Contacts of the helix formed by residues 207 - 221 (chain A) in PDB entry 1ORR
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 GLY 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A MET 5.4 3.1 - - - -
200A GLN* 3.8 23.1 - - - -
202A ALA* 3.3 7.9 - - - +
203A THR 4.7 0.2 - - - -
206A GLN* 1.3 76.5 - - - +
208A TRP* 1.3 61.3 + - - +
209A VAL 3.3 2.9 - - - -
210A GLY 3.3 2.1 + - - -
211A TRP* 2.8 31.3 + - - +
1200A NAD 6.2 0.7 - - - -
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Residues in contact with TRP 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A SER* 2.9 26.9 + - - -
207A GLY* 1.3 71.0 - - - +
209A VAL* 1.3 80.3 + - + +
211A TRP* 3.6 5.3 - - - +
212A PHE* 3.0 33.8 + + + -
235A GLN 5.8 0.2 - - - -
237A ARG* 3.8 16.1 - - + +
239A VAL* 3.7 20.6 - - + -
274A LEU* 3.8 29.8 - - + -
275A SER 4.5 0.4 - - - -
276A LEU* 3.0 36.3 - - + -
279A LEU* 3.6 28.0 - - + -
1201A CDP 3.6 66.7 - - + +
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A SER* 5.2 2.7 - - - -
195A MET 5.5 1.5 + - - +
196A TYR* 3.8 37.5 - - + -
207A GLY 3.3 0.6 - - - -
208A TRP* 1.3 116.7 - - + +
210A GLY* 1.3 60.0 + - - +
212A PHE* 3.3 2.4 + - - +
213A CYS* 2.9 36.1 + - - -
239A VAL* 3.9 17.5 - - + -
274A LEU* 5.8 0.4 - - + -
279A LEU* 4.3 9.9 - - + +
329A VAL* 4.1 20.6 - - + -
332A MET* 4.7 1.1 - - + -
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Residues in contact with GLY 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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200A GLN* 4.2 4.1 - - - +
202A ALA* 3.6 12.3 - - - +
207A GLY 3.3 6.2 + - - -
208A TRP 3.3 0.2 - - - -
209A VAL* 1.3 81.6 - - - +
211A TRP* 1.3 62.0 + - - +
213A CYS* 3.2 5.6 + - - +
214A GLN* 3.1 22.0 + - - +
332A MET* 3.4 31.2 - - - +
336A THR* 4.7 2.6 + - - +
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Residues in contact with TRP 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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202A ALA* 3.3 9.7 - - + +
203A THR* 3.5 20.6 - - - +
204A TYR* 3.4 47.6 - + + +
207A GLY 2.8 21.5 + - - +
208A TRP* 3.6 5.4 - - - +
210A GLY* 1.3 73.3 - - - +
212A PHE* 1.3 82.4 + + - +
214A GLN* 3.0 16.4 + - + +
215A LYS* 2.9 60.9 + - + +
227A PHE* 5.3 4.9 - - + +
228A THR 5.2 1.2 + - - -
1201A CDP 3.3 28.1 + + - -
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Residues in contact with PHE 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 TRP* 3.0 36.4 + + + +
211A TRP* 1.3 91.7 - + - +
213A CYS* 1.3 62.0 + - - +
215A LYS* 3.1 8.8 + - + +
216A ALA* 3.0 21.0 + - - +
227A PHE* 3.7 32.3 - + - -
228A THR 3.9 7.2 - - - -
229A ILE* 4.2 1.3 - - + -
276A LEU* 3.7 28.5 - - + -
279A LEU* 3.7 19.1 - - + -
280A PHE* 3.6 26.2 - + + -
283A LEU* 3.8 7.4 - - + +
291A MET* 4.2 1.7 - - + +
1201A CDP 3.6 36.6 - + - -
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Residues in contact with CYS 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 VAL* 2.9 22.1 + - - -
210A GLY 3.6 8.5 - - - +
211A TRP 3.2 0.4 - - - -
212A PHE* 1.3 77.2 - - - +
214A GLN* 1.3 58.1 + - - +
216A ALA* 3.2 5.2 + - - +
217A VAL* 3.0 30.8 + - - +
279A LEU* 5.4 0.2 - - - -
283A LEU* 4.1 25.6 - - - -
329A VAL* 4.3 9.0 - - - -
332A MET* 3.7 24.2 - - + -
333A TYR* 3.8 16.4 - - - -
