Contacts of the helix formed by residues 220 - 234 (chain C) in PDB entry 5TXV
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 ASP 220 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217C LYS* 3.3 28.1 - - + +
218C ILE 3.1 0.8 - - - -
219C LYS* 1.3 83.1 - - - +
221C ALA* 1.3 64.6 + - - +
222C MET 3.3 0.2 - - - -
223C LYS* 3.2 30.7 + - + +
224C LEU* 3.5 19.9 - - + +
235D ASN* 5.8 3.6 - - - +
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Residues in contact with ALA 221 (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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131C ILE* 5.2 8.7 - - + -
217C LYS 3.8 15.6 + - - +
218C ILE* 2.8 15.8 + - - +
220C ASP* 1.3 79.0 - - - +
222C MET* 1.3 61.8 + - - +
223C LYS 3.2 0.9 + - - -
224C LEU* 3.3 17.5 + - - +
225C LEU* 3.4 21.4 + - + +
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Residues in contact with MET 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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124C GLU* 5.2 5.8 - - - +
127C ALA* 3.5 29.8 - - - +
128C GLU* 4.5 5.6 - - + +
131C ILE* 3.7 40.3 - - + +
163C LEU* 4.0 20.6 - - + -
218C ILE 3.9 3.9 + - - +
219C LYS* 4.4 8.5 - - - +
220C ASP 3.3 1.2 - - - -
221C ALA* 1.3 78.2 - - - +
223C LYS* 1.3 62.1 + - + +
225C LEU* 3.8 5.1 + - + +
226C ILE* 3.3 30.8 + - + +
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Residues in contact with LYS 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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219C LYS 4.2 14.8 - - - +
220C ASP* 3.6 23.1 + - + +
221C ALA 3.1 0.8 - - - -
222C MET* 1.3 78.6 - - + +
224C LEU* 1.3 69.5 + - + +
226C ILE* 3.3 24.7 + - + +
227C GLU* 3.6 6.1 + - - +
238D GLU* 4.7 17.8 + - - +
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Residues in contact with LEU 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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220C ASP* 3.5 20.9 - - + +
221C ALA* 3.3 10.8 + - - +
223C LYS* 1.3 80.6 - - + +
225C LEU* 1.3 63.3 + - + +
227C GLU* 3.2 23.5 + - - +
228C GLU* 3.2 33.0 + - + +
235D ASN* 5.0 27.8 - - + +
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Residues in contact with LEU 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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127C ALA* 3.7 39.9 - - + +
130C ARG* 3.7 29.2 - - + -
131C ILE* 4.5 9.9 - - + +
221C ALA* 3.4 19.3 + - + +
222C MET* 3.8 5.1 + - - +
223C LYS 3.3 0.6 - - - -
224C LEU* 1.3 76.0 - - + +
226C ILE* 1.3 60.9 + - - +
228C GLU* 3.9 22.2 - - + +
229C GLU* 2.8 34.8 + - + +
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Residues in contact with ILE 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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119C ASN 5.6 0.9 - - - +
120C ARG* 5.9 4.5 - - - -
123C ALA* 4.3 24.4 - - + +
124C GLU* 5.1 13.2 - - + +
127C ALA* 4.9 7.4 - - + -
222C MET* 3.3 25.8 - - + +
223C LYS* 3.6 14.8 - - + +
224C LEU 3.2 0.8 - - - -
225C LEU* 1.3 78.4 - - - +
227C GLU* 1.3 56.1 + - - +
230C ALA* 2.9 37.9 + - + +
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Residues in contact with GLU 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 LYS 3.6 5.9 + - - +
224C LEU* 3.2 25.8 + - - +
225C LEU 3.2 0.4 - - - -
226C ILE* 1.3 77.2 - - - +
228C GLU* 1.3 61.8 + - + +
230C ALA* 4.1 2.2 - - - +
231C ALA* 2.7 43.0 + - + +
237D GLU* 4.3 27.7 - - + +
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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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224C LEU* 3.2 22.6 + - + +
225C LEU* 3.9 22.7 - - + +
227C GLU* 1.3 81.7 - - + +
229C GLU* 1.3 58.6 + - - +
231C ALA* 3.9 5.3 - - - +
232C LYS* 2.9 28.2 + - - +
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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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123C ALA* 3.8 24.0 - - + +
126C LEU* 3.3 43.9 - - + +
127C ALA* 5.3 1.6 - - - +
130C ARG* 4.7 14.7 + - - +
225C LEU* 2.8 19.9 + - + +
228C GLU* 1.3 76.8 - - - +
230C ALA* 1.3 54.2 + - - +
232C LYS* 3.0 23.0 + - - +
233C LEU* 2.6 57.7 + - + +
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Residues in contact with ALA 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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116C ILE* 6.5 1.3 - - + -
119C ASN* 3.8 31.9 + - + +
123C ALA* 4.4 4.5 - - + +
226C ILE* 2.9 25.5 + - + +
227C GLU* 4.1 2.7 - - - +
229C GLU* 1.3 76.5 - - - +
231C ALA* 1.3 53.2 + - - +
233C LEU* 4.2 3.1 - - - +
234C VAL* 2.7 38.3 + - - +
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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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227C GLU* 2.7 28.7 + - + +
228C GLU* 3.9 5.8 - - - +
230C ALA* 1.3 73.7 - - - +
232C LYS* 1.3 60.9 + - - +
233C LEU 3.4 0.3 + - - -
234C VAL* 3.4 26.5 - - + +
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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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130C ARG* 5.1 13.0 - - - +
228C GLU 2.9 21.1 + - - +
229C GLU* 3.0 27.1 + - - +
231C ALA* 1.3 77.4 - - - +
233C LEU* 1.3 61.2 + - + +
234C VAL 4.1 2.6 - - - +
235C ASN* 5.2 2.3 + - - -
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Residues in contact with LEU 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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119C ASN* 3.9 20.3 - - - +
122C ARG* 3.6 44.4 - - + +
123C ALA* 4.0 8.5 - - + +
126C LEU* 5.3 5.2 - - + -
229C GLU* 2.6 52.5 + - + +
230C ALA* 4.0 4.0 - - - +
232C LYS* 1.3 75.6 - - + +
234C VAL* 1.3 66.2 + - - +
235C ASN* 3.7 13.5 + - - +
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Residues in contact with VAL 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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112C ARG* 5.8 6.7 - - - +
115C ALA* 5.0 3.4 - - + -
119C ASN* 4.0 18.2 - - - +
230C ALA 2.7 23.9 + - - +
231C ALA* 3.4 23.5 - - + +
232C LYS 4.1 2.3 - - - +
233C LEU* 1.3 74.4 - - - +
235C ASN* 1.3 71.4 + - - +
236C PRO* 3.9 13.9 - - + +
239C LEU* 3.8 28.5 - - + -
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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
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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