Contacts of the helix formed by residues 221 - 235 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129E ILE* 3.7 14.1 - - - +
130E ALA 2.9 20.4 + - - -
132E SER* 3.3 12.3 + - - -
198E LEU* 3.3 30.3 + - - +
199E ILE* 3.0 16.8 + - - -
200E GLY* 3.9 3.4 - - - +
219E ILE 3.6 0.6 + - - -
220E PRO* 1.4 70.6 - - - +
222E ASN* 1.4 54.0 + - - +
224E ALA* 3.7 7.3 - - - +
225E ARG* 2.7 37.6 + - - +
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Residues in contact with ASN 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E ALA 3.4 2.0 + - - -
131E ASP* 2.7 24.0 + - - +
132E SER* 3.1 33.0 + - - +
133E ASP* 3.3 20.7 - - - +
220E PRO* 5.4 0.2 - - + -
221E SER* 1.4 72.6 + - - +
223E MET* 1.3 58.4 + - - +
225E ARG* 3.2 37.7 + - - +
226E THR* 2.8 34.3 + - - -
304E ARG* 6.0 1.6 - - - +
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Residues in contact with MET 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E SER* 5.0 7.6 - - - -
172E LEU* 5.2 6.5 - - - +
173E GLU* 5.7 0.2 - - - -
174E ASN* 3.6 39.0 - - + +
219E ILE* 4.0 18.2 - - + -
220E PRO* 3.1 21.9 + - + +
222E ASN* 1.3 80.0 - - - +
224E ALA* 1.3 61.5 + - - +
226E THR* 3.8 1.6 - - - -
227E LEU* 3.1 39.8 + - + +
303E SER* 3.9 27.1 - - - +
304E ARG* 4.7 5.4 - - + +
307E THR* 3.8 32.1 - - + +
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Residues in contact with ALA 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E LEU* 3.8 25.7 - - + +
113E ILE* 3.7 23.1 - - + +
198E LEU* 5.5 1.3 - - + -
201E ILE* 4.0 15.5 - - + -
219E ILE* 4.2 2.6 - - + +
220E PRO 3.0 15.9 + - - +
221E SER* 3.3 8.0 + - - +
223E MET* 1.3 76.4 - - - +
225E ARG* 1.4 56.3 + - - +
227E LEU* 3.9 1.2 - - - +
228E ALA* 2.9 30.8 + - - +
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Residues in contact with ARG 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E ILE* 4.8 6.1 - - + -
78E LEU* 4.8 0.6 - - - +
129E ILE* 3.6 39.4 + - + +
130E ALA 3.4 18.2 + - - -
131E ASP* 4.4 3.0 - - - +
221E SER 2.7 20.9 + - - +
222E ASN* 3.2 46.5 + - - +
224E ALA* 1.4 68.8 - - - +
226E THR* 1.3 63.7 + - - +
228E ALA* 3.2 7.6 + - - +
229E GLN* 3.0 35.1 + - + +
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Residues in contact with THR 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222E ASN* 2.8 18.4 + - - +
223E MET* 3.8 5.2 - - - -
225E ARG* 1.3 78.2 + - - +
227E LEU* 1.3 65.9 + - - +
229E GLN* 3.3 9.7 + - - +
230E GLN* 3.2 29.8 + - + +
307E THR* 3.4 28.9 - - + +
308E THR* 4.8 6.3 - - + -
309E GLU* 5.3 1.6 - - + +
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Residues in contact with LEU 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E ASP* 3.7 5.4 - - + +
111E SER* 3.3 29.2 - - - +
113E ILE* 3.7 26.9 - - + -
223E MET* 3.1 35.1 + - + +
224E ALA 3.9 2.7 - - - +
226E THR* 1.3 74.6 - - - +
228E ALA* 1.4 61.8 + - - +
230E GLN* 3.2 11.2 + - - +
231E LEU* 3.1 27.9 + - - +
237E ILE* 3.8 14.5 - - + +
239E ARG* 3.5 28.0 - - - +
307E THR* 4.1 22.4 - - + +
