Contacts of the helix formed by residues 193 - 210 (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 SER 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B ALA* 3.4 5.7 - - - +
190B THR* 2.7 37.3 + - - +
191B VAL 3.8 0.4 - - - +
192B SER* 1.4 76.8 + - - +
194B GLU* 1.3 59.3 + - - +
195B TRP* 3.5 5.2 - - - +
196B ALA* 3.5 19.0 - - - +
197B TRP* 3.3 31.4 + - - -
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Residues in contact with GLU 194 (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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14A OIC 5.6 3.8 - - + +
185B TYR* 3.3 48.3 + - + +
186B SER* 3.4 13.5 + - - -
189B ALA* 4.0 8.9 - - - +
190B THR 4.1 7.0 - - - +
191B VAL* 4.0 15.2 + - - +
192B SER 2.8 11.7 + - - +
193B SER* 1.3 72.8 - - - +
195B TRP* 1.4 63.1 + - + +
197B TRP* 3.7 1.9 + - - +
198B GLU* 3.6 17.7 + - - +
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Residues in contact with TRP 195 (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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192B SER* 3.2 30.6 + - - -
193B SER* 4.7 0.9 - - - +
194B GLU* 1.4 76.5 - - + +
196B ALA* 1.4 78.3 + - + +
198B GLU* 3.2 7.6 + - - +
199B VAL* 2.8 52.9 + - + +
276B LEU* 3.8 28.5 - - + -
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Residues in contact with ALA 196 (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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193B SER* 3.5 26.7 - - - +
194B GLU 3.3 0.2 - - - -
195B TRP* 1.4 95.5 - - + +
197B TRP* 1.3 59.0 + - + +
199B VAL* 3.5 11.6 - - - +
200B GLY* 2.9 25.5 + - - -
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Residues in contact with TRP 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LEU* 5.9 0.4 - - + -
185B TYR* 3.6 22.8 - - + -
188B VAL* 4.0 38.9 + - + -
189B ALA* 3.5 22.0 - - + +
193B SER* 3.3 31.0 + - - +
194B GLU 3.7 1.1 + - - +
195B TRP 3.3 0.4 - - - -
196B ALA* 1.3 78.5 - - + +
198B GLU* 1.3 60.7 + - - +
200B GLY* 4.4 1.6 - - - +
201B LEU* 3.1 63.1 + - + +
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Residues in contact with GLU 198 (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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14A OIC 3.6 38.3 - - + +
183B MET* 4.6 5.0 - - - +
185B TYR* 2.7 41.9 + - + -
194B GLU 3.6 8.0 + - - +
195B TRP* 3.2 11.7 + - - +
197B TRP* 1.3 77.4 - - - +
199B VAL* 1.4 56.9 + - - +
202B GLY* 3.0 31.0 + - - -
268B LYS* 4.6 11.1 - - - -
272B MET* 3.4 27.4 - - + +
1102B OLC 4.7 6.8 + - - -
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B TRP* 2.8 36.3 + - + +
196B ALA* 3.5 14.1 - - - +
198B GLU* 1.4 75.2 - - - +
200B GLY* 1.3 62.4 + - - +
203B VAL* 3.2 45.7 + - + +
272B MET* 3.9 24.6 - - + -
273B LEU* 6.1 0.7 - - + -
276B LEU* 3.8 26.5 - - + -
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Residues in contact with GLY 200 (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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196B ALA 2.9 19.4 + - - -
197B TRP* 4.1 1.3 - - - -
198B GLU 3.3 0.2 - - - -
199B VAL* 1.3 77.4 - - - +
201B LEU* 1.3 60.1 + - - +
203B VAL* 4.4 1.5 - - - +
204B SER* 3.0 26.7 + - - -
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Residues in contact with LEU 201 (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 PRO* 4.4 14.1 - - + -
167B LEU* 3.8 17.9 - - + -
183B MET* 4.5 5.4 - - + -
185B TYR* 3.7 24.0 - - + +
197B TRP* 3.1 45.0 + - + +
200B GLY* 1.3 72.6 - - - +
202B GLY* 1.3 59.3 - - - +
204B SER* 3.2 14.0 + - - +
205B SER* 3.2 19.8 + - - -
1102B OLC 3.2 47.3 - - + +
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Residues in contact with GLY 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B GLU* 3.0 26.1 + - - -
