Contacts of the helix formed by residues 217 - 229 (chain B) in PDB entry 2VLH
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 ARG 217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B THR* 5.5 0.2 + - - -
50B ASP* 2.8 39.9 + - - -
182B VAL 3.0 9.8 + - - -
183B THR* 3.5 24.5 + - - +
185B ASN* 3.4 25.1 - - - +
216B THR* 1.3 85.1 - - + +
218B CYS* 1.3 55.9 + - - +
219B VAL 3.2 0.2 + - - -
220B GLU* 3.4 26.5 + - - +
221B ASN 3.0 22.9 + - - -
257B LYS* 3.6 15.1 - - - +
258B ASP* 3.0 13.9 - - - +
343B HIS* 3.3 27.8 - - - -
404B ARG* 5.8 2.0 - - - +
406B THR* 5.3 0.4 - - - +
409B ARG* 3.9 10.5 - - - +
1257B PLP 2.9 32.2 + - - +
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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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88B PHE* 3.8 29.2 - - - -
182B VAL* 3.3 20.6 + - + -
215B ALA 2.9 20.4 + - - +
216B THR 3.5 0.2 - - - -
217B ARG* 1.3 76.8 - - - +
219B VAL* 1.3 72.6 + - - +
221B ASN* 3.4 4.8 - - - +
222B ALA* 3.0 25.3 + - - +
241B VAL* 4.5 3.7 - - + +
244B MET* 3.6 10.1 - - + +
245B PHE* 3.7 23.1 - - + -
253B MET* 4.1 6.5 - - - -
258B ASP* 3.5 0.2 + - - -
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Residues in contact with VAL 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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218B CYS* 1.3 86.6 - - - +
220B GLU* 1.3 63.8 + - - +
221B ASN 3.1 1.3 - - - -
222B ALA* 3.1 5.6 + - - +
223B TYR 2.9 18.7 + - - -
237B ILE* 4.0 15.5 - - + -
241B VAL* 4.7 2.2 - - + -
258B ASP* 2.8 30.0 + - + +
306B LEU* 4.7 4.9 - - + -
309B ALA* 3.3 35.7 - - + +
310B MET* 3.7 21.8 - - + -
315B ILE* 3.7 20.1 - - + +
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Residues in contact with GLU 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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183B THR* 4.4 4.8 + - + -
217B ARG* 3.4 27.6 - - + +
219B VAL* 1.3 73.5 - - - +
221B ASN* 1.3 62.6 + - - +
223B TYR* 3.1 11.4 + - - +
224B PHE* 3.2 20.7 + - - -
258B ASP* 2.9 19.4 + - - +
315B ILE* 3.8 15.8 - - + +
318B ARG* 2.7 35.6 + - - +
319B VAL* 4.3 8.5 - - + +
342B GLY* 3.3 28.5 - - - +
343B HIS* 3.4 2.2 + - - +
409B ARG* 2.9 22.7 + - - -
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Residues in contact with ASN 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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182B VAL* 3.6 25.9 - - + +
183B THR* 3.7 11.9 - - + +
191B PRO* 3.2 9.2 - - - +
192B VAL 2.8 46.5 + - - -
197B MET* 3.6 9.3 - - - +
217B ARG 3.0 14.2 + - - +
218B CYS 3.4 9.6 - - - +
219B VAL 3.1 0.2 - - - -
220B GLU* 1.3 77.6 - - - +
222B ALA* 1.3 61.0 + - - +
224B PHE* 3.2 15.9 + - - +
225B ILE* 3.2 21.4 + - - +
244B MET* 3.8 2.6 - - + +
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Residues in contact with ALA 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 CYS 3.0 15.3 + - - +
219B VAL* 3.1 8.3 + - - +
221B ASN* 1.3 76.1 - - - +
223B TYR* 1.3 63.4 + - - +
225B ILE* 3.4 3.5 + - - +
226B LYS* 3.0 23.0 + - - +
237B ILE* 4.2 9.6 - - + -
240B ILE* 3.6 30.5 - - + +
241B VAL* 3.7 22.7 - - + -
244B MET* 4.0 5.2 - - - -
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Residues in contact with TYR 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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219B VAL 2.9 6.9 + - - -
