Contacts of the helix formed by residues 209 - 224 (chain A) in PDB entry 1YNU
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 THR 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A GLN* 3.0 28.0 + - - +
207A THR 4.7 5.2 - - - +
208A MET* 1.3 75.4 - - - +
210A ARG* 1.3 65.2 + - - +
211A ASN* 3.6 8.9 + - - +
212A GLU* 3.0 37.1 + - - +
213A LEU* 3.1 12.3 + - - +
244A ILE* 5.1 2.0 - - - -
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Residues in contact with ARG 210 (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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106A LYS* 5.6 0.8 - - - +
208A MET 3.9 0.8 + - - -
209A THR* 1.3 73.2 - - - +
211A ASN* 1.3 61.3 + - - +
213A LEU* 3.2 12.3 + - - +
214A TYR* 2.9 67.8 + - + -
244A ILE* 3.4 36.5 - - + +
248A GLU* 3.7 21.8 + - - +
249A VAL* 5.2 10.5 - - + +
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Residues in contact with ASN 211 (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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209A THR* 3.2 8.9 + - - +
210A ARG* 1.3 82.0 - - - +
212A GLU* 1.3 57.1 + - + +
214A TYR* 3.4 14.1 + - - +
215A LEU* 2.9 29.7 + - - +
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Residues in contact with GLU 212 (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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171A PHE 4.9 0.2 - - - +
172A GLN* 3.4 29.5 + - + +
173A ILE* 2.9 46.9 + - + +
207A THR 4.5 1.2 - - - +
208A MET* 3.3 28.3 - - + +
209A THR* 3.0 38.7 + - - +
211A ASN* 1.3 76.3 - - + +
213A LEU* 1.3 58.1 - - - +
215A LEU* 3.3 11.3 + - - +
216A LEU* 3.0 32.6 + - - +
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Residues in contact with LEU 213 (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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197A VAL* 6.1 1.8 - - + -
199A ASN* 4.3 11.7 - - + +
208A MET* 3.5 30.3 - - + +
209A THR 3.1 16.2 + - - +
210A ARG* 3.5 9.2 - - - +
212A GLU* 1.3 74.3 - - - +
214A TYR* 1.3 65.4 + - - +
216A LEU* 3.1 8.6 + - + +
217A LEU* 2.9 29.5 + - + +
227A LEU* 5.4 1.2 - - + +
229A SER* 5.8 0.9 - - - +
244A ILE* 3.3 36.3 - - + +
245A SER 4.4 0.4 - - - +
246A VAL* 4.4 20.6 - - + -
249A VAL* 3.4 30.5 - - + -
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Residues in contact with TYR 214 (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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210A ARG* 2.9 58.3 + - + +
211A ASN* 3.9 13.9 - - - +
213A LEU* 1.3 75.7 - - - +
215A LEU* 1.3 57.3 - - - +
217A LEU* 3.3 9.7 + - + +
218A SER* 2.9 32.0 + - - -
249A VAL* 3.5 30.4 + - + +
252A ASP* 4.0 28.5 + - - +
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Residues in contact with LEU 215 (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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173A ILE* 3.3 30.7 - - + +
174A THR* 3.8 2.9 - - - -
175A GLU* 3.5 44.6 - - + +
178A LEU* 3.5 22.9 - - + -
211A ASN 2.9 18.0 + - - +
212A GLU* 3.4 10.1 - - - +
213A LEU 3.2 0.2 - - - -
214A TYR* 1.3 77.3 - - - +
216A LEU* 1.3 57.4 + - - +
218A SER* 3.5 6.0 + - - -
219A PHE* 3.0 25.8 + - + +
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Residues in contact with LEU 216 (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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173A ILE* 4.0 18.2 - - + -
178A LEU* 4.2 27.4 - - + -
195A VAL* 4.3 12.8 - - + -
197A VAL* 3.8 32.8 - - + -
208A MET* 3.3 34.5 - - + -
212A GLU 3.0 10.7 + - - +
213A LEU* 3.1 9.8 + - + +
215A LEU* 1.3 75.2 - - + +
