Contacts of the helix formed by residues 219 - 224 (chain C) in PDB entry 1YI2
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 ASN 219 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6720 G 3.9 17.0 + - - +
6750 U 5.7 1.0 + - - -
6760 C 2.5 54.3 + - - +
6770 C 4.1 8.5 - - - +
111C VAL* 5.0 3.8 - - - -
217C GLU 3.2 2.5 + - - +
218C VAL* 1.3 74.2 - - - +
220C THR* 1.3 61.7 + - - +
221C GLU* 3.1 21.5 + - - +
222C ASP* 2.3 55.2 + - - +
223C LEU* 3.1 22.0 + - - +
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Residues in contact with THR 220 (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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6770 C 5.0 2.1 + - - -
31C ILE* 3.5 36.1 - - + +
34C ALA* 3.8 21.4 - - + +
35C VAL* 3.7 13.9 - - + -
107C ARG* 4.5 1.6 + - - +
110C ALA* 4.4 8.7 - - - +
111C VAL* 3.6 25.4 + - - +
114C ALA* 4.4 4.3 - - + -
219C ASN* 1.3 77.6 - - - +
221C GLU* 1.3 52.7 + - - +
223C LEU* 4.4 5.2 - - - -
224C ALA* 2.6 34.0 + - - +
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Residues in contact with GLU 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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6720 G 6.1 0.7 - - - +
6750 U 4.4 3.5 + - - +
6760 C 5.5 1.6 - - - +
35C VAL* 4.3 16.4 - - + +
38C ALA* 3.6 25.1 - - + +
39C GLN* 3.7 15.6 - - - +
42C ARG* 3.0 42.6 + - - -
219C ASN* 3.1 13.8 + - - +
220C THR* 1.3 76.5 - - - +
222C ASP* 1.3 61.8 + - - +
224C ALA 4.2 5.2 - - - -
225C PRO* 2.8 36.3 - - + +
226C GLY 5.3 2.6 + - - -
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Residues in contact with ASP 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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6720 G 2.8 41.3 + - - +
193C LEU* 3.4 29.1 - - + +
211C ASP* 5.2 3.8 - - + -
213C ALA* 3.9 3.8 - - - +
218C VAL* 3.7 5.4 - - - -
219C ASN* 2.3 56.3 + - - +
221C GLU* 1.3 73.7 - - - +
223C LEU* 1.3 55.5 + - - +
225C PRO* 3.4 1.0 - - - +
231C ARG* 2.9 40.2 + - - +
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Residues in contact with LEU 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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111C VAL* 3.9 24.9 - - + +
114C ALA* 3.6 21.1 - - + +
115C LEU* 3.5 40.8 - - + +
118C THR* 4.6 8.2 + - - +
193C LEU* 3.4 24.2 - - + -
195C VAL* 5.1 0.4 - - + -
218C VAL* 3.6 19.1 - - + -
219C ASN 3.1 23.7 + - - +
220C THR 3.8 0.4 - - - +
222C ASP* 1.3 79.3 - - - +
224C ALA* 1.3 58.2 + - - +
225C PRO* 3.6 0.4 - - - -
230C GLY 4.5 2.3 + - - -
231C ARG* 3.1 28.4 + - - +
233C THR* 4.9 3.1 - - - +
235C PHE* 5.0 5.2 - - + -
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Residues in contact with ALA 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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31C ILE* 3.5 28.7 - - + -
35C VAL* 3.6 4.5 - - - +
114C ALA* 4.3 5.8 - - + -
220C THR 2.6 19.1 + - - +
221C GLU 3.2 3.3 - - - +
223C LEU* 1.3 76.4 - - - +
225C PRO* 1.3 68.7 - - - +
226C GLY 3.3 0.2 + - - -
227C GLY* 2.8 13.7 + - - -
228C ALA 3.1 21.5 - - - +
229C PRO* 3.9 6.5 - - + -
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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