Contacts of the helix formed by residues 212 - 222 (chain B) in PDB entry 2VF8
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 PRO 212 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210B GLU 4.3 2.7 - - - +
211B LEU* 1.4 94.9 - - + +
213B GLU* 1.3 67.9 + - - +
214B GLU* 3.1 13.7 + - + +
215B THR* 3.2 17.3 + - - +
216B ARG* 3.2 12.4 + - - +
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Residues in contact with GLU 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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211B LEU 3.5 2.4 + - - -
212B PRO* 1.3 69.8 - - - +
214B GLU* 1.3 61.7 + - + +
216B ARG* 3.5 29.2 + - - +
217B HIS* 2.7 58.8 + - - +
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Residues in contact with GLU 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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212B PRO* 3.1 12.0 + - + +
213B GLU* 1.3 83.4 + - + +
215B THR* 1.3 60.4 + - - +
217B HIS* 3.5 7.8 + - - +
218B TRP* 2.9 33.2 + - - +
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Residues in contact with THR 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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202B ILE* 3.6 31.2 - - + -
211B LEU* 3.9 20.4 - - + -
212B PRO* 3.2 12.5 + - - +
214B GLU* 1.3 78.3 - - - +
216B ARG* 1.3 58.8 + - - +
218B TRP* 4.1 10.1 - - + +
219B ILE* 3.2 37.5 + - + +
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Residues in contact with ARG 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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165B GLU* 4.5 16.4 + - - -
208B TRP* 3.2 72.6 + - + +
209B ARG* 4.2 15.2 + - - +
211B LEU* 2.9 39.2 + - + +
212B PRO* 3.2 16.5 + - - +
213B GLU* 3.7 30.6 + - - +
215B THR* 1.3 75.0 - - - +
217B HIS* 1.3 64.4 + - - +
219B ILE* 4.7 4.7 - - + -
220B LEU* 3.5 5.8 + - - +
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Residues in contact with HIS 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 GLU* 2.7 44.1 + - - +
214B GLU* 3.5 7.0 + - - +
216B ARG* 1.3 70.3 - - - +
218B TRP* 1.3 63.6 + - - +
220B LEU* 2.7 29.5 + - - +
221B PHE* 3.0 49.0 + + + +
222B THR* 6.5 0.2 - - - -
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Residues in contact with TRP 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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197B LEU* 4.5 8.3 - - + -
200B LEU* 4.8 13.2 - - + -
202B ILE* 5.8 4.3 - - + -
214B GLU 2.9 21.0 + - - +
215B THR* 4.1 11.9 - - + +
217B HIS* 1.3 78.4 + - - +
219B ILE* 1.3 98.9 + - + +
222B THR* 2.7 61.4 + - + +
224B GLU* 2.6 28.9 + - - -
226B PRO* 4.1 23.1 - - + -
255B PHE* 4.0 23.6 - + - -
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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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176B ILE* 5.8 3.1 - - + -
181B VAL* 6.1 2.5 - - + -
184B TRP* 4.0 24.0 - - + -
197B LEU* 3.7 25.1 - - + -
202B ILE* 4.2 17.5 - - + -
208B TRP* 5.2 13.9 - - + -
211B LEU* 5.6 2.0 - - + -
215B THR* 3.2 23.1 + - + +
216B ARG* 4.8 6.7 - - + +
217B HIS 3.3 0.4 - - - -
218B TRP* 1.3 102.0 - - + +
220B LEU* 1.3 61.1 + - + +
221B PHE 3.2 3.5 + - - -
255B PHE* 4.0 16.4 - - + -
257B SER* 3.4 8.8 - - - -
258B ALA* 3.3 19.4 + - + +
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Residues in contact with LEU 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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165B GLU* 3.7 27.6 - - + +
168B MET* 3.9 22.1 - - + +
169B VAL* 3.8 15.7 - - + -
181B VAL* 4.5 9.6 - - + -
208B TRP* 3.5 34.8 - - + -
216B ARG 3.5 10.3 - - - +
217B HIS* 2.7 15.3 + - - +
219B ILE* 1.3 75.7 - - + +
221B PHE* 1.3 86.2 + - + -
258B ALA* 4.1 13.2 - - + -
259B ARG 3.5 18.2 + - - -
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Residues in contact with PHE 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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163B VAL* 3.3 37.7 - - + -
164B THR* 4.3 1.3 - - - -
165B GLU* 3.8 23.8 - - + -
168B MET* 4.8 1.1 - - - -
217B HIS* 3.0 47.0 + + + +
219B ILE 3.2 0.4 + - - -
220B LEU* 1.3 107.9 - - + +
222B THR* 1.3 64.8 + - - +
257B SER* 4.1 2.5 - - - -
259B ARG* 2.9 50.7 + - + +
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Residues in contact with THR 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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217B HIS* 6.5 0.2 - - - -
218B TRP* 2.7 66.1 + - + +
221B PHE* 1.3 73.0 - - - +
223B ASP* 1.3 61.4 + - - +
224B GLU* 3.2 35.3 + - + +
255B PHE* 4.3 7.4 - - + -
257B SER* 2.2 45.7 + - - -
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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