Contacts of the helix formed by residues 200 - 213 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ALA 3.7 11.8 + - - -
57B ASP* 4.0 14.3 + - - +
58B VAL 3.7 11.9 - - - +
59B GLU* 3.6 24.0 - - + -
60B PHE* 3.9 5.4 - - - -
148B ARG* 4.0 6.3 - - - +
199B VAL* 1.3 77.4 - - - +
201B VAL* 1.3 66.9 + - - +
202B LYS* 3.4 10.4 + - - +
203B ASP* 2.7 43.6 + - - +
204B LEU* 3.1 12.6 + - - +
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLY 3.8 6.3 - - - +
41B ILE* 3.5 5.6 - - - +
42B ALA* 3.1 23.6 - - + +
55B ASP 4.7 0.9 - - - +
56B ALA* 3.7 15.7 + - + -
58B VAL 4.5 0.8 + - - -
60B PHE* 3.7 5.9 - - + -
200B THR* 1.3 72.9 - - - +
202B LYS* 1.3 62.9 + - - +
204B LEU* 3.3 4.2 + - - -
205B ALA* 3.0 19.6 + - - +
276B GLY* 2.8 33.0 - - - +
277B VAL* 3.3 15.7 - - - +
278B PHE* 3.1 36.8 - - + +
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Residues in contact with LYS 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA* 3.9 14.4 - - + -
50B LEU* 4.3 24.4 - - + +
52B CYS* 3.6 26.1 - - + -
56B ALA* 3.3 22.0 + - + +
57B ASP* 2.9 40.2 + - - +
200B THR* 3.0 7.7 + - - +
201B VAL* 1.3 79.5 - - - +
203B ASP* 1.3 62.7 + - - +
205B ALA* 3.2 2.6 + - - +
206B VAL* 3.1 30.0 + - + +
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Residues in contact with ASP 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ALA* 3.9 19.4 - - + +
148B ARG* 2.8 44.6 + - - -
150B LEU* 4.5 2.0 - - - -
199B VAL* 3.5 12.1 - - + -
200B THR* 2.7 40.7 + - - +
202B LYS* 1.3 74.1 - - - +
204B LEU* 1.3 58.3 + - - +
206B VAL* 3.1 7.9 + - - +
207B MET* 2.8 43.0 + - - +
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Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PHE* 4.0 19.5 - - + -
62B ILE* 3.6 33.0 - - + -
65B ALA* 4.7 3.6 - - + -
199B VAL* 3.9 11.9 - - + -
200B THR 3.1 11.1 + - - +
201B VAL* 3.6 7.0 - - - +
203B ASP* 1.3 78.7 - - - +
205B ALA* 1.3 54.3 + - - +
207B MET* 3.6 8.5 - - + -
208B GLY* 2.7 31.2 + - - -
264B GLY 4.3 2.0 - - - -
265B VAL 3.5 40.2 - - - +
266B LEU* 3.5 22.6 - - + +
275B ILE 3.9 4.3 - - - +
276B GLY* 3.8 8.1 - - - -
277B VAL 4.3 3.1 - - - +
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Residues in contact with ALA 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA* 3.8 32.3 - - + +
43B LEU 4.0 0.7 - - - +
44B ALA* 3.4 13.8 - - + +
50B LEU* 4.4 2.2 - - + -
201B VAL 3.0 13.2 + - - +
202B LYS* 3.4 9.6 - - - +
203B ASP 3.2 0.2 - - - -
204B LEU* 1.3 76.8 - - - +
206B VAL* 1.3 57.3 + - - +
209B ALA 2.9 22.9 + - - -
274B GLY* 3.3 17.5 - - - +
275B ILE 3.7 12.3 - - - -
276B GLY* 3.9 0.4 - - - +
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA* 3.8 16.2 - - + -
50B LEU* 4.4 16.8 - - + -
145B LEU 3.8 5.2 - - - +
146B ALA 4.6 9.0 - - - +
202B LYS 3.1 18.5 + - - +
203B ASP* 3.6 7.4 - - - +
205B ALA* 1.3 73.0 - - - +
207B MET* 1.3 66.4 + - - +
209B ALA* 3.1 4.0 + - - +
210B CYS* 3.1 22.2 + - - -
217B HIS* 3.5 35.9 - - + +
218B PRO* 4.4 6.0 - - + +
219B MET* 4.4 12.6 - - + -
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Residues in contact with MET 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ILE* 4.4 1.1 - - + -
69B PHE* 3.5 47.0 - - + -
