 + - - +
233C GLY 3.4 9.9 - - - +
235C ALA* 1.3 75.4 - - - +
237C GLY* 1.3 62.6 + - - +
239C ASP* 3.3 8.8 + - - +
240C ASP* 3.0 30.3 + - - +
392C TYR* 3.2 26.7 - - - +
396C TYR* 3.8 12.8 - - + -
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Residues in contact with GLY 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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233C GLY 3.0 11.2 + - - -
234C ALA 3.2 4.0 + - - -
236C ALA* 1.3 77.6 - - - +
238C ARG* 1.3 56.3 + - - +
241C PHE* 2.8 48.0 + - - +
396C TYR* 3.6 19.0 - - - -
399C TYR* 3.6 13.2 - - - -
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Residues in contact with ARG 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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36C HIS* 6.0 5.2 - - + -
49C VAL* 3.5 10.8 - - + -
50C ASP* 2.6 38.8 + - - +
52C PRO* 4.5 6.3 - - + -
53C LEU* 3.6 44.4 - - - +
234C ALA 2.9 14.6 + - - +
235C ALA* 3.2 12.3 + - - +
237C GLY* 1.3 75.6 - - - +
239C ASP* 1.3 76.4 + - - +
241C PHE 3.8 0.9 - - - -
242C GLY* 3.2 21.5 + - - -
399C TYR* 3.4 30.2 + - + +
403C LYS* 5.6 0.3 + - - -
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Residues in contact with ASP 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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235C ALA* 3.1 14.3 + - - +
236C ALA* 3.5 11.8 - - - +
237C GLY 3.2 0.2 - - - -
238C ARG* 1.3 93.3 + - - +
240C ASP* 1.3 69.0 + - - +
242C GLY* 3.3 14.1 + - - -
243C THR* 4.4 1.2 + - - -
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Residues in contact with ASP 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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4C HIS* 2.6 6.9 + - + -
236C ALA* 3.0 14.7 + - - +
237C GLY 4.0 2.0 - - - +
239C ASP* 1.3 87.7 - - - +
241C PHE* 1.3 70.2 + - + +
242C GLY 3.3 2.1 + - - -
243C THR* 3.8 16.1 - - - +
248C GLU 4.3 6.6 - - - +
249C ASN* 4.4 0.3 + - - -
250C PRO* 4.9 1.5 - - + +
396C TYR* 2.8 23.7 + - - +
451C LI 1.8 47.5 - - - +
440F GLU* 3.2 4.4 - - - +
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Residues in contact with PHE 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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5C VAL 5.1 2.9 - - - -
237C GLY* 2.8 35.8 + - - +
238C ARG 3.8 2.9 - - - -
240C ASP* 1.3 78.1 - - + +
242C GLY* 1.3 51.0 + - - +
249C ASN* 3.0 40.3 + - - +
250C PRO* 3.8 30.3 - - + -
251C ALA* 3.9 9.4 - - + -
252C TYR* 3.7 0.3 + - - -
396C TYR* 3.6 38.1 - + - -
399C TYR* 4.1 7.2 - + + -
400C PHE* 3.6 43.5 - + + -
403C LYS* 2.8 45.0 + - + +
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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