Contacts of the helix formed by residues 214 - 226 (chain B) in PDB entry 3G29
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 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B ILE* 4.0 3.8 - - - -
213B THR* 1.3 91.8 - - + +
215B PRO* 1.3 75.2 - - - +
216B GLY* 3.5 4.9 + - - -
217B GLU* 3.1 40.3 + - - +
218B ILE* 3.3 14.9 + - - +
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Residues in contact with PRO 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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172B ILE* 5.3 4.3 - - + -
186B ALA* 3.8 38.4 - - + +
189B ILE* 3.9 29.4 - - + -
190B ILE* 4.0 13.7 - - + -
193B PHE* 3.9 10.4 - - + -
214B THR* 1.3 87.4 - - - +
216B GLY* 1.3 60.6 + - - +
218B ILE* 3.5 2.4 + - + +
219B ILE* 3.0 34.9 + - + +
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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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214B THR* 3.1 6.7 + - - -
215B PRO* 1.3 81.4 - - - +
217B GLU* 1.3 56.4 + - - +
219B ILE* 3.4 9.6 + - - +
220B LYS* 3.1 30.6 + - - +
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Residues in contact with GLU 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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211B THR 4.1 4.5 - - - +
212B LEU* 3.6 29.9 - - + +
213B THR* 2.8 33.5 + - - -
214B THR* 3.1 30.4 + - - +
216B GLY* 1.3 72.2 - - - +
218B ILE* 1.3 62.1 + - - +
220B LYS* 3.5 9.0 + - + +
221B TYR* 2.9 31.5 + - - +
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Residues in contact with ILE 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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164B PHE* 4.7 1.1 - - + -
190B ILE* 4.5 18.4 - - + -
193B PHE* 3.7 27.8 - - + -
194B ARG* 5.3 4.9 - - - +
205B ILE* 3.9 40.8 - - + -
208B ALA* 5.6 4.5 - - + -
212B LEU* 4.0 33.0 - - + +
214B THR 3.3 16.3 + - - +
215B PRO 3.8 5.2 - - - +
217B GLU* 1.3 73.6 - - - +
219B ILE* 1.3 66.1 + - - +
221B TYR* 3.2 7.5 + - + +
222B VAL* 2.9 24.9 + - + +
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Residues in contact with ILE 219 (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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164B PHE* 3.9 19.7 - - + -
165B VAL* 5.3 7.9 - - + -
168B ALA* 4.3 11.9 - - + -
172B ILE* 4.4 14.4 - - + -
193B PHE* 3.9 25.6 - - + -
215B PRO* 3.0 28.4 + - + +
216B GLY* 3.8 8.3 - - - +
218B ILE* 1.3 75.6 - - - +
220B LYS* 1.3 58.4 + - - +
222B VAL* 3.1 4.7 + - - +
223B LEU* 2.9 48.4 + - + +
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Residues in contact with LYS 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 GLY 3.1 17.8 + - - +
217B GLU* 3.8 9.6 - - + +
219B ILE* 1.3 77.0 - - - +
221B TYR* 1.3 60.7 - - - +
223B LEU* 3.5 6.8 + - - +
224B ASP* 3.1 53.1 + - - +
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Residues in contact with TYR 221 (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* 4.0 26.1 - - + +
205B ILE* 5.6 1.3 - - + -
207B THR* 4.6 4.9 + - - -
208B ALA* 3.7 31.7 + - + -
209B PRO* 3.8 17.6 - - + +
212B LEU* 3.8 22.4 - - + -
217B GLU 2.9 19.8 + - - +
218B ILE* 3.5 6.3 - - + +
220B LYS* 1.3 76.8 - - - +
222B VAL* 1.3 69.0 + - + +
224B ASP* 5.1 0.2 - - - -
225B ARG* 2.6 70.6 + - - +
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Residues in contact with VAL 222 (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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164B PHE* 3.7 42.0 - - + -
201B ILE* 4.1 26.2 - - + -
204B LEU* 4.6 12.9 - - + +
205B ILE* 4.1 26.5 - - + -
218B ILE* 2.9 17.6 + - + +
219B ILE 3.7 6.1 - - - +
221B TYR* 1.3 81.9 - - + +
223B LEU* 1.3 63.5 - - + +
225B ARG* 3.2 2.1 + - - +
226B GLN* 3.0 31.9 + - + +
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Residues in contact with LEU 223 (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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164B PHE* 4.5 15.0 - - + +
165B VAL* 4.5 30.7 - - + +
219B ILE* 2.9 35.8 + - + +
220B LYS* 4.1 6.1 - - - +
222B VAL* 1.3 77.6 - - - +
224B ASP* 1.3 64.1 + - - +
225B ARG 3.5 0.5 + - - -
226B GLN* 3.4 32.5 + - - +
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Residues in contact with ASP 224 (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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220B LYS* 3.1 45.6 + - - +
221B TYR* 5.1 0.2 - - - -
222B VAL 3.2 0.4 - - - -
223B LEU* 1.3 82.5 - - - +
225B ARG* 1.3 87.5 + - - +
226B GLN 5.2 0.8 - - - +
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Residues in contact with ARG 225 (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* 4.9 17.6 - - + +
221B TYR* 2.6 85.1 + - - +
222B VAL 3.2 2.6 + - - +
224B ASP* 1.3 111.7 + - + +
226B GLN* 1.3 68.3 + - - +
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Residues in contact with GLN 226 (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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158B GLN* 5.8 0.2 - - - +
163B SER* 5.6 2.8 - - - +
164B PHE* 4.3 18.3 + - - +
201B ILE* 4.3 15.1 - - + +
204B LEU* 4.7 8.3 - - + +
222B VAL* 3.0 32.6 + - + +
223B LEU* 3.4 32.2 - - - +
224B ASP 3.8 0.9 - - - +
225B ARG* 1.3 82.5 - - - +
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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