Contacts of the helix formed by residues 224 - 237 (chain B) in PDB entry 2VUU
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 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B PRO 2.7 16.7 + - - -
184B ASP* 3.1 24.2 - - - -
185B ILE 3.0 22.7 - - - -
186B PRO* 3.7 2.4 - - - +
223B LEU 1.3 68.6 - - - -
225B PRO* 1.3 64.7 - - - +
226B VAL* 3.4 4.7 + - - +
227B GLN* 2.4 52.4 + - - +
228B VAL* 2.9 9.6 + - - +
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Residues in contact with PRO 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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177B TRP* 3.5 22.0 - - + -
181B PHE* 3.8 20.2 - - + -
182B ASP 2.9 28.0 - - - +
183B PRO* 3.4 4.5 - - + +
185B ILE 3.1 7.9 - - - +
187B LEU* 4.3 7.6 - - + -
223B LEU 4.0 2.4 - - - +
224B SER* 1.3 81.5 - - - +
226B VAL* 1.3 62.7 + - - +
228B VAL* 3.1 7.0 + - + +
229B CYS* 3.0 26.3 + - - -
242B TYR* 3.3 33.4 - - + -
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Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B PRO* 3.0 39.0 + - + +
184B ASP* 3.7 11.2 - - - +
224B SER* 2.9 4.9 + - - +
225B PRO* 1.3 73.6 - - - +
227B GLN* 1.3 59.5 + - + +
229B CYS* 3.3 5.2 + - + +
230B ALA* 2.8 27.6 + - + +
242B TYR* 4.4 13.7 - - + +
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Residues in contact with GLN 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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186B PRO* 4.8 4.7 - - - +
222B THR 4.0 2.6 + - - +
223B LEU* 2.9 30.4 - - + +
224B SER* 2.4 51.3 + - - +
226B VAL* 1.3 70.7 - - + +
228B VAL* 1.3 66.4 + - - +
230B ALA* 2.9 10.6 + - - +
231B ALA* 2.8 24.1 + - - +
234B ARG* 4.8 4.1 + - - +
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Residues in contact with VAL 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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157B PHE* 3.7 33.7 - - + -
167B MET* 5.2 1.1 - - + -
177B TRP* 4.3 5.6 - - + -
189B TRP* 3.5 38.6 - - + +
223B LEU* 3.7 19.7 - - + +
224B SER 2.9 13.2 + - - +
225B PRO* 3.5 9.0 - - + +
227B GLN* 1.3 75.5 - - - +
229B CYS* 1.3 57.5 + - - +
231B ALA* 3.1 9.8 - - - +
232B PHE* 3.0 38.3 + - + -
331B MET* 4.0 6.3 - - + -
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Residues in contact with CYS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B MET* 4.5 3.6 - - - -
177B TRP* 3.9 20.2 - - - -
225B PRO 3.0 17.7 + - - -
226B VAL* 3.5 9.2 - - + +
228B VAL* 1.3 73.8 - - - +
230B ALA* 1.3 60.5 + - - +
231B ALA 3.0 2.2 - - - -
232B PHE 4.5 0.2 - - - +
233B SER* 2.8 31.6 + - - -
240B VAL* 3.2 37.6 - - + +
241B THR 3.9 2.0 - - - -
242B TYR* 3.5 34.1 - - - +
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Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B VAL* 2.8 17.7 + - + +
227B GLN* 2.9 14.3 + - - +
229B CYS* 1.3 76.2 - - - +
231B ALA* 1.3 56.3 + - - +
233B SER* 3.2 8.6 - - - -
234B ARG* 3.0 46.9 + - - +
240B VAL 5.4 0.7 - - - -
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Residues in contact with ALA 231 (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 LEU* 5.2 2.2 - - + -
227B GLN 2.8 10.7 + - - +
228B VAL* 3.1 11.7 - - - +
230B ALA* 1.3 73.9 - - - +
232B PHE* 1.3 68.2 + - - +
233B SER 2.9 0.9 - - - -
234B ARG* 2.7 30.1 + - - +
235B ALA* 3.1 11.6 + - - +
331B MET* 3.9 27.1 - - + -
332B GLU* 4.3 14.3 - - + +
335B ALA* 4.7 2.7 - - - -
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Residues in contact with PHE 232 (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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157B PHE* 3.6 34.1 - + + -
167B MET* 3.3 35.7 - - + -
228B VAL* 3.0 27.0 + - + +
229B CYS 4.1 0.7 - - - +
231B ALA* 1.3 77.9 - - - +
233B SER* 1.3 61.7 + - - +
236B LEU* 3.0 44.2 + - + +
240B VAL* 3.9 8.3 - - + -
331B MET* 3.8 25.1 - - + -
334B TYR* 4.0 13.0 - + - -
335B ALA* 3.7 22.2 - - + +
339B PHE* 3.6 34.1 - + + -
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Residues in contact with SER 233 (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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234A ARG* 5.3 11.6 + - - +
229B CYS 2.8 21.2 + - - -
230B ALA* 3.2 11.9 - - - -
232B PHE* 1.3 78.5 - - - +
234B ARG* 1.3 57.2 + - - +
237B ASN* 3.1 25.6 + - - -
238B ARG 2.6 27.6 + - - +
239B ARG* 4.4 0.9 - - - -
240B VAL* 3.5 23.7 + - - +
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Residues in contact with ARG 234 (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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233A SER 5.4 2.2 - - - +
234A ARG* 4.7 12.6 - - + +
237A ASN* 3.0 50.4 + - - +
336A ARG* 5.9 0.7 + - - -
227B GLN* 4.8 4.0 + - - +
230B ALA* 3.0 36.3 + - - +
231B ALA* 2.7 22.2 + - - +
233B SER* 1.3 72.6 - - - +
235B ALA* 1.3 60.1 + - - +
236B LEU 3.5 0.2 + - - -
237B ASN* 3.8 14.4 + - - +
332B GLU* 3.2 34.8 + - - +
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Residues in contact with ALA 235 (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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231B ALA 3.1 7.0 + - - +
232B PHE 4.1 0.7 - - - +
234B ARG* 1.3 78.2 - - - +
236B LEU* 1.3 62.8 + - - +
237B ASN* 3.5 5.8 + - - -
332B GLU* 3.6 14.3 - - + +
335B ALA* 3.9 12.8 - - + -
336B ARG* 3.2 56.0 - - + +
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Residues in contact with LEU 236 (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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175B PHE* 4.0 28.0 - - + -
232B PHE* 3.0 43.9 + - + +
235B ALA* 1.3 83.5 - - + +
237B ASN* 1.3 63.0 + - - +
238B ARG* 2.9 40.3 + - + +
240B VAL* 4.8 2.2 - - + -
335B ALA 3.8 21.8 - - - +
336B ARG* 5.1 0.9 - - - -
339B PHE* 4.4 8.5 - - + -
340B PRO* 4.9 7.2 - - + -
350B TRP* 4.0 20.2 - - + -
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Residues in contact with ASN 237 (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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234A ARG* 5.1 15.2 - - - +
332A GLU* 4.9 14.2 - - - +
336A ARG* 4.7 17.3 + - - -
233B SER 3.1 9.2 + - - -
234B ARG 3.8 10.8 + - - +
235B ALA 3.5 5.4 + - - -
236B LEU* 1.3 78.8 + - - +
238B ARG* 1.3 59.6 + - - +
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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