142B MET* 3.5 46.0 - - + +
145B LEU* 3.9 11.9 - - + -
146B ALA* 3.6 30.3 - - - +
150B LEU* 4.6 1.6 - - + -
199B VAL* 4.4 7.6 - - - -
203B ASP* 2.8 36.1 + - - +
204B LEU* 3.6 11.9 - - - +
206B VAL* 1.3 73.2 - - - +
208B GLY* 1.3 63.2 + - - +
210B CYS* 3.2 18.0 - - - +
211B LEU* 3.6 9.5 + - - +
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Residues in contact with GLY 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B LEU 2.7 20.7 + - - -
205B ALA 3.7 0.7 - - - -
207B MET* 1.3 72.2 - - - +
209B ALA* 1.3 65.1 + - - +
211B LEU* 2.9 15.4 + - - +
212B ALA* 3.0 9.4 + - - +
266B LEU* 3.6 18.4 - - - +
267B GLY 3.6 8.3 - - - -
268B ALA* 3.5 13.7 - - - +
274B GLY* 3.8 5.6 - - - -
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Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA* 3.7 28.7 - - + +
45B THR 4.5 2.7 - - - +
46B PRO* 5.4 0.4 - - + -
205B ALA 2.9 14.5 + - - +
206B VAL 3.4 9.4 - - - +
208B GLY* 1.3 76.2 - - - +
210B CYS* 1.3 56.5 + - - +
212B ALA* 3.5 6.2 - - - +
213B THR* 3.0 37.7 + - + +
218B PRO* 3.8 17.9 - - + -
273B VAL 5.0 0.4 - - - -
274B GLY* 3.4 8.6 - - - +
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Residues in contact with CYS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 3.7 48.9 - - + -
206B VAL 3.1 18.6 + - - -
207B MET 3.2 11.4 - - - +
208B GLY 3.0 0.6 - - - -
209B ALA* 1.3 77.7 - - - +
211B LEU* 1.3 57.9 + - + +
213B THR* 3.1 3.8 + - - -
215B GLY* 2.9 33.3 + - - -
216B ILE 3.9 10.1 - - - +
217B HIS* 3.7 27.1 - - - -
218B PRO* 4.0 4.3 - - - -
224B MET* 4.6 0.7 - - - -
225B LEU* 5.3 1.1 - - + +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PRO* 4.8 0.9 - - + -
69B PHE* 3.9 30.1 - - + -
72B ALA* 5.4 1.3 - - + -
145B LEU* 4.9 1.3 - - + -
207B MET 3.8 10.8 - - - +
208B GLY* 2.9 6.5 + - - +
210B CYS* 1.3 75.7 - - - +
212B ALA* 1.3 65.6 + - - +
213B THR 3.2 0.4 - - - -
214B GLY* 3.3 12.8 + - - -
225B LEU* 3.8 27.8 - - + -
230B ALA* 4.3 14.7 - - + +
233B VAL* 4.3 22.7 - - + -
234B VAL* 3.7 24.3 - - + +
237B MET* 4.1 25.4 - - - -
266B LEU* 4.5 4.0 - - + -
268B ALA* 4.2 7.6 - - + -
270B PRO* 5.4 1.7 - - - +
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PRO* 5.9 2.2 - - + -
208B GLY 3.0 10.3 + - - +
209B ALA* 3.1 11.9 + - - +
211B LEU* 1.3 80.1 - - - +
213B THR* 1.3 59.8 + - + +
214B GLY 3.6 0.2 + - - -
234B VAL* 5.5 0.2 - - - -
268B ALA* 4.4 2.4 - - - +
269B LEU 3.2 29.6 - - - +
270B PRO* 3.5 9.8 - - - +
271B GLY* 2.7 28.3 + - - +
272B ARG 4.8 0.7 - - - +
273B VAL* 3.9 17.5 - - - +
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Residues in contact with THR 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PRO* 4.2 34.1 - - + +
209B ALA 3.0 15.7 - - - +
210B CYS 3.1 5.7 + - - -
212B ALA* 1.3 80.4 - - + +
214B GLY* 1.3 58.2 - - - +
216B ILE* 2.5 58.4 + - + +
218B PRO* 4.7 3.8 - - + -
223B ARG* 5.7 0.5 + - - -
271B GLY* 5.4 2.2 - - - -
416B ARG* 4.9 7.8 + - - -
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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
------------------------------------------------------------
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