336A THR* 3.7 18.2 - - - +
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Residues in contact with GLN 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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202A ALA* 5.9 2.7 - - + +
210A GLY 3.1 11.6 + - - +
211A TRP* 3.0 21.1 + - + +
213A CYS* 1.3 73.4 - - - +
215A LYS* 1.4 73.3 + - - +
217A VAL* 3.3 7.9 + - - +
218A GLU* 2.9 63.3 + - - +
336A THR* 3.3 25.9 - - + +
339A ILE* 5.5 5.0 - - - +
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Residues in contact with LYS 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 TRP* 2.9 58.1 + - + +
212A PHE* 3.1 20.4 + - + +
214A GLN* 1.4 83.9 - - - +
216A ALA* 1.3 55.9 + - - +
218A GLU* 2.7 35.9 + - - +
219A ILE* 3.0 34.2 + - - +
225A LYS* 4.6 9.8 + - - +
227A PHE* 3.9 50.0 - - + -
291A MET* 4.3 2.5 - - + -
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Residues in contact with ALA 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 PHE 3.0 11.7 + - - +
213A CYS 3.4 9.4 - - - +
214A GLN 3.2 0.2 - - - -
215A LYS* 1.3 75.8 - - - +
217A VAL* 1.3 60.2 + - - +
219A ILE* 3.3 2.4 + - - +
220A LYS* 2.9 30.7 + - - +
283A LEU* 4.2 12.6 - - + -
287A CYS* 4.5 1.5 - - - -
289A ILE* 3.9 25.3 - - + +
291A MET* 4.1 10.9 - - - +
333A TYR* 3.9 17.2 + - + -
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Residues in contact with VAL 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 CYS 3.0 16.4 + - - +
214A GLN* 3.3 12.3 + - - +
216A ALA* 1.3 75.8 - - - +
218A GLU* 1.3 63.1 + - + +
220A LYS* 3.2 1.7 + - - +
221A ASN* 3.1 42.4 + - - +
223A ILE* 6.1 0.4 - - + -
333A TYR* 3.0 38.8 - - + +
336A THR* 3.6 23.1 - - + +
337A SER* 3.9 26.2 - - - +
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Residues in contact with GLU 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 GLN* 2.9 40.8 + - - +
215A LYS* 2.7 43.0 + - - +
217A VAL* 1.3 77.0 - - + +
219A ILE* 1.3 62.4 + - + +
221A ASN 3.1 1.4 + - - -
223A ILE* 2.8 61.2 + - + +
225A LYS* 3.7 35.4 + - + +
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Residues in contact with ILE 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 LYS 3.0 19.6 + - - +
216A ALA* 3.3 4.7 + - - +
218A GLU* 1.3 80.2 - - + +
220A LYS* 1.3 63.4 + - - +
222A GLY* 3.0 14.5 + - - +
223A ILE 4.4 9.0 - - - +
227A PHE* 4.1 20.2 - - + -
289A ILE* 3.9 31.1 - - + +
290A ASP 3.7 22.7 - - - +
291A MET* 4.1 14.6 - - + -
292A ARG 4.6 2.9 - - - +
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Residues in contact with LYS 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 ALA 2.9 17.5 + - - +
217A VAL 3.5 5.8 - - - +
218A GLU 3.2 0.2 - - - -
219A ILE* 1.3 77.0 - - - +
221A ASN* 1.3 67.1 + - - +
222A GLY 3.6 0.2 + - - -
287A CYS* 2.9 32.7 + - + +
288A ASN* 4.4 10.7 + - - +
289A ILE* 4.0 12.6 - - + -
333A TYR* 3.7 20.0 - - + +
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Residues in contact with ASN 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 VAL* 3.1 35.8 + - - +
218A GLU 3.1 0.8 + - - -
220A LYS* 1.3 88.9 - - - +
222A GLY* 1.3 61.7 + - - +
223A ILE* 3.0 22.4 - - + +
333A TYR* 5.5 0.6 + - - -
337A SER* 6.0 0.6 - - - -
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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