Contacts of the helix formed by residues 221 - 235 (chain C) in PDB entry 3STJ
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 221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129C ILE* 3.7 13.4 - - - +
130C ALA 2.8 21.0 + - - -
132C SER* 3.3 12.3 + - - -
198C LEU* 3.4 30.4 + - - +
199C ILE* 3.0 18.2 + - - -
200C GLY* 4.0 3.4 - - - +
219C ILE 3.6 1.2 + - - -
220C PRO* 1.4 67.6 - - - +
222C ASN* 1.3 56.7 + - - +
224C ALA* 3.7 7.1 - - - +
225C ARG* 2.7 38.3 + - - +
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Residues in contact with ASN 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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130C ALA 3.4 1.6 + - - -
131C ASP* 2.7 24.4 + - - +
132C SER* 3.2 33.0 + - - +
133C ASP* 3.3 19.9 - - - +
220C PRO* 5.5 0.2 - - + -
221C SER* 1.3 75.2 + - - +
223C MET* 1.3 58.9 + - - +
225C ARG* 3.2 36.3 + - - +
226C THR* 2.8 35.0 + - - +
304C ARG* 6.2 0.9 - - - +
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Residues in contact with MET 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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111C SER* 5.0 7.4 - - - -
172C LEU* 5.2 7.6 - - - +
174C ASN* 3.5 39.0 - - + +
219C ILE* 4.0 17.7 - - + -
220C PRO* 3.1 21.3 + - + +
222C ASN* 1.3 78.5 - - - +
224C ALA* 1.3 63.6 + - - +
226C THR* 3.6 1.2 + - - -
227C LEU* 3.1 39.7 + - + +
303C SER* 3.9 26.0 - - - +
304C ARG* 4.6 6.1 - - + +
307C THR* 3.7 30.3 - - + +
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Residues in contact with ALA 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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78C LEU* 3.8 26.0 - - + +
113C ILE* 3.7 22.4 - - + +
198C LEU* 5.5 1.3 - - + -
201C ILE* 4.0 15.9 - - + -
219C ILE* 4.2 2.2 - - + +
220C PRO 3.0 16.3 + - - +
221C SER* 3.7 8.1 - - - +
223C MET* 1.3 76.9 - - - +
225C ARG* 1.4 55.6 + - - +
227C LEU* 3.5 1.4 + - - +
228C ALA* 2.9 30.7 + - - +
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Residues in contact with ARG 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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70C ILE* 4.8 7.2 - - + -
78C LEU* 4.7 0.4 - - - +
129C ILE* 3.5 40.1 + - + +
130C ALA 3.4 18.0 + - - -
131C ASP* 4.4 3.4 - - - +
221C SER 2.7 20.9 + - - +
222C ASN* 3.2 46.1 + - - +
224C ALA* 1.4 69.6 - - - +
226C THR* 1.4 62.6 + - - +
228C ALA* 3.3 8.2 + - - +
229C GLN* 2.9 34.4 + - + +
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Residues in contact with THR 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 ASN 2.8 20.5 + - - -
223C MET 3.8 3.4 - - - -
225C ARG* 1.4 75.7 + - - +
227C LEU* 1.3 65.9 + - - +
229C GLN* 3.3 9.1 + - - +
230C GLN* 3.1 29.0 + - - +
307C THR* 3.4 32.3 - - + +
308C THR* 5.0 4.5 - - + -
309C GLU* 5.5 1.1 - - + +
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Residues in contact with LEU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ASP* 3.7 6.3 - - + +
111C SER* 3.3 29.2 - - - +
113C ILE* 3.8 25.6 - - + -
223C MET* 3.1 34.9 + - + +
224C ALA 4.0 2.9 - - - +
226C THR* 1.3 74.6 - - - +
228C ALA* 1.4 62.1 + - - +
230C GLN* 3.2 14.9 + - - +
231C LEU* 3.1 28.0 + - + +
237C ILE* 3.8 15.3 - - + +
239C ARG* 3.6 27.1 - - - +
307C THR* 4.0 19.5 - - + +
