Contacts of the helix formed by residues 218 - 227 (chain A) in PDB entry 1I4A
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 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A PHE 5.7 0.2 - - - +
211A TYR* 4.1 0.4 - - - -
212A LYS* 3.2 28.4 + - - +
217A LYS* 1.3 74.1 - - - +
219A ILE* 1.3 67.4 + - - +
220A GLU* 3.0 22.7 + - - +
221A GLN* 2.5 40.7 + - + +
222A SER* 3.2 8.1 + - - -
243A ARG* 2.7 44.0 + - - -
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Residues in contact with ILE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LEU* 3.9 19.7 - - + -
192A PHE* 3.8 27.8 - - + -
196A LEU* 5.4 1.6 - - + -
208A PHE* 3.7 34.3 + - + -
211A TYR* 3.8 32.4 - - + -
217A LYS 3.8 1.8 + - - -
218A ASP* 1.3 73.2 + - - +
220A GLU* 1.3 59.9 + - - +
222A SER* 3.2 2.0 + - - -
223A ILE* 2.9 45.7 + - + +
239A VAL* 4.0 15.9 - - + -
243A ARG* 3.6 23.1 - - - +
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Residues in contact with GLU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ASP* 3.0 9.7 + - - +
219A ILE* 1.3 83.3 - - - +
221A GLN* 1.3 60.4 + - - +
223A ILE* 3.4 8.4 + - - +
224A LYS* 3.1 41.3 + - - +
236A LEU* 4.1 9.9 - - + +
239A VAL* 3.6 29.1 - - + +
240A LYS* 3.4 36.0 - - - +
243A ARG* 2.8 28.9 + - - +
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Residues in contact with GLN 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A LYS* 4.8 0.7 - - - -
217A LYS* 3.3 20.8 - - + +
218A ASP* 2.5 53.0 + - + +
220A GLU* 1.3 76.1 - - - +
222A SER* 1.3 64.8 + - - +
224A LYS* 3.4 10.7 + - - +
225A SER* 3.2 24.8 + - - -
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Residues in contact with SER 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A PHE* 5.2 2.7 - - - -
211A TYR* 2.6 37.9 + - - -
217A LYS* 4.2 15.3 - - - +
218A ASP 3.2 8.1 + - - -
219A ILE* 3.6 10.1 - - - -
221A GLN* 1.3 74.6 - - - +
223A ILE* 1.3 59.5 + - - +
225A SER* 3.3 6.0 + - - -
226A GLU* 2.8 51.7 + - - +
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Residues in contact with ILE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A PHE* 4.0 21.8 - - + -
196A LEU* 4.1 12.8 - - + -
219A ILE* 2.9 31.5 + - + +
220A GLU* 3.7 1.1 - - - +
222A SER* 1.3 77.4 - - - +
224A LYS* 1.3 56.2 + - - +
226A GLU* 4.9 1.8 - - - -
227A THR* 2.6 50.9 + - - +
232A GLU* 3.8 4.9 - - + +
235A LEU* 3.8 20.0 - - + -
236A LEU* 3.3 28.0 - - + -
239A VAL* 3.7 31.0 - - + -
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Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLU* 3.1 37.4 + - - +
221A GLN* 3.8 9.4 - - - +
222A SER 3.2 0.4 - - - -
223A ILE* 1.3 77.3 - - - +
225A SER* 1.3 59.1 + - - +
227A THR 3.5 10.8 - - - +
232A GLU* 3.4 21.6 - - - +
236A LEU* 4.0 26.5 - - + -
240A LYS* 5.1 7.8 - - - +
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Residues in contact with SER 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A GLN 3.2 18.4 + - - -
222A SER* 3.4 7.8 + - - -
224A LYS* 1.3 77.1 - - - +
226A GLU* 1.3 68.1 + - - +
227A THR 3.6 1.3 - - - -
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Residues in contact with GLU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LEU 4.6 0.9 - - - +
178A TYR 5.5 0.3 - - - +
181A GLY* 3.2 33.9 + - - +
187A THR* 2.8 35.9 + - + +
189A GLU* 4.6 1.7 - - - +
192A PHE* 3.5 22.2 - - + -
211A TYR* 4.0 4.9 + - - -
222A SER* 2.8 39.4 + - - +
223A ILE* 4.9 0.4 - - - -
225A SER* 1.3 86.7 + - - +
227A THR* 1.3 63.4 + - + +
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Residues in contact with THR 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A THR* 4.4 12.3 - - + -
189A GLU* 4.0 8.3 - - - +
192A PHE* 4.6 7.6 - - + -
223A ILE* 2.6 31.8 + - + +
224A LYS 3.5 8.5 - - - +
225A SER 4.6 0.7 - - - -
226A GLU* 1.3 85.4 + - + +
228A SER* 1.3 64.9 + - - +
231A PHE* 3.8 32.8 - - + -
232A GLU* 3.2 28.0 - - - +
235A LEU* 4.1 8.9 - - + +
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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