Contacts of the helix formed by residues 210 - 226 (chain A) in PDB entry 4XNW
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 TYR 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A PHE* 4.0 30.8 - + - -
189A TYR* 4.1 11.2 - + + -
206A THR* 3.7 21.3 - - - +
207A SER* 2.9 23.1 + - - -
209A GLU* 1.3 103.2 + - + +
211A LEU* 1.3 65.2 + - - +
212A ARG 3.3 2.9 - - - -
213A SER* 3.2 9.9 + - - +
214A TYR* 3.1 19.8 + - - +
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Residues in contact with LEU 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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205A THR* 4.9 0.4 - - - +
206A THR* 3.8 13.2 - - + -
207A SER 3.3 7.5 + - - +
208A ASP* 3.1 22.7 + - + +
210A TYR* 1.3 76.8 - - - +
212A ARG* 1.3 57.2 + - - +
214A TYR* 3.5 2.6 - - + +
215A PHE* 2.8 31.2 + - - +
284A LEU* 3.3 32.5 - - + -
287A ARG* 3.5 59.0 - - + +
288A LEU* 3.9 26.8 - - + +
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Residues in contact with ARG 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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208A ASP 4.8 1.2 + - - +
209A GLU 5.3 1.1 + - - +
210A TYR 3.2 1.6 + - - -
211A LEU* 1.3 77.9 - - - +
213A SER* 1.3 62.8 + - - +
215A PHE* 3.3 12.6 + - - +
216A ILE* 3.3 20.6 + - + +
288A LEU* 3.6 38.7 + - + +
289A ASP* 3.3 26.2 + - - -
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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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189A TYR* 2.7 28.3 + - - -
210A TYR* 3.2 13.6 + - - +
212A ARG* 1.3 75.1 - - - +
214A TYR* 1.3 68.5 + - - +
216A ILE* 3.1 16.5 + - - +
217A TYR* 2.9 22.3 + - - +
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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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132A HIS* 4.9 4.2 + - - -
186A ILE* 4.8 11.7 - - + +
189A TYR* 3.5 40.6 - + + -
204A ASP 3.9 4.9 + - - -
205A THR* 3.6 37.9 - - + +
206A THR* 3.7 13.9 - - + -
210A TYR 3.1 11.2 + - - +
211A LEU 3.5 7.6 - - - +
213A SER* 1.3 83.3 + - - +
215A PHE* 1.3 63.7 + - - +
217A TYR* 3.0 18.6 + + - +
218A SER* 2.8 34.0 + - - -
280A LYS* 2.8 35.0 + - - -
284A LEU* 4.1 18.2 - - + -
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Residues in contact with PHE 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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211A LEU 2.8 17.2 + - - +
212A ARG* 3.4 10.8 - - - +
213A SER 3.2 0.2 - - - -
214A TYR* 1.3 77.9 - - - +
216A ILE* 1.3 64.8 + - + +
218A SER* 3.2 2.0 + - - -
219A MET* 2.9 61.1 + - + +
281A THR* 4.2 12.8 - - + -
284A LEU* 3.9 31.9 - - + -
285A ARG* 3.5 38.1 - - + -
288A LEU* 4.1 18.6 - - + -
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Residues in contact with ILE 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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212A ARG* 3.3 17.0 + - + +
213A SER* 3.1 15.4 + - - +
215A PHE* 1.3 82.2 - - + +
217A TYR* 1.3 64.0 + - - +
219A MET* 3.4 7.8 + - - +
220A CYS* 3.1 37.5 + - - -
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Residues in contact with TYR 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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182A ALA 2.6 29.0 + - - -
183A ILE* 3.3 22.2 + - + +
185A PRO* 3.5 26.3 - - + +
186A ILE* 4.1 22.4 - - + +
189A TYR* 4.2 21.5 - + + +
213A SER 2.9 12.1 + - - +
214A TYR* 3.4 24.2 - + - +
216A ILE* 1.3 78.2 - - - +
218A SER* 1.3 65.8 + - - +
220A CYS* 3.1 19.4 + - + +
221A THR* 3.2 30.4 + - + -
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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* 2.8 38.8 + - - -
