Contacts of the helix formed by residues 208 - 223 (chain A) in PDB entry 6AU8
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 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A LEU 5.2 0.6 + - - -
169A SER 3.7 16.6 + - - -
170A ALA* 4.5 4.0 - - - +
203A PHE* 2.9 29.0 + - + +
204A LEU* 4.3 1.7 + - - +
206A LEU* 4.3 8.3 - - + +
207A LYS* 1.3 76.4 - - - +
209A LYS* 1.3 59.0 + - - +
210A SER* 3.6 8.1 + - - -
211A SER* 2.8 41.4 + - - -
212A ALA* 3.2 18.9 + - - +
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Residues in contact with LYS 209 (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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204A LEU* 3.7 24.8 - - + +
207A LYS 3.6 4.6 + - - +
208A ASN* 1.3 74.6 - - - +
210A SER* 1.3 61.2 + - - +
212A ALA* 3.6 1.4 - - - +
213A SER* 3.0 28.9 + - - -
244A LEU* 4.6 3.9 - - + +
247A VAL* 4.6 13.1 + - + -
248A ASP* 3.1 47.7 + - + +
283A PHE* 4.5 16.0 - - + -
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Residues in contact with SER 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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208A ASN* 3.2 6.8 - - - -
209A LYS* 1.3 85.0 - - - +
211A SER* 1.3 62.2 + - - +
213A SER* 3.3 6.7 + - - -
214A VAL* 3.1 30.6 + - - +
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Residues in contact with SER 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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170A ALA* 3.5 24.5 + - - +
172A GLY* 3.9 9.5 - - - +
203A PHE* 3.8 20.0 - - - -
208A ASN* 2.8 34.5 + - - -
210A SER* 1.3 76.3 + - - +
212A ALA* 1.3 60.9 + - - +
214A VAL* 3.7 7.0 - - - +
215A VAL* 2.8 33.3 + - - +
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Residues in contact with ALA 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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200A VAL* 3.6 14.5 - - + +
203A PHE* 3.7 16.9 - - + +
204A LEU* 3.9 19.1 - - + -
208A ASN 3.2 18.0 + - - +
209A LYS 3.6 5.6 - - - +
210A SER 3.2 0.4 - - - -
211A SER* 1.3 79.4 - - - +
213A SER* 1.3 61.4 + - - +
215A VAL* 3.3 11.6 - - - +
216A PHE* 3.2 22.3 + - - +
244A LEU* 3.9 10.2 - - + +
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Residues in contact with SER 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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209A LYS 3.0 17.8 + - - -
210A SER* 3.6 5.6 - - - -
212A ALA* 1.3 76.8 - - - +
214A VAL* 1.3 63.6 + - - +
216A PHE* 3.3 3.3 + - - +
217A THR* 3.0 29.2 + - - -
244A LEU* 4.0 20.5 - - - +
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Residues in contact with VAL 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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172A GLY* 3.8 2.2 - - - +
173A GLU* 3.4 36.8 - - + +
210A SER* 3.1 21.7 + - - +
211A SER* 3.8 7.0 - - - +
213A SER* 1.3 75.6 - - - +
215A VAL* 1.3 65.2 + - - +
217A THR* 4.7 3.4 - - - -
218A THR* 2.9 35.4 + - - +
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Residues in contact with VAL 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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172A GLY 3.5 21.8 - - - +
175A CYS* 4.2 14.6 - - + -
176A ALA* 3.6 19.2 - - + +
179A LEU* 4.5 4.3 - - + -
196A VAL* 4.4 4.5 - - + -
199A ALA* 4.4 10.3 - - + -
200A VAL* 3.8 20.0 - - + +
203A PHE* 4.0 15.3 - - + -
211A SER 2.8 19.7 + - - +
212A ALA* 3.3 16.6 - - - +
214A VAL* 1.3 74.1 - - - +
216A PHE* 1.3 68.2 + - - +
219A TYR* 2.9 29.6 + - + +
