Contacts of the helix formed by residues 200 - 213 (chain A) in PDB entry 3IH9
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 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ALA 3.4 13.7 + - - -
57A ASP* 3.7 23.6 + - - +
58A VAL 3.7 8.5 - - - +
59A GLU* 3.8 18.4 - - + -
60A PHE* 4.0 5.4 - - - -
148A ARG* 4.2 4.9 - - - +
199A VAL* 1.3 78.8 - - - +
201A VAL* 1.3 66.9 + - - +
202A LYS* 3.2 9.4 + - - +
203A ASP* 2.7 42.8 + - - +
204A LEU* 3.1 12.8 + - - +
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Residues in contact with VAL 201 (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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40A GLY 4.0 2.7 - - - -
41A ILE* 3.4 7.9 - - - -
42A ALA* 3.4 13.2 - - - +
55A ASP 3.3 26.9 - - - +
56A ALA* 3.4 14.4 - - + -
58A VAL 5.0 0.7 - - - +
60A PHE* 3.8 8.7 - - + -
200A THR* 1.3 73.7 - - - +
202A LYS* 1.3 62.8 + - - +
204A LEU* 3.4 1.6 + - - -
205A ALA* 3.0 19.2 + - - +
276A GLY* 2.6 51.9 - - - +
277A VAL* 3.4 4.9 - - - +
278A PHE* 3.4 23.6 - - + -
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Residues in contact with LYS 202 (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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42A ALA* 3.9 19.1 - - + -
50A LEU* 4.2 24.1 - - + +
52A CYS* 3.1 33.1 - - - -
56A ALA* 3.4 10.5 + - + +
57A ASP* 3.0 40.0 + - - +
200A THR* 3.0 7.7 + - - +
201A VAL* 1.3 75.2 - - - +
203A ASP* 1.3 66.2 + - - +
205A ALA* 3.2 3.6 + - - +
206A VAL* 3.0 27.6 + - + +
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Residues in contact with ASP 203 (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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146A ALA* 4.2 15.2 - - + +
148A ARG* 2.9 45.6 + - - +
150A LEU* 4.5 3.8 - - - -
199A VAL* 3.4 13.4 - - + -
200A THR* 2.7 39.8 + - - +
202A LYS* 1.3 74.6 - - - +
204A LEU* 1.3 58.4 + - - +
206A VAL* 3.2 6.9 + - - +
207A MET* 2.8 41.1 + - - +
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Residues in contact with LEU 204 (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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60A PHE* 3.8 25.6 - - + -
62A ILE* 3.6 34.3 - - + -
65A ALA* 4.5 2.9 - - + -
69A PHE* 5.0 0.2 - - + -
199A VAL* 3.9 9.9 - - + -
200A THR 3.1 10.6 + - - +
201A VAL* 3.6 7.0 - - - +
203A ASP* 1.3 77.0 - - - +
205A ALA* 1.3 60.3 + - - +
207A MET* 3.6 10.1 - - + +
208A GLY* 2.8 28.9 + - - -
264A GLY 4.5 1.3 - - - -
265A VAL 3.7 31.0 - - - +
266A LEU* 3.7 23.3 - - + +
275A ILE 4.1 4.5 - - - +
276A GLY* 3.8 9.4 - - - -
277A VAL 4.5 2.2 - - - +
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Residues in contact with ALA 205 (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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42A ALA* 3.4 36.6 - - + +
43A LEU 4.3 0.2 - - - -
44A ALA* 3.3 14.4 - - + +
50A LEU* 4.5 1.3 - - + -
201A VAL 3.0 12.9 + - - +
202A LYS* 3.2 8.3 + - - +
204A LEU* 1.3 75.7 - - - +
206A VAL* 1.3 57.1 + - - +
209A ALA 3.1 21.1 + - - -
274A GLY* 3.2 17.4 - - - +
275A ILE 3.6 13.0 - - - +
276A GLY 3.6 1.5 - - - +
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Residues in contact with VAL 206 (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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44A ALA* 3.9 10.8 - - + -
50A LEU* 4.4 13.2 - - + -
145A LEU 3.2 21.1 - - - +
146A ALA 4.0 12.6 - - - +
202A LYS 3.0 15.5 + - - +
203A ASP* 3.6 7.4 - - - +
205A ALA* 1.3 76.0 - - - +
207A MET* 1.3 65.1 + - - +
209A ALA* 3.2 12.5 + - - +
210A CYS* 3.3 13.7 + - - -
217A HIS* 3.6 21.1 - - + +
218A PRO* 4.5 2.0 - - + +
219A MET* 4.1 26.0 - - + -
