Contacts of the helix formed by residues 213 - 228 (chain A) in PDB entry 2O07
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 HIS 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A LEU* 2.6 52.0 + - + +
28A TRP* 6.0 1.1 - + - -
29A PRO* 5.9 1.6 - - + -
208A GLU* 3.4 30.1 - - - +
209A CYS 2.9 13.9 + - - +
212A LEU* 1.3 102.0 + - + +
214A LEU* 1.3 65.2 + - - +
215A ASP* 3.3 10.6 + - - -
216A LEU* 3.2 21.3 + - + +
217A ILE* 3.1 24.5 + - - +
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Residues in contact with LEU 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 GLN* 3.8 14.4 + - + +
212A LEU 3.9 1.0 - - - -
213A HIS* 1.3 73.9 - - - +
215A ASP* 1.3 60.8 + - - +
217A ILE* 3.2 15.7 + - + -
218A LYS* 2.9 28.2 + - + +
293A PHE* 3.5 35.2 - - + +
294A ALA* 4.0 21.8 - - + -
297A ALA* 3.8 24.9 - - + -
298A LEU* 4.1 21.1 - - + -
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Residues in contact with ASP 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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213A HIS* 3.7 13.0 + - - +
214A LEU* 1.3 74.2 - - - +
216A LEU* 1.3 80.9 + - - +
218A LYS* 3.3 10.9 + - - +
219A GLU* 3.1 29.8 + - - +
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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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27A LEU* 6.1 3.8 - - + -
208A GLU* 3.4 30.7 - - + +
213A HIS* 3.2 28.4 + - + +
215A ASP* 1.3 95.5 + - - +
217A ILE* 1.3 66.5 + - - +
219A GLU* 3.3 32.2 - - + +
220A MET* 3.0 27.7 + - - +
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Residues in contact with ILE 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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207A GLY 3.7 6.7 - - - +
208A GLU* 3.6 20.0 - - + +
209A CYS 3.9 1.3 - - - -
210A GLN* 3.5 36.8 - - + +
213A HIS 3.1 15.0 + - - +
214A LEU* 3.2 10.9 + - + +
216A LEU* 1.3 75.6 - - - +
218A LYS* 1.3 54.0 + - - +
220A MET* 3.8 4.6 - - - +
221A ARG* 2.8 38.1 + - + +
233A TYR* 3.5 42.8 - - + +
249A MET* 4.8 6.6 - - + +
298A LEU* 3.9 24.7 - - + -
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Residues in contact with LYS 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 LEU 2.9 13.0 + - - +
215A ASP* 3.4 14.1 - - - +
217A ILE* 1.3 77.2 - - - +
219A GLU* 1.3 57.4 + - - +
221A ARG* 3.5 3.2 + - - +
222A GLN* 3.0 59.5 + - + +
297A ALA* 3.5 34.2 + - + +
298A LEU* 3.8 15.0 - - + +
300A ASP 5.8 2.2 + - - -
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Residues in contact with GLU 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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187A GLU* 4.8 9.1 - - - +
215A ASP* 3.1 15.5 + - - +
216A LEU* 3.3 39.1 - - - +
218A LYS* 1.3 73.4 - - - +
220A MET* 1.3 69.5 + - + +
222A GLN* 3.3 13.8 + - - +
223A PHE* 2.8 30.5 + - - +
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Residues in contact with MET 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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187A GLU* 3.6 30.1 - - + +
190A TYR* 4.2 29.2 - - + +
208A GLU* 6.4 1.3 - - + -
216A LEU 3.0 19.0 + - - +
217A ILE* 3.9 4.3 - - - +
219A GLU* 1.3 84.8 - - + +
221A ARG* 1.3 56.6 + - - +
223A PHE* 3.2 20.8 + - - +
224A CYS* 2.8 36.7 + - - +
249A MET* 4.3 16.4 - - + -