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Residues in contact with PHE 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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196A VAL* 3.8 19.1 - - + -
200A VAL* 3.9 3.1 - - + -
212A ALA 3.2 14.2 + - - +
213A SER 3.6 3.8 - - - +
215A VAL* 1.3 82.7 - - - +
217A THR* 1.3 67.5 + - - +
219A TYR* 4.0 0.3 - - - +
220A THR* 2.9 49.5 + - + +
230A PRO* 5.7 1.8 - - + -
232A PHE* 3.7 24.5 - + - -
237A LEU* 3.5 31.6 - - + -
240A ILE* 3.4 29.4 - - + -
241A TRP* 3.9 25.6 - + + -
244A LEU* 3.7 18.8 - - + -
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Residues in contact with THR 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 SER* 3.0 21.6 + - - -
214A VAL* 4.0 4.5 - - - -
216A PHE* 1.3 83.1 - - - +
218A THR* 1.3 65.2 + - - +
220A THR* 3.4 6.7 + - - -
221A GLN* 3.2 49.7 + - - +
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Residues in contact with THR 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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173A GLU* 4.0 23.1 - - + +
176A ALA* 3.5 20.4 - - + -
177A ASN* 4.1 5.4 - - - +
214A VAL* 2.9 29.4 + - - +
217A THR* 1.3 81.3 - - - +
219A TYR* 1.3 56.0 + - - +
221A GLN* 3.9 3.9 - - - -
222A LYS* 2.9 55.9 + - + +
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Residues in contact with TYR 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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176A ALA* 3.6 11.0 - - + +
179A LEU* 3.8 38.8 - - + -
180A VAL* 3.8 16.8 - - + -
183A SER* 3.4 14.4 + - - -
192A VAL 2.7 29.3 + - - -
195A PHE* 3.5 12.2 - - + +
196A VAL* 3.4 31.9 - - + -
215A VAL* 2.9 20.5 + - + +
218A THR* 1.3 78.2 - - - +
220A THR* 1.3 60.4 + - - +
223A HIS* 2.9 58.5 + + - +
226A ILE* 3.8 18.2 - - + -
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Residues in contact with THR 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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216A PHE* 2.9 55.1 + - + +
217A THR* 3.4 8.3 + - - -
219A TYR* 1.3 80.9 - - + +
221A GLN* 1.3 67.8 + - - +
223A HIS 4.0 1.4 + - - -
226A ILE* 3.6 43.6 - - + +
227A GLU 4.8 1.9 - - - +
229A GLY 5.3 1.2 + - - -
232A PHE* 4.0 27.3 - - + -
237A LEU* 4.3 7.6 - - + -
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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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217A THR* 3.2 39.4 + - - +
218A THR* 4.0 4.4 - - - +
220A THR* 1.3 86.9 + - - +
222A LYS* 1.3 63.5 + - + +
223A HIS 3.7 3.3 + - - +
226A ILE 5.0 1.9 - - - +
229A GLY 5.6 6.1 - - - +
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Residues in contact with LYS 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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173A GLU* 4.6 8.7 + - - -
177A ASN* 3.2 38.0 + - - +
180A VAL* 4.2 17.4 - - + +
218A THR* 2.9 32.5 + - + +
219A TYR 4.4 0.4 - - - +
221A GLN* 1.3 79.3 - - + +
223A HIS* 1.3 63.8 + - - +
224A PRO* 3.4 7.8 - - - +
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Residues in contact with HIS 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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180A VAL* 4.2 14.8 - - + +
183A SER* 3.1 21.6 + - - -
184A THR* 3.6 19.2 - - + +
192A VAL* 3.4 33.1 - - + +
219A TYR* 2.9 47.3 + + + +
220A THR 4.0 1.1 + - - +
221A GLN 3.5 2.7 - - - +
222A LYS* 1.3 77.0 - - - +
224A PRO* 1.3 68.9 - - + +
225A SER* 3.0 39.7 + - - -
226A ILE* 3.2 30.9 + - + +
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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