Contacts of the helix formed by residues 224 - 237 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183C PRO 3.1 20.3 + - - -
184C ASP* 3.3 28.1 + - - -
185C ILE 3.2 8.3 - - - -
186C PRO* 3.6 2.3 - - - +
223C LEU* 1.3 74.9 - - - +
225C PRO* 1.3 69.1 - - - +
226C VAL* 3.9 2.8 - - - +
227C GLN* 2.6 45.5 + - - +
228C VAL* 2.9 10.2 + - - +
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Residues in contact with PRO 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C TRP* 3.6 14.1 - - + -
181C PHE* 3.8 13.5 - - + -
182C ASP 2.9 28.7 - - - +
183C PRO* 3.3 6.3 - - + +
185C ILE 3.2 8.7 - - - +
187C LEU* 3.9 11.2 - - + -
223C LEU 4.0 0.2 - - - -
224C SER* 1.3 80.4 - - - +
226C VAL* 1.3 61.3 + - - +
228C VAL* 3.1 6.1 + - + +
229C CYS* 3.0 26.5 + - - -
242C TYR* 3.3 45.3 - - + -
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Residues in contact with VAL 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C PRO* 3.0 37.7 - - + +
184C ASP* 4.1 10.1 - - - +
224C SER* 3.0 4.4 + - - +
225C PRO* 1.3 75.8 - - - +
227C GLN* 1.3 58.5 + - + +
229C CYS* 3.3 4.4 + - - +
230C ALA* 2.8 27.4 + - + +
242C TYR* 4.4 13.2 - - + +
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Residues in contact with GLN 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C PRO* 4.8 3.3 - - - +
222C THR 4.0 3.3 - - - +
223C LEU* 3.0 27.9 - - + +
224C SER* 2.6 48.6 + - - +
226C VAL* 1.3 73.0 - - + +
228C VAL* 1.3 65.1 + - - +
230C ALA* 3.0 9.4 + - - +
231C ALA* 2.8 24.1 + - - +
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Residues in contact with VAL 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C PHE* 3.7 26.0 - - + -
167C MET* 4.9 0.4 - - + -
177C TRP* 3.9 4.7 - - + -
189C TRP* 3.4 37.7 - - + +
223C LEU* 3.9 11.2 - - + +
224C SER 2.9 19.4 + - - +
225C PRO* 3.1 12.1 + - + +
227C GLN* 1.3 74.9 - - - +
229C CYS* 1.3 62.0 + - - +
231C ALA* 3.1 14.2 + - - +
232C PHE* 3.0 44.8 + - + -
331C MET* 3.8 9.0 - - + -
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Residues in contact with CYS 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C MET* 4.2 2.7 - - - -
177C TRP* 3.9 22.4 - - - -
225C PRO 3.0 16.3 + - - +
226C VAL* 3.5 9.2 - - - +
228C VAL* 1.3 73.1 - - - +
230C ALA* 1.3 59.5 + - - +
231C ALA 3.0 1.6 - - - -
232C PHE* 3.1 4.0 + - - +
233C SER* 2.8 31.5 + - - -
240C VAL* 3.4 40.2 - - + +
241C THR 3.9 3.4 - - - -
242C TYR* 3.8 28.7 - - - +
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Residues in contact with ALA 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C VAL* 2.8 18.0 + - + +
227C GLN* 3.4 14.4 - - - +
229C CYS* 1.3 76.1 - - - +
231C ALA* 1.3 56.4 + - - +
233C SER* 3.4 8.1 + - - -
234C ARG* 2.9 29.8 + - - +
240C VAL 5.5 0.9 - - - -
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Residues in contact with ALA 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C LEU* 5.1 2.9 - - + -
227C GLN 2.8 11.7 + - - +
228C VAL* 3.1 11.7 - - - +
229C CYS 3.0 0.2 - - - -
230C ALA* 1.3 74.0 - - - +
232C PHE* 1.3 60.1 + - - +
234C ARG* 3.1 8.0 + - - +
235C ALA* 2.8 30.9 + - - +
331C MET* 3.9 26.9 - - + -
332C GLU* 4.3 15.3 - - + +
335C ALA* 4.8 1.3 - - - -
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Residues in contact with PHE 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C PHE* 3.9 22.0 - + + -
167C MET* 3.8 28.9 - - + -
228C VAL* 3.0 46.6 + - + -
229C CYS 3.1 5.1 + - - +
231C ALA* 1.3 78.6 - - - +
233C SER* 1.3 59.0 + - - +
236C LEU* 2.8 49.6 + - + +
240C VAL* 3.9 17.9 - - + +
331C MET* 3.7 20.9 - - + -
334C TYR* 4.2 9.0 - + - -
335C ALA* 3.8 21.3 - - + -
339C PHE* 3.9 27.8 - + - -
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Residues in contact with SER 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C CYS 2.8 17.1 + - - -
230C ALA* 3.5 9.6 - - - -
232C PHE* 1.3 77.7 - - - +
234C ARG* 1.3 58.1 + - - +
237C ASN* 3.0 28.9 + - - -
238C ARG 2.6 26.1 + - - +
239C ARG* 3.9 2.8 - - - -
240C VAL* 3.7 19.4 + - - +
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Residues in contact with ARG 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C ALA 2.9 18.8 + - - +
231C ALA* 3.4 8.1 - - - +
233C SER* 1.3 78.7 - - - +
235C ALA* 1.3 59.4 + - - +
237C ASN* 4.0 6.1 + - - +
332C GLU* 3.7 26.9 + - - +
336C ARG* 3.5 15.2 + - - +
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Residues in contact with ALA 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C ALA 2.8 16.4 + - - +
232C PHE 4.0 0.2 - - - +
234C ARG* 1.3 79.2 - - - +
236C LEU* 1.3 61.8 + - - +
237C ASN* 3.8 0.7 + - - +
332C GLU* 3.5 14.1 - - + +
335C ALA* 3.6 9.4 - - + -
336C ARG* 3.4 58.8 + - + +
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Residues in contact with LEU 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C PHE* 4.2 24.5 - - + -
232C PHE* 2.8 36.5 + - + +
235C ALA* 1.3 77.5 - - + +
237C ASN* 1.3 65.6 + - - +
238C ARG* 3.1 29.0 + - + +
240C VAL* 5.9 0.2 - - + -
335C ALA 3.8 9.0 - - - +
336C ARG* 5.0 0.4 - - - -
339C PHE* 4.1 20.6 - - + -
340C PRO* 3.7 30.7 - - + -
350C TRP* 4.1 17.7 - - + -
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Residues in contact with ASN 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C SER 3.0 13.7 + - - -
234C ARG 4.5 4.5 - - - +
235C ALA 3.4 3.2 - - - +
236C LEU* 1.3 80.8 - - - +
238C ARG* 1.3 62.4 + - - +
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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