Contacts of the helix formed by residues 210 - 229 (chain B) in PDB entry 5VBL
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 PHE 210 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B THR* 2.9 11.7 + - + +
209B GLY* 1.4 79.1 - - - +
211B VAL* 1.4 68.2 + - + +
213B PRO* 3.5 6.5 - - - +
214B PHE* 3.0 56.7 + + + +
257B PHE* 4.0 23.7 - + - -
258B ALA* 4.5 11.7 - - - -
261B LYS* 3.7 30.1 - - + -
262B MET* 3.7 44.4 - - + -
265B HIS* 3.7 32.3 - + + +
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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
----------------------------------------------------------
206B THR* 2.9 34.9 + - + +
207B THR* 3.8 20.2 - - + +
210B PHE* 1.4 78.4 - - + +
212B VAL* 1.4 63.2 + - + +
214B PHE* 4.0 1.8 - - - +
215B THR* 2.9 40.3 + - + +
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B THR* 2.8 42.1 + - + +
208B VAL* 4.7 8.7 - - + +
211B VAL* 1.4 72.1 - - + +
213B PRO* 1.4 64.9 - - + +
215B THR* 2.7 21.1 + - - +
216B ILE* 3.2 30.6 + - + +
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Residues in contact with PRO 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ALA* 4.0 15.5 - - + +
118B PHE* 4.2 9.4 - - + -
121B THR* 3.3 31.0 - - + +
207B THR 3.5 8.3 - - - +
208B VAL 3.4 20.0 - - - +
209B GLY 3.8 10.5 - - - +
210B PHE* 3.5 16.6 - - - +
212B VAL* 1.4 90.3 - - + +
214B PHE* 1.4 56.0 + - - +
216B ILE* 3.2 5.5 + - + -
217B MET* 3.1 35.6 + - + +
257B PHE* 5.7 0.4 - - + -
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Residues in contact with PHE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B PHE* 3.0 45.0 + + + +
211B VAL* 4.1 2.0 - - - +
213B PRO* 1.4 75.2 - - - +
215B THR* 1.4 59.1 + - + +
217B MET* 3.5 11.9 + - + +
218B LEU* 3.1 61.3 + - + +
254B VAL* 4.0 24.5 - - + -
257B PHE* 5.3 5.2 - + + -
258B ALA* 3.8 31.6 - - + -
262B MET* 5.7 4.7 - - - -
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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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211B VAL* 2.9 26.0 + - + +
212B VAL* 2.7 25.3 + - - +
214B PHE* 1.4 74.7 - - + +
216B ILE* 1.4 60.2 + - - +
218B LEU* 3.6 11.1 + - + +
219B THR* 2.9 36.1 + - - +
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Residues in contact with ILE 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B THR* 4.3 20.9 - - + +
125B PHE* 5.3 7.0 - - + -
212B VAL* 3.2 36.3 + - + +
213B PRO* 3.2 9.6 + - + +
215B THR* 1.4 76.0 - - - +
217B MET* 1.4 57.7 + - - +
219B THR* 3.0 9.3 + - - +
220B CYS* 2.9 44.0 + - - -
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Residues in contact with MET 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ALA 3.6 23.1 - - - +
120B LEU* 3.8 16.6 - - + -
121B THR* 3.8 11.2 - - + -
124B SER* 3.7 26.9 + - - +
213B PRO* 3.1 32.7 + - + +
214B PHE* 3.6 14.1 - - + +
215B THR 3.4 0.2 - - - -
216B ILE* 1.4 75.3 - - - +
218B LEU* 1.4 55.7 + - - +
220B CYS* 3.6 2.9 + - - +
221B TYR* 3.1 27.7 + - - +
254B VAL* 3.8 40.2 - - + -
257B PHE* 4.1 18.6 - - + -
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Residues in contact with LEU 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 PHE* 3.1 60.5 + - + +
215B THR* 3.9 11.9 - - + +
217B MET* 1.4 73.7 - - - +
219B THR* 1.4 60.7 + - + +
221B TYR* 3.3 13.0 + - + +
222B PHE* 3.0 27.2 + - - +
254B VAL* 6.4 0.2 - - + -
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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
----------------------------------------------------------
215B THR* 2.9 24.3 + - - +
216B ILE* 3.0 16.6 + - - +
218B LEU* 1.4 72.0 - - + +
220B CYS* 1.4 64.2 + - - +
222B PHE* 3.2 9.3 + - + +
223B PHE* 3.1 42.3 + - + -
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Residues in contact with CYS 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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124B SER* 3.9 18.8 - - - +
125B PHE* 3.8 42.6 - - - -
128B TYR* 4.0 16.3 - - + -
