Contacts of the helix formed by residues 220 - 227 (chain A) in PDB entry 1YFL
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 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A LEU* 3.0 43.3 - - + +
176A ILE* 3.7 10.8 - - + +
190A GLU* 4.1 12.1 + - - +
211A ASN* 5.4 5.4 + - - +
212A VAL 4.0 15.3 - - - +
213A LEU* 2.8 19.5 + - - +
219A GLU* 1.3 68.5 - - - +
221A THR* 1.3 57.9 + - - +
222A LEU* 4.6 2.8 - - - +
223A LEU* 2.6 46.2 + - - +
224A LYS* 2.9 22.1 + - - +
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Residues in contact with THR 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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219A GLU* 3.3 32.2 + - - +
220A ASN* 1.3 69.0 - - - +
222A LEU* 1.3 69.4 + - - +
223A LEU 3.0 2.2 - - - -
224A LYS* 2.7 21.4 + - + +
225A GLU* 2.9 17.2 + - + +
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Residues in contact with LEU 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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175A LEU* 5.7 2.2 - - + -
187A GLU* 5.7 6.7 - - + +
190A GLU* 5.0 9.0 - - + -
194A LEU* 4.5 11.4 - - + +
220A ASN* 4.4 5.2 - - - +
221A THR* 1.3 78.7 - - - +
223A LEU* 1.3 56.2 - - - +
225A GLU* 4.2 3.8 - - - +
226A TRP* 3.2 24.0 + - - +
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Residues in contact with LEU 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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190A GLU* 4.3 7.9 - - - +
194A LEU* 4.3 18.4 - - + -
209A LEU* 6.0 1.8 - - + -
211A ASN* 5.7 4.5 - - - +
213A LEU* 4.5 8.5 - - + -
220A ASN* 2.6 28.9 + - + +
222A LEU* 1.3 71.1 - - - +
224A LYS* 1.3 51.6 + - - +
225A GLU 3.0 2.7 - - - -
226A TRP* 3.9 9.0 - - + -
227A SER* 2.5 43.9 + - - +
257A ILE* 5.1 9.0 - - + -
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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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213A LEU* 4.0 26.1 - - + +
214A GLU* 2.8 44.1 + - - +
219A GLU* 3.0 32.6 + - + +
220A ASN 2.9 19.0 + - - +
221A THR* 2.7 19.6 + - + +
223A LEU* 1.3 72.1 - - - +
225A GLU* 1.3 55.0 + - - +
227A SER* 2.4 17.2 + - - -
228A LYS* 4.5 2.6 + - - +
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Residues in contact with GLU 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 THR* 2.9 15.3 + - + +
222A LEU* 4.2 3.4 - - - +
224A LYS* 1.3 74.4 - - - +
226A TRP* 1.3 66.6 + - - +
227A SER 3.0 1.3 - - - -
228A LYS* 3.0 24.3 + - - +
229A LYS* 4.3 1.6 + - - +
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Residues in contact with TRP 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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194A LEU* 3.3 66.7 + - + +
195A ASN* 5.1 2.4 - - - +
197A LEU* 3.8 16.6 - - + -
198A ASP* 3.6 6.7 + - - -
207A PHE* 3.8 14.8 - + - -
209A LEU* 5.0 4.9 - - + -
222A LEU 3.2 18.6 + - - +
223A LEU* 3.3 8.5 + - + -
225A GLU* 1.3 78.5 - - - +
227A SER* 1.3 63.3 + - - +
228A LYS 3.0 5.5 + - - -
229A LYS* 3.2 47.9 + - - +
230A TYR* 3.4 33.0 - + - -
257A ILE* 3.9 20.4 - - + -
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Residues in contact with SER 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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213A LEU* 4.6 7.0 - - - +
223A LEU 2.5 19.9 + - - -
224A LYS* 2.4 32.6 + - - -
226A TRP* 1.3 81.2 - - - +
228A LYS* 1.3 55.7 + - - +
229A LYS 3.5 0.2 - - - -
230A TYR* 2.9 22.4 + - - +
231A ASN 3.4 9.0 - - - +
232A VAL* 4.6 10.1 - - - +
257A ILE* 3.8 28.1 - - - +
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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