199B VAL* 5.0 0.2 - - - -
201B LEU* 1.3 75.6 - - - +
203B VAL* 1.4 62.8 + - - +
205B SER* 3.5 3.8 + - - -
206B THR* 3.3 25.1 + - - -
268B LYS* 5.8 5.4 - - - +
272B MET* 5.5 7.2 - - - -
1102B OLC 3.4 13.8 + - - -
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Residues in contact with VAL 203 (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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199B VAL* 3.2 35.2 + - + +
200B GLY* 4.5 1.3 - - - +
202B GLY* 1.4 71.2 - - - +
204B SER* 1.4 58.2 + - - +
206B THR* 3.2 8.3 + - - -
207B THR* 2.7 43.7 + - - +
269B THR* 5.9 5.2 - - + -
272B MET* 5.1 10.5 - - + -
273B LEU* 5.4 9.0 - - + -
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Residues in contact with SER 204 (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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200B GLY 3.0 18.5 + - - -
201B LEU* 3.2 16.3 + - - +
203B VAL* 1.4 78.4 - - - +
205B SER* 1.4 54.5 + - - +
207B THR* 3.8 7.1 - - - -
208B VAL* 2.9 37.2 + - - +
1102B OLC 3.7 20.9 - - - +
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Residues in contact with SER 205 (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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110B PHE* 3.5 14.2 - - - -
113B MET* 3.4 20.3 - - - +
114B TYR* 3.0 26.2 + - - -
201B LEU 3.2 20.9 + - - -
202B GLY 3.5 7.2 - - - -
203B VAL 3.2 0.4 - - - -
204B SER* 1.4 77.0 + - - +
206B THR* 1.3 56.7 + - - +
208B VAL* 4.6 0.2 - - - -
209B GLY* 3.0 27.4 + - - -
265B HIS* 5.1 0.2 - - - -
1102B OLC 3.7 13.0 - - - -
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Residues in contact with THR 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLY 3.3 10.5 + - - -
203B VAL* 3.2 11.3 + - - -
205B SER* 1.3 75.0 - - - +
207B THR* 1.3 59.8 + - - +
210B PHE* 2.9 11.2 + - + -
211B VAL* 2.9 36.9 + - + -
265B HIS* 3.3 44.1 + - + +
268B LYS* 5.5 7.8 - - - +
269B THR* 4.0 19.4 + - + +
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Residues in contact with THR 207 (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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203B VAL* 2.7 33.3 + - - +
204B SER* 3.8 7.6 - - - -
205B SER 3.4 0.2 - - - -
206B THR* 1.3 77.3 - - - +
208B VAL* 1.3 61.7 + - + +
211B VAL* 3.4 18.1 + - + +
212B VAL* 2.8 49.1 + - + +
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Residues in contact with VAL 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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114B TYR* 3.7 20.2 - - + +
118B PHE* 3.3 32.4 - - + -
156B LEU* 5.9 1.8 - - + -
160B LEU* 3.9 39.9 - - + -
204B SER* 2.9 23.8 + - - +
207B THR* 1.3 73.1 - - + +
209B GLY* 1.3 57.6 + - - +
210B PHE 3.7 0.2 - - - -
212B VAL* 4.7 8.7 - - + +
213B PRO* 3.4 8.1 - - - +
1102B OLC 5.0 1.6 - - + -
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Residues in contact with GLY 209 (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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113B MET* 4.1 12.6 - - - +
114B TYR* 3.7 18.6 - - - -
117B ALA* 3.5 20.7 - - - +
205B SER 3.0 19.6 + - - -
206B THR 3.9 0.2 - - - -
208B VAL* 1.3 79.2 - - - +
210B PHE* 1.4 59.6 + - - +
213B PRO* 3.8 6.7 - - - -
257B PHE* 4.5 5.0 - - - -
261B LYS* 6.1 0.2 - - - +
265B HIS* 4.7 3.3 + - - -
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Residues in contact with PHE 210 (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 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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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