Contacts of the helix formed by residues 221 - 233 (chain C) in PDB entry 4I5L
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 221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204C ASP 3.7 1.8 - - - -
206C ARG 3.2 23.3 - - - -
208C GLY 3.2 11.9 + - - -
220C PHE* 1.3 72.6 - - - +
222C GLN* 1.3 67.5 + - - -
223C ASP* 3.2 9.6 - - - -
224C ILE* 3.0 13.5 + - - +
225C SER* 3.2 9.2 + - - -
252C HIS* 3.2 15.0 - - - -
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Residues in contact with GLN 222 (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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204C ASP 4.5 0.6 + - - -
206C ARG 4.6 0.8 + - - -
207C GLY* 5.5 0.4 - - - -
221C GLY* 1.3 71.2 - - - -
223C ASP* 1.3 62.2 + - - +
225C SER* 3.1 4.3 + - - -
226C GLU* 3.0 48.2 + - - +
252C HIS* 3.4 54.1 + - + +
253C ASP* 3.5 18.3 + - - +
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Residues in contact with ASP 223 (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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207C GLY* 3.6 9.2 - - - -
208C GLY* 2.9 38.2 + - - -
221C GLY 3.8 3.8 - - - -
222C GLN* 1.3 74.1 + - - +
224C ILE* 1.3 72.3 + - - +
226C GLU* 3.7 12.4 + - - +
227C THR* 3.0 30.0 + - - -
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Residues in contact with ILE 224 (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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170C LEU* 3.9 10.3 - - + -
208C GLY* 3.8 29.2 - - - +
209C TRP* 3.5 57.2 - - + +
220C PHE* 3.7 13.2 - - + -
221C GLY 3.0 10.7 + - - +
223C ASP* 1.3 87.4 - - - +
225C SER* 1.3 59.1 + - - +
227C THR* 3.5 5.8 + - - +
228C PHE* 3.0 30.2 + - + +
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Residues in contact with SER 225 (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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170C LEU* 4.0 9.9 - - - -
220C PHE* 3.5 9.9 - - - -
221C GLY 3.2 1.0 + - - -
222C GLN 3.1 5.6 + - - -
224C ILE* 1.3 78.1 - - - +
226C GLU* 1.3 57.7 + - - +
228C PHE* 3.9 1.0 - - - +
229C ASN* 2.9 37.3 + - - +
237C VAL* 5.6 0.9 - - - -
252C HIS* 2.7 35.6 + - - -
255C ASN* 3.9 11.7 - - - -
256C VAL* 3.4 21.5 - - - +
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Residues in contact with GLU 226 (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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222C GLN* 3.0 46.4 + - - +
223C ASP* 4.0 11.4 - - - +
225C SER* 1.3 73.4 - - - +
227C THR* 1.3 66.6 + - - +
229C ASN* 3.2 1.6 + - - -
230C HIS* 2.9 49.1 + - + +
253C ASP* 4.7 4.2 - - - +
255C ASN* 3.3 29.8 + - - +
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Residues in contact with THR 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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223C ASP* 3.0 18.0 + - - +
224C ILE* 3.9 7.5 - - - +
226C GLU* 1.3 76.3 - - - +
228C PHE* 1.3 65.1 + - - +
230C HIS* 4.1 3.4 - - - +
231C ALA* 3.1 32.0 + - + +
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Residues in contact with PHE 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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164C PHE* 3.9 28.3 - + - -
170C LEU* 3.8 33.2 - - + -
171C SER 6.2 0.4 - - - -
174C ILE* 3.8 35.0 - - + -
175C ASP* 3.8 12.8 - - - -
177C LEU* 4.3 12.6 - - + -
180C ILE* 4.7 0.4 - - + -
209C TRP* 6.6 0.2 - + - -
224C ILE* 3.0 19.4 + - + +
225C SER 3.9 1.3 - - - +
227C THR* 1.3 79.4 - - - +
229C ASN* 1.3 68.4 + - - +
231C ALA* 4.7 1.3 - - - -
232C ASN* 2.8 49.3 + - - +
234C LEU* 3.6 26.5 - - + -
237C VAL* 4.7 0.7 - - + -
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Residues in contact with ASN 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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225C SER 2.9 21.9 + - - +
226C GLU* 3.2 2.2 + - - +
228C PHE* 1.3 71.2 - - - +
230C HIS* 1.3 66.5 + - + +
232C ASN 3.1 1.4 + - - -
233C GLY 2.8 27.5 + - - -
234C LEU* 3.0 44.3 + - - +
235C THR 4.5 1.4 - - - -
236C LEU 4.1 9.4 - - - +
237C VAL* 3.2 23.8 - - - +
255C ASN* 3.3 47.6 + - - +
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Residues in contact with HIS 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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226C GLU* 2.9 42.1 + - + +
227C THR* 4.2 3.1 - - - +
229C ASN* 1.3 78.7 - - + +
231C ALA* 1.3 62.7 + - - +
232C ASN 3.3 0.9 + - - -
233C GLY* 3.6 8.1 + - - -
234C LEU 5.5 3.1 - - - -
255C ASN* 5.1 4.3 + - - -
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Residues in contact with ALA 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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175C ASP* 4.6 6.7 - - + +
176C THR* 5.7 4.3 - - + +
227C THR* 3.1 24.7 + - + +
228C PHE* 3.9 3.8 - - - +
230C HIS* 1.3 77.9 - - - +
232C ASN* 1.3 67.8 + - - +
233C GLY 3.6 0.2 - - - -
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Residues in contact with ASN 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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161C GLY 4.9 1.6 - - - +
175C ASP 2.7 25.4 + - - -
176C THR* 3.1 9.8 - - - +
177C LEU* 3.0 42.6 + - + +
228C PHE* 2.8 36.9 + - - +
229C ASN 3.1 2.8 + - - -
231C ALA* 1.3 81.3 - - - +
233C GLY* 1.3 64.3 + - - +
234C LEU* 3.4 24.1 - - + +
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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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161C GLY 3.5 17.5 - - - +
162C GLN* 4.2 8.7 + - - +
229C ASN 2.8 4.7 + - - -
230C HIS* 3.6 8.9 + - - -
231C ALA 3.6 0.6 - - - -
232C ASN* 1.3 78.4 - - - +
234C LEU* 1.3 60.0 + - - +
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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