Contacts of the helix formed by residues 211 - 219 (chain B) in PDB entry 2F37
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 LEU 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A GLY 5.1 1.3 - - - +
168B HIS* 4.1 2.5 - - - -
189B VAL 4.8 1.1 - - - +
190B HIS* 3.5 37.5 - - + +
191B ALA 4.0 0.4 - - - +
192B ARG* 4.0 11.4 - - + +
209B GLY 2.8 12.8 + - - +
210B GLU* 1.3 74.3 - - - +
212B PRO* 1.3 59.0 - - + +
213B LEU* 4.2 6.1 - - + +
214B SER* 3.1 23.1 + - - +
215B LEU* 2.7 35.3 + - - +
240B ALA* 3.6 34.5 - - + +
241B THR 3.5 33.7 - - - +
242B ASP 4.2 0.7 - - - +
246B ASN 5.0 1.3 - - - +
248B VAL 5.7 0.2 - - - +
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Residues in contact with PRO 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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167B LEU* 3.8 20.9 - - + -
168B HIS* 3.5 19.0 - - + +
171B ILE* 3.5 31.3 - - + +
188B ASN 4.3 1.8 - - - +
189B VAL* 3.2 31.6 - - - +
191B ALA 3.1 19.3 - - - +
211B LEU* 1.3 82.9 - - + +
213B LEU* 1.3 62.0 + - - +
215B LEU* 3.3 6.4 + - + +
216B ALA* 3.0 20.1 + - - +
228B LEU* 3.9 5.8 - - + -
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B VAL 4.6 2.0 + - - +
211B LEU* 3.3 6.5 - - + +
212B PRO* 1.3 78.8 - - - +
214B SER* 1.3 59.9 + - - +
216B ALA* 3.2 3.1 + - - +
217B ALA* 2.9 27.4 + - - +
225B VAL* 3.9 43.3 - - + +
228B LEU* 3.8 14.7 - - + +
229B LEU* 3.8 25.6 - - + -
236B ALA* 4.1 17.2 - - + +
237B SER 4.0 20.2 - - - +
238B LEU* 4.1 14.1 - - + -
248B VAL* 4.9 13.2 - - + -
273B LEU* 4.9 2.0 - - + -
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Residues in contact with SER 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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208B PHE 3.0 21.3 - - - -
209B GLY 4.1 9.5 + - - -
211B LEU* 3.1 24.0 + - - +
213B LEU* 1.3 74.5 - - - +
215B LEU* 1.3 60.6 + - - +
217B ALA* 3.3 0.7 + - - +
218B CYS* 2.8 35.5 + - - +
247B THR 4.5 1.0 - - - -
248B VAL* 3.5 39.0 + - - +
251B ALA* 4.4 3.8 - - - -
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Residues in contact with LEU 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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164B HIS* 6.0 0.7 - - + -
168B HIS* 3.4 43.3 - - + +
171B ILE* 3.7 20.2 - - + -
172B GLU* 4.1 10.5 - - + +
206B PHE* 4.4 11.2 - - + -
208B PHE* 3.4 41.3 - - + -
211B LEU 2.7 20.5 + - - +
212B PRO* 3.5 5.4 - - + +
214B SER* 1.3 73.4 - - - +
216B ALA* 1.3 60.0 + - - +
218B CYS 3.3 0.3 + - - -
219B THR* 2.8 49.6 + - + +
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Residues in contact with ALA 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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171B ILE* 3.8 7.6 - - + +
212B PRO 3.0 12.7 + - - +
213B LEU 3.6 6.5 - - - +
215B LEU* 1.3 75.9 - - - +
217B ALA* 1.3 60.0 + - - +
219B THR* 3.4 6.1 + - - -
220B LYS 3.4 4.0 + - - -
221B GLN* 3.0 29.1 + - - +
224B VAL* 3.6 34.1 - - + -
225B VAL* 3.7 16.6 - - + +
228B LEU* 4.2 4.3 - - + -
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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 LEU 2.9 12.1 + - - +
214B SER 3.7 0.9 - - - +
216B ALA* 1.3 78.3 - - - +
218B CYS* 1.3 60.0 + - - +
219B THR 3.4 0.5 + - - -
220B LYS* 3.4 20.4 + - - -
225B VAL* 3.5 11.2 - - + +
248B VAL* 3.4 32.5 - - + -
252B LEU* 3.9 5.9 - - + +
269B MSE 3.5 33.2 - - + +
273B LEU* 4.1 4.7 - - + -
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Residues in contact with CYS 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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207B TYR 5.3 0.2 - - - +
208B PHE* 3.9 18.2 - - + -
214B SER* 2.8 22.7 + - - +
215B LEU 3.3 3.1 + - - +
217B ALA* 1.3 77.5 - - - +
219B THR* 1.3 61.2 + - + +
220B LYS* 3.4 17.3 + - - -
248B VAL 5.2 0.2 - - - -
251B ALA* 3.9 29.6 - - - -
252B LEU* 4.2 11.4 - - - -
255B ILE* 3.9 39.2 - - + +
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Residues in contact with THR 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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172B GLU* 5.9 4.9 - - + -
174B ARG* 2.8 38.6 + - - -
206B PHE* 5.3 8.5 - - + -
208B PHE* 5.9 0.2 - - + -
215B LEU* 2.8 39.4 + - + +
216B ALA 3.5 2.4 + - - -
217B ALA 3.2 0.2 - - - -
218B CYS* 1.3 81.6 - - + +
220B LYS* 1.3 69.0 + - - +
221B GLN* 2.9 25.4 + - - +
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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