Contacts of the helix formed by residues 224 - 237 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183F PRO 3.2 14.4 - - - -
184F ASP* 3.4 25.0 - - - -
185F ILE 3.5 7.6 - - - -
186F PRO* 3.7 3.1 - - - +
223F LEU* 1.3 74.6 - - - +
225F PRO* 1.3 59.3 - - - +
226F VAL* 2.8 24.9 - - - +
227F GLN* 2.7 49.5 + - - +
228F VAL* 2.9 10.0 + - - +
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Residues in contact with PRO 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177F TRP* 3.5 18.3 - - + -
181F PHE* 3.7 22.2 - - + -
182F ASP 3.2 20.6 - - - +
183F PRO 3.1 11.0 - - - +
185F ILE 3.4 8.7 - - - +
187F LEU* 4.0 12.8 - - + -
224F SER* 1.3 81.0 - - - +
226F VAL* 1.3 61.8 + - - +
228F VAL* 3.2 6.0 + - + +
229F CYS* 3.0 27.0 + - - -
242F TYR* 3.4 32.5 - - + -
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Residues in contact with VAL 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183F PRO* 3.0 20.9 + - + +
184F ASP* 3.6 18.8 - - - +
224F SER* 2.8 23.8 - - - +
225F PRO* 1.3 74.0 - - - +
227F GLN* 1.3 59.8 + - + +
229F CYS* 3.3 5.0 + - - +
230F ALA* 2.8 28.2 + - + +
242F TYR* 4.4 12.2 - - + +
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Residues in contact with GLN 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F PRO* 4.5 6.4 - - - +
222F THR 4.5 3.0 + - - +
223F LEU* 3.5 25.4 - - + +
224F SER* 2.7 50.4 + - - +
226F VAL* 1.3 74.3 - - + +
228F VAL* 1.3 56.7 + - - +
230F ALA* 2.9 8.4 + - - +
231F ALA* 2.7 36.8 + - - +
234F ARG* 4.8 1.2 + - - -
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Residues in contact with VAL 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157F PHE* 3.7 34.3 - - + -
167F MET* 4.8 0.7 - - + -
177F TRP* 4.0 5.8 - - + -
189F TRP* 3.8 26.2 - - + +
223F LEU* 3.7 29.1 - - + +
224F SER 2.9 18.8 + - - +
225F PRO* 3.4 8.7 - - + +
227F GLN* 1.3 75.8 - - - +
229F CYS* 1.3 58.0 + - - +
231F ALA* 3.2 3.6 + - - +
232F PHE* 2.9 41.4 + - + -
331F MET* 4.0 10.3 - - + -
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Residues in contact with CYS 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F MET* 4.6 2.2 - - - -
177F TRP* 3.6 26.5 - - - -
225F PRO 3.0 16.5 + - - -
226F VAL* 3.5 9.2 - - - +
228F VAL* 1.3 75.5 - - - +
230F ALA* 1.3 53.8 + - - +
232F PHE* 3.0 5.5 + - - +
233F SER* 2.6 35.9 + - - -
240F VAL* 3.4 35.9 - - + +
241F THR* 3.8 5.2 - - - -
242F TYR* 3.6 27.8 - - - +
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Residues in contact with ALA 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226F VAL* 2.8 18.9 + - + +
227F GLN* 2.9 12.5 + - - +
229F CYS* 1.3 75.4 - - - +
231F ALA* 1.3 58.0 + - - +
233F SER* 3.1 9.0 + - - -
234F ARG* 2.8 43.8 + - + +
240F VAL 5.5 0.7 - - - -
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Residues in contact with ALA 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F LEU* 4.9 4.0 - - + -
227F GLN 2.7 16.1 + - - +
228F VAL* 3.3 9.4 - - - +
230F ALA* 1.3 73.0 - - - +
232F PHE* 1.3 58.6 + - - +
234F ARG* 3.2 23.3 + - - +
235F ALA* 2.8 30.2 + - - +
331F MET* 4.0 25.8 - - + -
332F GLU* 4.2 13.9 - - - +
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Residues in contact with PHE 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F PHE* 4.1 20.6 - + + -
167F MET* 3.4 35.2 - - + -
228F VAL* 2.9 28.6 + - + +
229F CYS 3.0 7.8 + - - +
231F ALA* 1.3 76.7 - - - +
233F SER* 1.3 56.9 + - - +
236F LEU* 3.0 54.7 + - + +
240F VAL* 3.6 10.9 - - + +
331F MET* 3.7 28.5 - - + -
334F TYR* 4.1 11.2 - + - -
335F ALA* 3.9 21.5 - - + -
339F PHE* 3.8 31.2 - + - -
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Residues in contact with SER 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229F CYS 2.6 16.1 + - - -
230F ALA* 3.2 15.0 - - - -
232F PHE* 1.3 74.8 - - - +
234F ARG* 1.3 54.6 + - - +
237F ASN* 2.7 35.7 + - - -
238F ARG 3.2 16.4 + - - -
239F ARG* 4.5 2.1 - - - -
240F VAL* 3.4 20.9 + - - -
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Residues in contact with ARG 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227F GLN 4.8 1.0 + - - -
230F ALA* 2.8 30.5 + - + +
231F ALA* 3.3 31.7 - - - +
233F SER* 1.3 77.3 - - - +
235F ALA* 1.3 68.1 + - - +
237F ASN* 3.8 6.4 + - - +
332F GLU* 2.7 52.2 + - - +
336F ARG* 5.1 1.0 - - - -
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Residues in contact with ALA 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231F ALA 2.8 17.5 + - - +
232F PHE 3.8 1.8 - - - +
233F SER 3.3 0.2 - - - -
234F ARG* 1.3 80.3 - - - +
236F LEU* 1.3 60.9 + - + +
237F ASN* 5.0 0.9 - - - +
332F GLU* 3.6 7.8 - - - +
335F ALA* 3.4 27.8 - - + -
336F ARG* 3.2 47.6 + - + +
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Residues in contact with LEU 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F PHE* 4.2 21.8 - - + -
232F PHE* 3.0 47.5 + - + +
235F ALA* 1.3 78.8 - - + +
237F ASN* 1.3 73.7 + - - +
238F ARG* 3.8 21.5 + - + +
240F VAL* 4.7 2.2 - - + -
335F ALA 3.9 18.2 - - - +
336F ARG* 5.4 0.4 - - - -
339F PHE* 4.1 5.2 - - + -
340F PRO* 4.3 6.3 - - + -
350F TRP* 3.5 33.9 - - + -
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Residues in contact with ASN 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233F SER 2.7 21.3 + - - -
234F ARG* 3.8 5.3 + - - +
235F ALA 3.5 1.9 - - - +
236F LEU* 1.3 76.1 - - - +
238F ARG* 1.3 66.9 + - - +
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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