217A LEU* 1.3 66.5 + - - +
219A PHE* 3.4 3.2 + - + +
220A VAL* 3.1 31.8 + - + +
227A LEU* 4.3 17.3 - - + -
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Residues in contact with LEU 217 (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 2.9 17.0 + - - +
214A TYR* 3.7 8.3 - - + +
216A LEU* 1.3 77.3 - - - +
218A SER* 1.3 61.8 + - - +
220A VAL* 3.4 8.4 - - + +
221A GLU* 3.2 26.1 + - - +
227A LEU* 3.8 22.7 - - + -
246A VAL* 4.2 8.1 - - + +
249A VAL* 3.4 40.8 - - + +
250A LEU* 3.9 22.9 - - + -
261A VAL* 4.2 8.8 - - + +
265A VAL* 3.8 22.9 - - + -
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Residues in contact with SER 218 (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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214A TYR 2.9 17.1 + - - -
215A LEU* 3.8 7.2 - - - -
217A LEU* 1.3 76.3 - - - +
219A PHE* 1.3 65.8 + - - +
221A GLU* 3.0 9.9 + - - +
222A ASP* 3.0 36.6 + - - +
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Residues in contact with PHE 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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139A LEU* 4.0 19.5 - - + -
178A LEU* 3.6 56.1 - - + -
179A GLU* 3.3 21.1 - - - -
182A TYR* 3.8 16.4 - + + -
195A VAL* 4.4 15.5 - - + -
215A LEU* 3.0 20.2 + - + +
216A LEU* 3.8 4.0 - - + +
218A SER* 1.3 78.1 + - - +
220A VAL* 1.3 60.5 + - + +
222A ASP* 3.2 8.0 + - + +
223A LYS* 3.0 66.5 + - + +
225A ILE* 4.7 2.9 - - + -
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Residues in contact with VAL 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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195A VAL* 4.1 21.3 - - + -
216A LEU* 3.1 17.4 + - - +
217A LEU* 3.4 18.2 - - + +
219A PHE* 1.3 76.5 - - + +
221A GLU* 1.3 61.6 + - - +
222A ASP 3.3 0.2 - - - -
223A LYS 3.8 0.9 - - - -
224A GLY 3.1 9.4 + - - -
225A ILE* 3.2 34.8 + - + +
226A HIS 4.2 7.9 - - - +
227A LEU* 4.2 22.2 - - + +
261A VAL* 4.0 14.8 - - + -
264A ARG* 3.1 24.5 + - - +
265A VAL* 5.8 0.4 - - + -
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Residues in contact with GLU 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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217A LEU* 3.2 19.6 + - - +
218A SER* 3.0 10.0 + - - +
220A VAL* 1.3 78.2 - - - +
222A ASP* 1.3 67.3 - - - +
224A GLY* 3.8 6.1 + - - -
259A SER* 5.6 4.8 + - - -
261A VAL* 4.0 27.2 - - + +
264A ARG* 3.7 12.4 + - - +
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Residues in contact with ASP 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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218A SER* 3.0 32.2 + - - +
219A PHE* 3.2 8.3 + - + +
221A GLU* 1.3 86.8 - - - +
223A LYS* 1.3 69.4 + - + +
224A GLY 3.5 0.2 - - - -
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Residues in contact with LYS 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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179A GLU* 3.3 17.6 + - - -
182A TYR* 3.2 44.2 + - + +
183A GLN* 5.4 0.8 - - - +
219A PHE* 3.0 53.9 + - + +
221A GLU 3.3 0.2 - - - -
222A ASP* 1.3 88.8 - - + +
224A GLY* 1.3 64.8 + - - +
225A ILE* 3.4 28.1 + - + +
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Residues in contact with GLY 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 VAL 3.1 5.0 + - - -
221A GLU 3.8 4.6 + - - -
222A ASP 3.5 2.6 - - - -
223A LYS* 1.3 79.8 - - - +
225A ILE* 1.3 59.0 + - - +
226A HIS* 5.5 1.4 + - - -
264A ARG* 2.6 25.8 + - - -
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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