Contacts of the helix formed by residues 218 - 225 (chain E) in PDB entry 6I53
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 ILE 218 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E PRO* 4.5 3.8 - - - +
145E LEU* 3.7 30.7 - - + -
216E ARG 4.0 8.7 - - - +
217E ASN* 1.3 76.9 - - - +
219E GLY* 1.3 66.2 + - - +
220E TYR 3.2 4.2 + - - -
221E PHE* 3.4 14.5 + - + +
222E ILE* 3.4 38.0 + - + +
226E TYR* 5.9 0.2 - - - -
443E TRP* 5.5 2.9 - - + -
508E POV 3.6 44.0 - - - +
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Residues in contact with GLY 219 (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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280A VAL 4.4 3.4 - - - -
281A ALA* 4.0 21.8 + - - +
282A TYR* 4.8 3.7 - - - +
217E ASN* 3.6 4.4 - - - +
218E ILE* 1.3 82.1 - - - +
220E TYR* 1.3 61.8 + - - +
222E ILE* 4.1 9.2 + - - +
223E LEU* 4.0 24.8 + - - +
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Residues in contact with TYR 220 (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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274A ARG* 3.3 56.4 + - + +
277A LEU* 6.0 0.7 - - + -
279A LYS* 3.6 55.9 - - + +
280A VAL 3.5 16.4 + - - +
281A ALA* 4.4 0.8 - - - +
282A TYR 5.7 0.2 - - - -
185E GLN* 4.9 3.1 - - - +
217E ASN 5.0 1.5 + - - +
218E ILE 3.2 1.0 - - - -
219E GLY* 1.3 78.4 - - - +
221E PHE* 1.3 88.0 + + + +
222E ILE 3.3 0.5 + - - -
223E LEU* 3.4 5.8 + - - +
224E GLN* 3.1 60.3 + - + +
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Residues in contact with PHE 221 (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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279A LYS* 5.0 5.4 - - + -
143E TYR* 3.2 38.1 - + - -
144E PRO* 3.6 35.9 - - + -
185E GLN* 3.5 35.7 - - - -
216E ARG* 3.8 6.3 - - - -
217E ASN 4.2 11.2 - - - -
218E ILE* 3.4 7.4 + - + +
220E TYR* 1.3 94.9 - + + +
222E ILE* 1.3 59.5 + - - +
224E GLN* 3.8 4.9 - - + -
225E THR* 2.5 42.8 + - + +
226E TYR* 3.0 11.2 + - + -
268E LEU* 5.6 6.1 - - + -
281E ILE* 4.5 10.5 - - + -
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Residues in contact with ILE 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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218E ILE* 3.4 33.9 - - + +
219E GLY* 4.3 8.3 - - - +
220E TYR 3.2 1.0 - - - -
221E PHE* 1.3 79.2 - - - +
223E LEU* 1.3 69.0 + - + +
224E GLN 3.2 0.7 + - - -
226E TYR* 3.3 17.0 + - + -
227E MET* 2.8 49.2 + - + +
228E PRO* 3.5 0.5 - - - +
443E TRP* 5.1 3.6 - - + -
508E POV 3.6 38.6 - - + +
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Residues in contact with LEU 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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270A SER* 4.5 12.8 - - - +
274A ARG* 5.3 10.1 - - - +
282A TYR 4.4 3.1 - - - +
283A ALA* 3.8 36.6 - - + +
287A ASP* 4.0 22.0 - - + +
291A ALA* 5.4 13.0 - - + -
219E GLY 4.0 14.1 + - - +
220E TYR* 3.4 7.2 + - - +
222E ILE* 1.3 85.5 - - + +
224E GLN* 1.3 59.0 + - - +
227E MET* 4.7 11.7 - - + -
228E PRO* 3.9 9.9 - - - +
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Residues in contact with GLN 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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270A SER 4.5 3.7 - - - +
271A ILE* 3.1 61.8 + - - +
274A ARG* 3.9 19.2 - - - +
220E TYR* 3.1 52.2 + - + +
221E PHE* 4.1 7.2 - - + -
223E LEU* 1.3 80.1 - - - +
225E THR* 1.3 72.1 + - + +
228E PRO* 3.4 13.7 - - - +
264E ILE* 5.3 1.4 - - - +
267E HIS 5.4 2.4 + - - -
268E LEU* 5.8 2.2 - - + -
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Residues in contact with THR 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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221E PHE* 2.5 30.9 + - + +
224E GLN* 1.3 90.0 - - + +
226E TYR* 1.3 71.7 + - - +
228E PRO* 3.4 4.4 - - - +
229E SER* 3.3 23.0 + - - -
264E ILE* 4.5 16.2 - - + +
268E LEU* 3.8 24.0 - - + -
281E ILE* 3.4 35.4 - - + +
285E LEU* 4.7 5.4 - - - +
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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