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Residues in contact with ALA 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E ILE* 4.1 23.3 - - + -
78E LEU* 4.3 8.1 - - + -
113E ILE* 4.8 0.8 - - - +
115E LEU* 4.2 17.0 - - + +
224E ALA 2.9 18.9 + - - +
225E ARG 3.2 5.6 + - - +
227E LEU* 1.4 75.3 - - - +
229E GLN* 1.4 56.6 + - - +
231E LEU* 3.1 12.9 + - - +
232E ILE* 3.0 34.6 + - + +
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Residues in contact with GLN 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ASP* 5.9 2.3 + - - -
225E ARG* 3.0 19.1 + - + +
226E THR* 3.3 11.6 + - - +
228E ALA* 1.4 72.6 - - - +
230E GLN* 1.3 58.1 + - + +
232E ILE* 3.2 24.7 + - - +
233E ASP* 2.9 66.4 + - - +
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Residues in contact with GLN 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E THR* 3.2 23.3 + - + +
227E LEU* 3.4 13.8 - - - +
229E GLN* 1.3 77.4 - - + +
231E LEU* 1.3 56.7 + - - +
233E ASP* 5.0 0.2 - - - -
234E PHE* 2.9 47.0 + - + -
236E GLU 3.0 19.0 - - - +
237E ILE* 3.5 14.2 - - - +
238E LYS 2.8 41.2 + - - +
239E ARG* 5.0 0.6 - - - +
307E THR 3.2 23.2 + - - +
309E GLU* 4.1 21.8 + - + +
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Residues in contact with LEU 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E ILE* 3.5 10.9 - - - +
106E GLY* 3.6 27.1 - - - +
107E SER* 3.5 32.8 - - - +
108E ASP 4.9 0.4 - - - +
113E ILE* 4.2 18.4 - - + +
115E LEU* 3.9 24.2 - - + +
227E LEU 3.1 19.9 + - - +
228E ALA* 3.1 6.7 + - - +
230E GLN* 1.3 73.9 - - - +
232E ILE* 1.3 62.8 + - - +
235E GLY* 3.0 25.3 + - - +
236E GLU* 3.8 27.6 - - - -
237E ILE* 4.1 9.9 - - + -
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Residues in contact with ILE 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E ILE* 6.3 0.7 - - + -
71E ASN* 5.9 2.5 - - - +
74E LYS* 5.9 2.7 - - - +
76E TYR* 4.0 39.8 + - + +
105E ILE* 4.5 4.8 - - - +
115E LEU* 3.2 29.8 - - + -
228E ALA* 3.0 12.5 + - + +
229E GLN* 3.2 34.5 + - - +
231E LEU* 1.3 78.1 - - - +
233E ASP* 1.4 76.0 + - - +
235E GLY 4.7 0.7 + - - -
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Residues in contact with ASP 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E GLN* 2.9 42.3 + - - +
230E GLN* 5.0 0.2 - - - -
232E ILE* 1.4 86.0 - - - +
234E PHE* 1.3 90.5 + - + +
309E GLU* 5.3 2.6 - - - +
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Residues in contact with PHE 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E GLN* 2.9 36.1 + - + +
233E ASP* 1.3 99.4 - - + +
235E GLY* 1.3 59.0 + - - +
236E GLU* 3.0 31.8 + - + +
238E LYS* 3.6 47.1 - - + -
309E GLU* 3.9 28.0 - - - -
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Residues in contact with GLY 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E ILE* 3.9 14.7 - - - +
106E GLY* 3.9 15.6 - - - -
107E SER 4.9 0.3 + - - -
230E GLN 3.7 0.2 + - - -
231E LEU* 3.0 27.4 + - - -
232E ILE 4.7 0.6 + - - -
233E ASP 3.9 0.4 - - - -
234E PHE* 1.3 75.9 - - - +
236E GLU* 1.4 58.2 + - - +
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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