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Residues in contact with ALA 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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70C ILE* 4.2 23.1 - - + -
78C LEU* 4.3 6.7 - - + -
113C ILE* 4.8 1.9 - - - +
115C LEU* 4.2 18.2 - - + +
224C ALA 2.9 19.5 + - - +
225C ARG 3.4 5.6 - - - +
227C LEU* 1.4 75.4 - - - +
229C GLN* 1.4 55.9 + - - +
231C LEU* 3.1 13.7 + - - +
232C ILE* 2.9 34.3 + - + +
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Residues in contact with GLN 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 ARG* 2.9 20.7 + - + +
226C THR* 3.3 11.6 + - - +
228C ALA* 1.4 73.9 - - - +
230C GLN* 1.3 57.7 + - + +
232C ILE* 3.2 26.2 + - - +
233C ASP* 2.9 66.7 + - - +
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Residues in contact with GLN 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 THR* 3.1 24.6 + - + +
227C LEU* 3.2 15.0 + - - +
229C GLN* 1.3 74.4 - - - +
231C LEU* 1.3 57.7 + - - +
234C PHE* 2.8 47.3 + - + -
236C GLU 3.0 20.6 - - - +
237C ILE* 3.5 14.2 - - + +
238C LYS 2.8 42.0 + - - +
239C ARG* 5.2 0.6 - - - +
307C THR 3.1 22.8 + - - +
309C GLU* 4.2 21.6 + - + +
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Residues in contact with LEU 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ILE* 3.5 11.4 - - + +
106C GLY* 3.7 27.8 - - - +
107C SER* 3.5 31.6 - - - +
108C ASP 4.9 0.2 - - - +
113C ILE* 4.2 17.9 - - + +
115C LEU* 3.9 24.9 - - + +
227C LEU 3.1 20.3 + - - +
228C ALA* 3.1 6.7 + - - +
230C GLN* 1.3 74.7 - - - +
232C ILE* 1.4 60.9 + - - +
235C GLY* 3.0 25.8 + - - +
236C GLU* 3.8 26.7 - - - +
237C ILE* 4.1 9.6 - - + -
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Residues in contact with ILE 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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70C ILE* 6.1 1.3 - - + -
71C ASN* 6.1 1.3 - - - +
74C LYS* 5.5 5.6 - - - +
76C TYR* 3.9 41.5 + - + +
105C ILE* 4.6 4.1 - - - +
115C LEU* 3.4 24.0 - - + -
228C ALA* 2.9 22.4 + - + +
229C GLN* 3.2 37.4 + - - +
231C LEU* 1.4 76.4 - - - +
233C ASP* 1.4 71.7 + - - +
235C GLY 4.7 0.7 + - - -
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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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229C GLN* 2.9 42.5 + - - +
232C ILE* 1.4 85.1 - - - +
234C PHE* 1.4 87.7 + - + +
309C GLU* 5.4 1.2 - - - +
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Residues in contact with PHE 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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230C GLN* 2.8 37.5 + - + +
233C ASP* 1.4 97.5 - - + +
235C GLY* 1.3 59.4 + - - +
236C GLU* 3.0 26.0 + - + +
238C LYS* 3.5 45.8 - - + +
309C GLU* 3.9 31.0 - - - -
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Residues in contact with GLY 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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105C ILE* 3.8 21.2 - - - +
106C GLY* 3.9 8.5 - - - -
107C SER 5.0 0.2 + - - -
230C GLN 3.6 0.4 + - - -
231C LEU* 3.0 26.9 + - - +
232C ILE 4.7 1.2 + - - -
233C ASP 3.9 0.2 - - - -
234C PHE* 1.3 76.7 - - - +
236C GLU* 1.3 56.6 + - - +
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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