220B GLU 3.1 7.8 + - - +
222B ALA* 1.3 77.2 - - - +
224B PHE* 1.3 62.0 + + - +
226B LYS* 3.1 4.7 + - + +
227B GLU* 2.8 70.9 + - + +
237B ILE* 3.9 8.5 - - + +
312B TYR* 3.7 26.3 + + - -
315B ILE* 3.8 30.1 - - + -
316B GLU* 3.6 34.4 - - + +
319B VAL* 3.8 33.7 - - + -
320B LYS* 3.2 19.3 + - + -
323B ARG* 4.2 1.3 - - - -
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Residues in contact with PHE 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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154B PHE* 3.7 4.7 - - + -
183B THR* 4.8 2.2 - - + -
189B GLY 4.5 1.3 - - - -
191B PRO* 3.5 49.4 - - + -
220B GLU 3.2 28.1 + - - -
221B ASN* 3.2 3.6 + - - +
223B TYR* 1.3 79.7 - + - +
225B ILE* 1.3 57.5 + - - +
227B GLU* 3.7 4.7 - - - +
228B GLN* 2.8 55.7 + - - +
319B VAL* 3.9 19.5 - - + -
323B ARG* 4.0 18.4 - - - -
340B VAL 4.2 11.7 - - - -
341B GLY* 3.9 7.0 - - - -
342B GLY* 3.8 32.5 - - - -
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Residues in contact with ILE 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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154B PHE* 3.8 11.2 - - + -
192B VAL 3.6 15.7 - - - +
194B MET* 3.8 8.7 - - + +
197B MET* 3.7 14.4 - - + -
221B ASN* 3.2 28.5 + - - +
222B ALA 3.7 5.8 - - - +
224B PHE* 1.3 75.7 - - - +
226B LYS* 1.3 64.6 + - - +
229B GLU* 2.9 47.6 + - - +
232B PHE* 3.5 33.8 - - + +
240B ILE* 4.0 12.1 - - + -
244B MET* 4.0 15.9 - - + -
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Residues in contact with LYS 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 ALA 3.0 14.1 + - - +
223B TYR* 3.3 11.7 - - + +
225B ILE* 1.3 79.9 - - - +
227B GLU* 1.3 63.6 + - - +
229B GLU 4.8 1.7 + - - +
232B PHE 3.6 19.8 - - - +
233B GLU* 3.1 28.4 + - - +
234B ASN 4.8 0.4 - - - -
235B LYS 2.9 29.1 + - - +
236B SER* 5.1 2.2 - - - +
237B ILE* 4.0 9.6 - - + -
240B ILE* 3.6 13.9 - - + +
312B TYR* 3.7 40.8 - - + +
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Residues in contact with GLU 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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223B TYR* 2.8 50.6 + - + +
224B PHE* 3.8 4.3 - - - +
226B LYS* 1.3 77.6 - - - +
228B GLN* 1.3 81.0 + - + +
320B LYS* 3.7 4.5 + - - -
323B ARG* 2.7 44.6 + - - -
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Residues in contact with GLN 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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153B ALA* 3.6 25.9 - - + +
154B PHE* 4.1 16.3 + - + -
191B PRO* 6.0 1.0 - - - +
224B PHE* 2.8 40.3 + - - +
227B GLU* 1.3 105.3 + - + +
229B GLU* 1.3 60.9 + - - +
230B GLN* 3.6 5.4 + - - +
323B ARG* 4.1 5.3 - - - +
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Residues in contact with GLU 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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154B PHE* 3.9 14.3 - - + -
193B SER* 3.5 13.7 - - - -
194B MET* 2.7 24.4 + - - +
195B ALA* 2.9 34.7 + - - +
224B PHE 4.0 0.2 + - - -
225B ILE* 2.9 32.1 + - + +
226B LYS 4.9 1.7 - - - +
227B GLU 3.9 0.2 - - - -
228B GLN* 1.3 77.2 - - - +
230B GLN* 1.3 70.3 + - + +
231B GLY 3.3 0.2 + - - -
232B PHE* 3.1 37.2 + - + +
233B GLU* 4.4 1.7 + - - +
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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