Contacts of the helix formed by residues 204 - 216 (chain B) in PDB entry 1IRD
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 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B HIS 3.8 0.8 + - - +
203B LEU* 1.3 75.7 - - - +
205B PRO* 1.3 71.5 - - - +
206B GLU* 3.5 12.1 + - - +
207B GLU* 3.0 39.3 + - - +
208B LYS* 2.8 26.5 + - - +
332B LYS* 4.9 5.4 - - - +
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Residues in contact with PRO 205 (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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203B LEU 4.4 1.3 - - - +
204B THR* 1.3 88.8 - - + +
206B GLU* 1.4 59.3 + - + +
208B LYS* 3.2 16.4 + - + +
209B SER* 2.9 29.5 + - - -
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Residues in contact with GLU 206 (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 THR* 3.2 11.4 + - - +
205B PRO* 1.4 79.1 - - + +
207B GLU* 1.3 63.9 + - + +
209B SER* 3.4 6.8 + - - -
210B ALA* 3.1 21.7 + - - +
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Residues in contact with GLU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LEU* 3.7 10.4 - - + -
204B THR* 3.0 35.5 + - - +
206B GLU* 1.3 76.4 - - + +
208B LYS* 1.4 54.4 + - - +
210B ALA* 3.1 6.0 + - - +
211B VAL* 2.7 37.8 + - - +
325B PRO 4.8 3.0 - - - +
328B ALA* 4.5 6.6 - - - +
329B ALA* 3.5 32.6 + - + -
332B LYS* 2.8 37.6 + - - -
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Residues in contact with LYS 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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203B LEU* 3.8 34.0 + - + +
204B THR 2.8 16.2 + - - +
205B PRO* 3.6 16.1 - - + +
207B GLU* 1.4 77.9 - - - +
209B SER* 1.3 58.3 + - - +
211B VAL* 3.7 2.4 - - - +
212B THR* 2.8 42.9 + - + +
278B LEU* 4.1 26.5 - - + -
279B ASP* 3.9 24.6 + - - -
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Residues in contact with SER 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B PRO 2.9 16.6 + - - -
206B GLU* 3.7 8.1 - - - -
208B LYS* 1.3 78.4 - - - +
210B ALA* 1.3 61.7 + - - +
212B THR* 3.7 5.5 + - - -
213B ALA* 2.9 31.0 + - - +
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Residues in contact with ALA 210 (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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206B GLU 3.1 13.2 + - - +
207B GLU* 3.1 12.1 + - - +
209B SER* 1.3 76.9 + - - +
211B VAL* 1.3 64.2 + - - +
213B ALA* 4.0 3.5 - - - +
214B LEU* 3.2 23.9 + - - +
325B PRO 5.6 0.7 - - - +
326B VAL* 4.1 33.2 - - + +
329B ALA* 4.9 2.9 - - + -
330B TYR* 4.6 2.3 - - - -
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Residues in contact with VAL 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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203B LEU* 3.8 14.1 - - + -
207B GLU 2.7 22.6 + - - +
208B LYS* 3.8 5.6 - - - +
210B ALA* 1.3 76.0 - - - +
212B THR* 1.3 68.0 + - + +
215B TRP* 3.0 8.8 + - - +
275B LEU* 3.4 35.9 - - + -
278B LEU* 5.8 1.1 - - + -
326B VAL 5.0 0.2 - - - +
329B ALA* 3.6 30.1 - - + +
330B TYR* 2.8 48.3 + - + +
333B VAL* 4.2 2.9 - - + -
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Residues in contact with THR 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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208B LYS* 2.8 33.3 + - + +
209B SER* 3.7 5.9 + - - -
211B VAL* 1.3 81.0 - - + +
213B ALA* 1.3 64.5 + - - +
215B TRP* 3.8 6.6 - - - +
216B GLY* 3.1 20.1 + - - -
275B LEU* 5.5 12.1 - - + +
278B LEU* 5.8 3.8 - - + -
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Residues in contact with ALA 213 (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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209B SER* 2.9 20.3 + - - +
210B ALA* 4.0 4.0 - - - +
212B THR* 1.3 77.3 + - - +
214B LEU* 1.3 63.5 + - - +
216B GLY* 3.6 6.2 + - - -
217B LYS* 3.2 26.3 - - - +
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Residues in contact with LEU 214 (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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210B ALA 3.2 13.6 + - - +
213B ALA* 1.3 78.4 - - + +
215B TRP* 1.3 67.7 + - - +
217B LYS* 2.9 20.6 + - - +
218B VAL* 3.5 7.0 + - - +
314B LEU* 4.8 3.1 - - + -
318B PHE* 3.7 49.6 - - + -
321B GLU* 3.9 28.5 - - - +
322B PHE* 3.6 34.3 - - + -
326B VAL* 4.2 7.0 - - + -
330B TYR* 3.6 20.2 - - + +
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Residues in contact with TRP 215 (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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211B VAL 3.0 17.9 + - - +
212B THR* 3.2 7.4 + - - +
214B LEU* 1.3 79.3 - - - +
216B GLY* 1.3 62.7 + - - +
217B LYS 3.0 0.2 - - - -
218B VAL* 3.1 34.9 + - + +
220B VAL* 5.1 7.7 - - + +
223B VAL* 5.7 0.2 - - + -
268B LEU* 3.7 37.2 - - + -
271B PHE* 4.2 10.1 - - + -
272B SER* 2.9 41.2 + - - -
275B LEU* 3.3 29.9 - - + +
310B LEU* 4.3 10.8 - - + -
314B LEU* 4.3 17.3 - - + -
330B TYR* 3.4 27.3 + + - +
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Residues in contact with GLY 216 (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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212B THR 3.1 14.1 + - - -
213B ALA* 3.6 3.6 + - - -
214B LEU 3.1 0.8 - - - -
215B TRP* 1.3 77.3 - - - +
217B LYS* 1.3 61.1 + - - +
218B VAL 3.5 3.5 + - - +
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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