215A PHE 3.6 3.8 - - - -
217A TYR* 1.3 77.4 - - - +
219A MET* 1.3 63.0 + - - +
221A THR* 3.2 8.2 + - - -
222A THR* 2.9 33.4 + - - -
280A LYS* 3.7 26.8 + - - +
281A THR* 5.4 3.5 + - - +
284A LEU* 3.9 11.3 - - - +
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Residues in contact with MET 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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215A PHE* 2.9 51.2 + - + +
216A ILE* 3.5 10.1 - - - +
217A TYR 3.2 0.2 - - - -
218A SER* 1.3 76.8 - - - +
220A CYS* 1.3 65.5 + - - +
222A THR* 3.5 9.4 + - + -
223A VAL* 3.0 44.3 + - + +
281A THR* 4.0 20.9 - - + +
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Residues in contact with CYS 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 ILE* 3.1 31.6 + - - -
217A TYR* 3.1 12.6 + - + +
219A MET* 1.3 77.7 - - - +
221A THR* 1.3 56.3 + - + +
223A VAL* 3.4 3.9 + - - +
224A ALA* 2.8 39.6 + - + +
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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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136A TYR* 3.9 19.4 + - - -
182A ALA* 4.3 5.2 - - + +
183A ILE* 4.6 2.7 - - + -
217A TYR* 3.2 42.2 + - + +
218A SER* 3.2 14.6 + - - -
220A CYS* 1.3 75.7 - - + +
222A THR* 1.3 62.0 + - - +
224A ALA* 4.8 0.2 - - - -
225A MET* 2.6 63.9 + - + +
226A PHE 3.4 0.7 + - - -
280A LYS* 6.1 0.7 - - - -
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Residues in contact with THR 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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136A TYR* 4.0 4.5 + - - -
218A SER* 2.9 25.4 + - - -
219A MET* 3.9 11.9 - - + +
221A THR* 1.3 81.5 + - - +
223A VAL* 1.3 52.3 + - + +
226A PHE* 3.2 13.8 + - + +
227A CYS* 2.7 46.8 + - - -
277A HIS* 3.3 35.1 + - + +
280A LYS* 4.9 3.1 - - - +
281A THR* 5.1 10.6 + - - +
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Residues in contact with VAL 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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219A MET* 3.0 38.3 + - + +
220A CYS* 3.8 4.5 - - - +
222A THR* 1.3 79.8 - - + +
224A ALA* 1.3 63.4 + - + +
227A CYS* 3.5 13.9 - - + +
228A VAL* 2.9 38.9 + - + +
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Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A LEU* 5.3 1.7 - - - +
220A CYS* 2.8 22.8 + - + +
221A THR* 4.8 0.4 - - - -
223A VAL* 1.3 77.5 - - + +
225A MET* 1.3 65.7 + - + +
228A VAL* 3.8 9.9 - - - +
229A PRO* 3.2 19.2 - - - +
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Residues in contact with MET 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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136A TYR* 3.3 35.8 - - + -
139A ILE* 3.3 21.7 - - - +
140A LEU* 4.5 24.5 - - + +
178A ILE* 4.6 10.8 - - + -
179A VAL* 4.6 4.9 - - - -
182A ALA* 3.4 27.4 - - + -
183A ILE* 3.4 35.7 - - + -
221A THR* 2.6 32.4 + - + +
224A ALA* 1.3 83.4 - - + +
226A PHE* 1.3 56.7 + - - +
229A PRO* 3.8 7.6 - - - +
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Residues in contact with PHE 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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136A TYR* 4.4 1.1 - - + -
139A ILE* 4.3 10.2 - - + +
221A THR 3.4 0.4 + - - -
222A THR* 3.2 13.1 + - + +
224A ALA 3.6 0.6 - - - -
225A MET* 1.3 80.7 - - - +
227A CYS* 1.3 87.9 + - - +
228A VAL 3.4 0.7 - - - -
229A PRO* 3.5 4.9 - - - +
230A LEU* 2.9 43.4 + - + +
269A PHE* 3.8 30.7 - + - -
273A TYR* 3.8 14.8 - - + -
274A ILE* 3.7 31.4 - - + -
277A HIS* 3.8 46.2 - + + +
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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