Contacts of the helix formed by residues 207 - 220 (chain B) in PDB entry 1IC8
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B GLN 6.0 0.2 - - - -
127B ASN* 3.0 18.8 - - - +
205B LYS 3.5 2.0 + - - -
206B TRP* 1.3 75.7 - - - +
208B PRO* 1.3 77.2 - - - +
209B ALA 3.4 2.5 - - - -
210B SER* 3.2 13.2 + - - -
211B GLN* 3.2 8.5 + - - +
240B GLU* 3.7 23.7 + - - -
243B GLN* 4.6 2.0 - - - -
244B ARG* 5.0 0.7 - - - -
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Residues in contact with PRO 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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124B GLN 5.6 4.9 - - - +
125B GLN* 5.5 2.2 - - - +
127B ASN* 5.9 0.4 - - - -
206B TRP 3.7 1.7 - - - +
207B GLY* 1.3 81.1 - - - +
209B ALA* 1.3 56.8 + - + +
211B GLN* 2.8 18.0 + - + +
212B GLN* 2.8 44.0 + - - +
243B GLN* 3.8 19.5 - - - +
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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
----------------------------------------------------------
207B GLY 3.4 0.6 - - - -
208B PRO* 1.3 80.4 - - + +
210B SER* 1.3 61.9 + - - +
212B GLN* 3.1 33.0 + - - +
213B ILE* 3.2 18.5 - - - +
239B ALA* 3.7 21.8 - - + -
240B GLU* 4.2 2.0 - - - +
243B GLN* 3.6 28.0 - - + +
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Residues in contact with SER 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B TRP* 3.4 31.6 - - - -
207B GLY 3.2 4.6 + - - -
208B PRO 3.2 0.8 - - - -
209B ALA* 1.3 78.0 - - - +
211B GLN* 1.3 59.3 + - - +
213B ILE* 3.2 2.1 + - - +
214B LEU* 3.0 24.8 + - - +
236B CYS* 3.1 32.8 + - - +
239B ALA* 4.6 0.4 - - - +
240B GLU* 2.3 43.3 + - - +
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Residues in contact with GLN 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LYS* 4.8 6.5 - - - +
206B TRP* 2.4 52.7 + - + +
207B GLY 3.3 11.1 + - - +
208B PRO* 2.8 12.3 + - + +
210B SER* 1.3 71.6 - - - +
212B GLN* 1.3 57.8 + - - +
213B ILE 2.9 5.2 - - - -
214B LEU* 2.8 26.3 + - - +
215B PHE* 3.0 26.3 + - + -
267B TRP* 4.6 11.7 + - - +
315E C 4.9 5.8 + - - -
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Residues in contact with GLN 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B PRO* 2.8 28.9 + - - +
209B ALA* 3.1 38.4 + - - +
211B GLN* 1.3 73.4 - - - +
213B ILE* 1.3 62.7 + - + +
215B PHE* 4.0 10.9 + - - +
216B GLN* 3.4 20.8 - - - +
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Residues in contact with ILE 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 ALA* 3.2 16.2 - - - +
210B SER* 3.2 9.1 + - - +
211B GLN 2.9 0.4 - - - -
212B GLN* 1.3 86.4 - - + +
214B LEU* 1.3 63.4 + - - +
215B PHE 3.3 0.8 + - - -
216B GLN* 3.4 30.5 + - - +
217B ALA* 3.6 8.1 + - - +
232B LEU* 4.9 7.8 - - + +
235B GLU* 4.0 36.6 - - + +
236B CYS* 3.8 15.5 - - - -
239B ALA* 3.9 21.5 - - + -
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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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206B TRP* 3.4 36.8 - - + -
210B SER 3.0 15.5 + - - +
211B GLN* 2.8 6.4 + - - +
213B ILE* 1.3 75.9 - - - +
215B PHE* 1.3 64.7 + - - +
216B GLN 3.3 0.2 + - - -
217B ALA* 3.5 5.4 + - - +
218B TYR 3.4 10.7 + - - -
232B LEU* 3.9 32.3 - - + -
236B CYS* 3.6 18.4 - - - -
264B VAL* 4.6 7.2 - - + -
267B TRP* 3.1 57.8 - - + +
268B PHE* 4.2 6.5 - - + -
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Residues in contact with PHE 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 GLN* 3.0 26.6 + - + +
212B GLN* 4.2 8.1 - - - +
213B ILE 3.3 0.4 - - - -
214B LEU* 1.3 76.8 - - - +
216B GLN* 1.3 52.0 + - + +
218B TYR* 3.0 5.8 + + - +
219B GLU* 2.5 59.6 + - + +
267B TRP* 3.1 34.8 - + - -
271B ARG* 4.8 25.4 - - + -
274B GLU* 5.3 4.9 - - - -
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Residues in contact with GLN 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 GLN 3.4 21.8 - - - +
213B ILE* 3.4 25.4 + - - +
214B LEU 3.2 0.2 - - - -
215B PHE* 1.3 72.6 - - + +
217B ALA* 1.3 53.5 + - - +
218B TYR 2.3 18.4 + - - -
219B GLU* 4.2 4.5 - - - +
220B ARG* 2.6 56.6 + - - +
235B GLU* 5.2 4.0 + - - -
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Residues in contact with ALA 217 (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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213B ILE 3.6 6.0 + - - +
214B LEU 3.5 6.8 + - - +
216B GLN* 1.3 74.8 - - - +
218B TYR* 1.3 55.7 + - - +
220B ARG* 3.5 21.1 - - - +
221B GLN 3.0 18.2 - - - +
223B ASN 4.5 2.8 - - - +
228B GLU* 5.7 0.5 - - - +
232B LEU* 3.5 44.2 - - + -
268B PHE* 3.2 15.4 - - + -
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Residues in contact with TYR 218 (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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214B LEU 3.4 10.5 - - - +
215B PHE* 3.2 11.0 - + - +
216B GLN 2.3 16.4 + - - -
217B ALA* 1.3 71.5 - - - +
219B GLU* 1.3 72.9 + - + +
220B ARG 2.9 4.3 - - - -
221B GLN* 3.0 13.5 + - - -
222B LYS* 3.1 39.4 + - + +
267B TRP* 3.9 11.7 - + + -
268B PHE* 3.5 26.2 - + + -
271B ARG* 3.7 35.8 - - + -
272B ARG* 3.4 45.2 + - + +
275B GLU* 2.8 23.6 + - - -
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Residues in contact with GLU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B PHE* 2.5 40.3 + - + +
216B GLN* 4.3 3.4 - - - +
218B TYR* 1.3 80.3 - - + +
220B ARG* 1.3 68.2 + - - +
271B ARG* 4.2 16.8 + - - +
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Residues in contact with ARG 220 (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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216B GLN* 2.6 55.5 + - - +
217B ALA* 3.5 29.2 - - - +
219B GLU* 1.3 77.8 - - - +
221B GLN* 1.3 72.3 + - + +
228B GLU* 6.0 1.3 - - - -
232B LEU* 5.9 1.0 - - - +
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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