Contacts of the helix formed by residues 214 - 225 (chain X) in PDB entry 3SI5
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 214 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ASN* 5.4 4.5 - - - -
133B ASN* 5.5 4.3 + - - -
212X LYS 3.8 2.4 + - - -
213X ILE* 1.3 73.8 - - - +
215X PHE* 1.3 63.5 + - - +
216X ASN* 3.4 11.3 + - - +
217X ASP* 3.1 43.1 + - + +
218X PHE* 2.9 21.8 + - - +
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Residues in contact with PHE 215 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A TRP* 3.9 14.4 - + - -
128A LEU* 4.0 21.8 - - + -
132A CYS* 3.9 17.2 - - + +
134A GLU 4.8 1.7 - - - +
137A ASP* 3.5 36.2 + - + +
138A MET* 3.7 29.8 - - + +
141A TYR* 3.5 39.7 - + + -
213X ILE* 3.6 5.4 + - - -
214X ASP* 1.3 72.8 + - - +
216X ASN* 1.3 71.9 + - - +
218X PHE* 3.1 9.9 + + - +
219X ILE* 3.0 47.3 + - + +
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Residues in contact with ASN 216 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ASP* 3.9 30.3 + - - +
214X ASP* 3.4 8.1 + - - +
215X PHE* 1.3 81.8 - - - +
217X ASP* 1.3 59.7 + - - +
219X ILE* 3.4 6.7 + - - +
220X LYS* 3.0 43.6 + - - +
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Residues in contact with ASP 217 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214X ASP* 3.1 37.7 + - + +
215X PHE 3.2 0.2 - - - -
216X ASN* 1.3 76.9 - - - +
218X PHE* 1.3 60.0 + - - +
220X LYS* 3.4 19.9 + - - +
221X ARG* 2.9 29.3 + - - +
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Residues in contact with PHE 218 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLU* 3.5 38.4 - - + +
106A VAL* 3.7 27.1 - - + -
125A TRP* 4.5 2.7 - + - -
128A LEU* 3.9 21.5 - - + -
213X ILE* 4.4 9.0 - - + -
214X ASP 2.9 12.3 + - - +
215X PHE* 3.3 14.6 - + - +
217X ASP* 1.3 76.5 - - - +
219X ILE* 1.3 69.8 + - + +
221X ARG* 3.0 40.7 + - - +
222X LEU* 2.9 57.4 + - + +
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Residues in contact with ILE 219 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A TRP* 4.2 2.7 - - + -
141A TYR* 3.7 44.2 - - + +
215X PHE* 3.0 45.9 + - + +
216X ASN* 3.8 6.3 - - - +
218X PHE* 1.3 77.6 - - + +
220X LYS* 1.3 68.1 + - + +
222X LEU* 3.4 26.3 + - + +
223X LYS* 3.2 46.2 + - - +
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Residues in contact with LYS 220 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216X ASN* 3.0 28.0 + - - +
217X ASP* 3.4 22.7 + - - +
219X ILE* 1.3 77.2 - - + +
221X ARG* 1.3 61.8 + - - +
223X LYS* 3.1 15.6 + - + +
224X THR* 3.1 25.6 + - - +
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Residues in contact with ARG 221 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLU* 3.1 32.3 + - - +
104A ARG* 6.4 0.2 - - - +
107A GLU* 3.6 32.6 + - - +
217X ASP 2.9 14.1 + - - +
218X PHE* 3.0 37.9 + - - +
220X LYS* 1.3 75.4 - - - +
222X LEU* 1.3 64.9 + - - +
224X THR* 3.2 22.5 + - + +
225X GLY 3.7 10.3 + - - +
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Residues in contact with LEU 222 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A VAL* 3.8 13.0 - - + -
107A GLU* 3.7 43.1 - - + +
110A GLN* 3.8 35.1 + - + +
125A TRP* 4.7 2.0 - - + -
141A TYR* 5.5 1.3 - - - +
218X PHE* 2.9 52.5 + - + +
219X ILE* 3.6 22.9 - - + +
220X LYS 3.3 0.2 - - - -
221X ARG* 1.3 79.7 - - - +
223X LYS* 1.3 62.3 + - + +
225X GLY* 3.4 14.2 + - - +
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Residues in contact with LYS 223 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLN* 5.6 0.7 - - - +
141A TYR* 5.7 3.6 - - - -
145A GLN* 6.3 0.4 - - - +
219X ILE* 3.2 34.3 + - + +
220X LYS* 3.1 12.9 + - + +
222X LEU* 1.3 78.4 - - + +
224X THR* 1.3 63.4 + - - +
225X GLY* 3.1 1.9 + - - -
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Residues in contact with THR 224 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220X LYS 3.1 14.3 + - - -
221X ARG* 3.2 15.1 + - + +
223X LYS* 1.3 77.3 - - - +
225X GLY* 1.3 58.9 + - - +
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Residues in contact with GLY 225 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLU* 4.3 13.7 - - - +
221X ARG* 3.7 9.6 + - - +
222X LEU* 3.4 10.6 + - - +
223X LYS 3.1 5.5 - - - -
224X THR* 1.3 84.0 - - - +
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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