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Residues in contact with MET 207 (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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62A ILE* 4.1 2.0 - - + -
69A PHE* 3.5 49.4 - - + -
142A MET* 3.7 39.3 - - + +
145A LEU* 3.9 11.1 - - + +
146A ALA* 3.6 31.6 - - - +
150A LEU* 4.9 0.2 - - + -
199A VAL* 4.4 7.0 - - - -
203A ASP* 2.8 37.0 + - - +
204A LEU* 3.6 13.9 - - - +
206A VAL* 1.3 75.8 - - - +
208A GLY* 1.3 62.1 + - - +
210A CYS* 3.3 18.4 + - - +
211A LEU* 3.6 10.0 + - - +
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Residues in contact with GLY 208 (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 2.8 14.5 + - - -
205A ALA 3.8 1.3 - - - -
207A MET* 1.3 76.3 - - - +
209A ALA* 1.3 58.5 + - - +
211A LEU* 3.3 5.9 + - - -
212A ALA* 2.9 23.0 + - - +
266A LEU* 3.6 10.7 - - - +
267A GLY 3.6 18.8 - - - -
268A ALA* 3.3 14.3 - - - +
274A GLY* 3.7 6.5 - - - -
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Residues in contact with ALA 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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44A ALA* 4.0 20.9 - - + +
45A THR 4.4 3.4 - - - +
46A PRO* 5.5 0.2 - - + -
205A ALA 3.1 13.5 + - - +
206A VAL 3.2 9.4 + - - +
208A GLY* 1.3 75.6 - - - +
210A CYS* 1.3 58.7 + - - +
212A ALA* 3.8 5.6 - - - -
213A THR* 2.8 38.6 + - + +
218A PRO* 3.7 24.0 - - + -
273A VAL* 5.0 0.4 - - - -
274A GLY* 3.5 6.9 - - - +
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Residues in contact with CYS 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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145A LEU* 3.7 37.5 - - + -
206A VAL 3.4 15.0 - - - -
207A MET 3.4 7.4 - - - +
208A GLY 3.2 0.2 - - - -
209A ALA* 1.3 77.8 - - - +
211A LEU* 1.3 54.9 + - + +
213A THR* 3.1 5.5 + - - -
215A GLY* 2.7 39.7 + - - +
216A ILE 3.5 11.7 - - - +
217A HIS* 3.6 40.2 - - - -
218A PRO* 4.0 1.1 - - - -
224A MET* 5.2 0.2 - - + -
225A LEU* 5.7 0.9 - - + -
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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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68A PRO* 4.9 1.1 - - + -
69A PHE* 4.0 29.2 - - + -
72A ALA* 5.4 1.6 - - + -
145A LEU* 4.7 2.9 - - + -
207A MET 3.8 11.0 - - - +
208A GLY* 3.3 6.0 + - - +
209A ALA 3.2 0.4 - - - -
210A CYS* 1.3 76.4 - - - +
212A ALA* 1.3 64.6 + - - +
214A GLY* 2.9 15.6 + - - -
225A LEU* 3.9 27.1 - - + -
230A ALA* 4.1 16.3 - - + +
233A VAL* 4.2 22.4 - - + -
234A VAL* 3.8 21.1 - - + +
237A MET* 4.1 25.8 - - - -
266A LEU* 4.8 2.7 - - + -
268A ALA* 4.2 8.7 - - + -
270A PRO* 5.4 1.2 - - - +
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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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46A PRO* 6.0 0.9 - - + -
208A GLY 2.9 17.0 + - - +
209A ALA* 3.1 9.6 + - - +
211A LEU* 1.3 77.9 - - - +
213A THR* 1.3 61.7 + - + +
214A GLY 3.5 0.2 + - - -
234A VAL* 5.5 0.2 - - - -
268A ALA* 4.3 3.1 - - - +
269A LEU 3.5 23.1 - - - +
270A PRO* 3.3 13.1 - - - +
271A GLY* 2.7 26.2 + - - +
272A ARG 4.8 0.7 - - - +
273A VAL* 3.7 20.4 - - - +
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Residues in contact with THR 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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46A PRO* 4.1 36.6 - - + +
209A ALA* 2.8 21.8 + - - +
210A CYS 3.1 3.8 + - - -
212A ALA* 1.3 77.5 - - + +
214A GLY* 1.3 58.8 + - - +
216A ILE* 2.5 56.5 + - + +
218A PRO* 4.8 4.3 - - + -
223A ARG* 5.5 0.3 + - - -
271A GLY* 4.9 4.0 - - - +
416A ARG* 4.7 9.9 + - - -
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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