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Residues in contact with ARG 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 ILE* 2.8 21.7 + - + +
218A LYS* 3.6 5.6 - - - +
220A MET* 1.3 73.9 - - - +
222A GLN* 1.3 58.1 + - + +
224A CYS* 3.3 2.3 + - - +
225A GLN* 2.9 58.0 + - - +
231A VAL* 4.1 27.2 + - + +
232A ALA* 3.7 5.3 - - - +
233A TYR* 3.3 39.4 - - - +
249A MET* 4.2 14.2 - - + +
260A GLN* 5.7 4.2 - - - +
290A LEU* 5.9 0.2 - - - +
298A LEU* 3.7 43.6 + - - +
299A ASN* 4.3 16.4 + - - +
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Residues in contact with GLN 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 LYS* 3.0 49.9 + - + +
219A GLU* 3.6 15.0 - - - +
220A MET 3.3 0.2 - - - -
221A ARG* 1.3 72.8 - - + +
223A PHE* 1.3 68.4 + - - +
225A GLN* 3.4 17.3 + - - +
226A SER* 3.3 19.1 + - - -
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Residues in contact with PHE 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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187A GLU* 3.2 64.6 - - + +
188A SER* 5.2 0.7 - - - -
190A TYR* 4.1 3.6 - - + -
191A GLN* 5.6 1.8 - - + -
219A GLU 2.8 21.1 + - - +
220A MET* 3.6 15.3 - - - +
222A GLN* 1.3 73.8 - - - +
224A CYS* 1.3 67.6 + - - +
226A SER* 3.1 22.6 + - - -
227A LEU* 3.5 35.8 + - + +
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Residues in contact with CYS 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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190A TYR* 3.5 42.8 - - - -
220A MET* 2.8 31.1 + - - +
221A ARG 3.8 2.2 - - - +
223A PHE* 1.3 75.5 - - - +
225A GLN* 1.3 56.6 + - - +
227A LEU* 3.1 3.9 + - - +
228A PHE* 2.8 36.0 + - - -
231A VAL* 3.5 14.7 - - + +
249A MET* 4.1 6.7 - - - -
251A CYS* 3.7 22.4 - - - -
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Residues in contact with GLN 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 ARG* 2.9 47.1 + - - +
222A GLN* 3.7 20.1 - - - +
223A PHE 3.2 0.6 - - - -
224A CYS* 1.3 76.2 - - - +
226A SER* 1.3 59.5 + - - +
228A PHE 3.3 14.7 + - - +
231A VAL* 3.7 23.1 + - + +
298A LEU 5.6 1.2 + - - -
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Residues in contact with SER 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 LYS* 5.4 0.2 + - - -
222A GLN 3.3 11.2 + - - -
223A PHE* 3.1 16.4 + - - -
225A GLN* 1.3 78.1 - - - +
227A LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 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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190A TYR* 4.1 8.7 - - + -
191A GLN* 3.9 40.8 - - + +
194A LYS* 2.7 46.0 + - + +
223A PHE* 3.5 41.9 + - + +
224A CYS* 3.1 7.7 + - - +
226A SER* 1.3 83.2 - - - +
228A PHE* 1.3 70.7 + - + +
229A PRO* 4.6 1.7 - - - +
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Residues in contact with PHE 228 (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 TYR* 3.7 16.4 - + - -
194A LYS* 3.7 35.9 - - + -
197A LEU* 4.5 3.1 - - + -
203A LEU* 3.6 24.9 - - + -
224A CYS* 2.8 23.3 + - - +
225A GLN* 3.3 21.0 - - - +
226A SER 3.8 0.2 - - - -
227A LEU* 1.3 91.8 - - + +
229A PRO* 1.3 68.4 - - - +
230A VAL 3.4 12.0 + - - +
231A VAL* 4.1 3.0 - - + +
251A CYS* 3.6 28.7 - - + -
252A SER 3.5 17.3 - - - +
253A LYS* 3.8 24.7 - - + -
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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