216B ILE* 2.9 33.4 + - - +
217B MET 3.7 5.2 - - - +
218B LEU 3.3 0.2 - - - -
219B THR* 1.4 76.2 + - - +
221B TYR* 1.4 56.4 + - - +
223B PHE* 3.4 4.9 + - - +
224B ILE* 3.1 35.1 + - + +
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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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217B MET 3.1 17.9 + - - +
218B LEU* 3.6 13.9 - - + +
219B THR 3.3 0.2 - - - -
220B CYS* 1.4 74.4 - - - +
222B PHE* 1.4 59.8 + - - +
224B ILE* 3.4 9.1 + - + +
225B ALA* 2.9 40.9 + - + +
247B LEU* 4.6 21.8 - - + -
251B VAL* 3.8 33.1 - - + +
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Residues in contact with PHE 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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218B LEU 3.0 13.2 + - - +
219B THR* 3.2 13.4 + - + +
221B TYR* 1.4 78.7 - - - +
223B PHE* 1.4 73.8 + + - +
225B ALA* 3.6 7.0 + - + +
226B GLN* 3.1 44.8 + - + +
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Residues in contact with PHE 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B TYR* 3.7 37.5 - + + -
132B VAL* 3.4 16.8 - - + +
219B THR* 3.1 35.4 + - + -
220B CYS* 3.9 1.3 - - - +
222B PHE* 1.4 86.6 - + - +
224B ILE* 1.4 65.4 + - - +
226B GLN* 3.4 25.0 + - - +
227B THR* 3.3 18.9 + - - +
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Residues in contact with ILE 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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124B SER* 3.9 5.4 - - - +
127B ARG* 3.6 21.3 - - + +
128B TYR* 3.5 35.9 - - - +
131B ILE* 3.8 15.0 - - + -
132B VAL* 3.8 10.1 - - + -
220B CYS* 3.1 28.0 + - + +
221B TYR* 3.7 12.1 - - + +
222B PHE 3.4 0.2 - - - -
223B PHE* 1.4 74.6 - - - +
225B ALA* 1.4 61.0 + - - +
227B THR* 2.9 18.5 + - - -
228B ILE* 3.1 31.9 + - + +
247B LEU* 3.8 18.8 - - + -
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Residues in contact with ALA 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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221B TYR* 2.9 34.1 + - + +
222B PHE* 3.7 9.0 - - + +
224B ILE* 1.4 77.2 - - - +
226B GLN* 1.4 55.1 + - - +
228B ILE* 3.9 8.3 - - - +
229B ALA* 3.0 32.3 + - - +
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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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222B PHE* 3.1 29.2 + - + +
223B PHE* 3.4 34.1 - - - +
224B ILE 3.3 0.2 - - - -
225B ALA* 1.4 77.6 - - - +
227B THR* 1.4 61.6 + - + +
229B ALA* 3.8 13.4 - - - +
1001B MET* 4.2 12.0 - - - +
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Residues in contact with THR 227 (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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131B ILE* 3.4 21.4 - - - +
132B VAL* 3.9 32.4 - - + +
223B PHE 3.3 11.6 + - - +
224B ILE* 2.9 16.1 + - - -
226B GLN* 1.4 78.1 - - + +
228B ILE* 1.4 62.8 + - - +
229B ALA 3.3 0.4 - - - -
244B ARG* 6.1 0.2 - - - -
1001B MET* 3.5 39.3 + - + +
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Residues in contact with ILE 228 (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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131B ILE* 4.0 7.6 - - + -
224B ILE* 3.1 38.5 + - + +
225B ALA* 4.0 6.7 - - - +
227B THR* 1.4 73.0 - - - +
229B ALA* 1.4 65.4 + - - +
244B ARG* 3.6 48.5 - - - +
247B LEU* 3.8 10.3 - - + -
1001B MET 3.2 4.7 + - - +
1002B LYS* 3.5 40.1 - - - +
1054B GLU* 6.0 0.2 - - + -
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Residues in contact with ALA 229 (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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225B ALA 3.0 17.9 + - - +
226B GLN* 3.8 12.1 - - - +
227B THR 3.3 0.2 - - - -
228B ILE* 1.4 76.5 - - - +
1001B MET* 1.4 57.7 + - + +
1002B LYS* 3.0 15.2 + - - +
1029B ASP* 4.0 10.0 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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