Contacts of the helix formed by residues 224 - 237 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183G PRO 3.1 17.0 + - - -
184G ASP* 3.5 11.9 + - - -
185G ILE 3.0 28.7 - - - -
186G PRO* 3.6 2.4 - - - +
223G LEU* 1.3 68.5 - - - +
225G PRO* 1.3 55.1 - - - -
226G VAL* 3.7 3.1 - - - +
227G GLN* 2.4 73.2 + - - +
228G VAL* 3.0 7.2 + - - -
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Residues in contact with PRO 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177G TRP* 3.4 15.3 - - + -
181G PHE* 3.6 24.0 - - + -
182G ASP 3.4 19.5 - - - +
183G PRO* 3.6 3.8 - - + +
185G ILE 3.1 13.7 - - - +
187G LEU* 4.0 14.6 - - + -
223G LEU 3.9 0.2 - - - -
224G SER* 1.3 80.8 - - - -
226G VAL* 1.3 62.7 + - - +
228G VAL* 3.1 6.9 + - + +
229G CYS* 3.0 25.8 + - - -
242G TYR* 3.4 37.2 - - + -
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Residues in contact with VAL 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239E ARG* 4.3 25.8 - - - +
183G PRO* 2.8 42.4 - - + +
184G ASP* 3.9 11.2 - - - +
224G SER* 2.7 7.6 + - - +
225G PRO* 1.3 73.4 - - - +
227G GLN* 1.3 53.7 + - + +
229G CYS* 3.2 5.8 + - - +
230G ALA* 2.8 34.2 + - + +
242G TYR* 4.4 13.0 - - + -
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Residues in contact with GLN 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E ARG* 6.2 1.3 - - - +
186G PRO* 4.4 7.6 - - - +
222G THR 4.3 1.2 + - - +
223G LEU* 3.1 26.5 - - + +
224G SER* 2.4 53.5 + - - +
226G VAL* 1.3 73.8 - - + +
228G VAL* 1.3 66.7 + - - +
230G ALA* 2.9 9.3 + - - +
231G ALA* 2.7 27.1 + - - +
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Residues in contact with VAL 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G PHE* 3.5 39.0 - - + -
167G MET* 4.7 0.4 - - + -
177G TRP* 3.6 6.1 - - + -
189G TRP* 3.4 38.1 - - + +
223G LEU* 3.9 14.1 - - + +
224G SER 3.0 12.0 + - - +
225G PRO* 3.2 13.7 - - + +
227G GLN* 1.3 75.5 - - - +
229G CYS* 1.3 62.2 + - - +
231G ALA* 3.5 3.3 + - - +
232G PHE* 3.1 33.8 + - + -
331G MET* 4.0 12.5 - - + +
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Residues in contact with CYS 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167G MET* 4.2 5.6 - - - -
177G TRP* 3.7 20.4 - - - -
225G PRO 3.0 16.6 + - - -
226G VAL* 3.4 8.7 - - - +
228G VAL* 1.3 75.6 - - - +
230G ALA* 1.3 59.7 + - - +
232G PHE* 3.1 2.6 + - - -
233G SER* 2.8 24.9 + - - -
240G VAL* 3.1 47.1 - - + +
241G THR* 4.0 1.1 - - - -
242G TYR* 3.7 31.2 - - + +
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Residues in contact with ALA 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E SER* 6.0 1.3 - - - +
226G VAL* 2.8 17.6 + - + +
227G GLN* 2.9 14.8 + - - +
229G CYS* 1.3 74.6 - - - +
231G ALA* 1.3 58.0 + - - +
233G SER* 2.8 30.5 + - - -
234G ARG* 3.2 6.9 + - - +
240G VAL 5.8 0.7 - - - -
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Residues in contact with ALA 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E ASN* 6.0 1.6 - - - +
223G LEU* 5.3 3.8 - - + -
227G GLN 2.7 14.8 + - - +
228G VAL* 3.6 9.2 - - - +
230G ALA* 1.3 71.3 - - - +
232G PHE* 1.3 52.2 + - - +
233G SER 3.2 0.2 + - - -
234G ARG* 3.2 4.9 + - - +
235G ALA* 2.7 37.4 + - - +
331G MET* 4.2 11.9 - - + -
332G GLU* 4.2 35.9 - - + +
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Residues in contact with PHE 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G PHE* 3.8 29.6 - + + -
167G MET* 3.5 27.8 - - + -
228G VAL* 3.1 22.7 + - + +
229G CYS 3.3 9.6 - - - +
231G ALA* 1.3 79.6 - - - +
233G SER* 1.3 56.5 + - - +
235G ALA* 3.9 5.8 - - - -
236G LEU* 2.8 55.8 + - + +
240G VAL* 3.5 12.7 - - + +
331G MET* 3.8 26.9 - - + -
334G TYR* 4.0 16.4 - + - -
335G ALA* 3.7 15.5 - - + -
339G PHE* 3.8 26.9 - + - -
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Residues in contact with SER 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234E ARG* 3.3 20.2 - - - +
229G CYS 2.8 11.3 + - - -
230G ALA* 2.8 19.1 + - - -
232G PHE* 1.3 76.2 - - - +
234G ARG* 1.3 55.2 + - - -
237G ASN* 2.8 30.0 + - - -
238G ARG 2.7 28.4 + - - +
239G ARG* 3.8 5.9 - - - +
240G VAL* 3.3 16.3 + - - +
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Residues in contact with ARG 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E ARG* 3.2 34.2 + - - +
235E ALA 3.5 18.2 + - - -
236E LEU 4.9 1.0 + - - -
237E ASN* 3.3 38.1 - - - +
336E ARG* 3.8 22.9 + - - +
230G ALA 3.2 5.7 + - - +
231G ALA* 3.8 5.8 - - - +
233G SER* 1.3 78.4 - - - +
235G ALA* 1.3 67.8 + - - +
237G ASN* 3.1 18.8 + - - +
332G GLU* 3.5 20.3 + - - +
336G ARG* 3.2 24.8 + - - +
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Residues in contact with ALA 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231G ALA 2.7 21.9 + - - +
232G PHE 3.7 1.1 - - - +
234G ARG* 1.3 76.9 - - - +
236G LEU* 1.3 58.8 + - - +
237G ASN* 3.1 4.3 + - - +
332G GLU* 3.5 17.4 - - - +
335G ALA* 3.3 31.6 - - + -
336G ARG* 3.4 38.5 + - - +
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Residues in contact with LEU 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167G MET* 5.1 0.2 - - + -
175G PHE* 4.3 22.0 - - + -
232G PHE* 2.8 48.0 + - + +
235G ALA* 1.3 73.1 - - + +
237G ASN* 1.3 64.6 + - - +
238G ARG* 3.0 28.1 + - + +
240G VAL* 5.1 2.2 - - + -
335G ALA 3.6 15.5 - - - +
336G ARG* 5.1 0.4 - - - -
339G PHE* 3.6 26.5 - - + -
340G PRO* 3.8 9.0 - - + -
350G TRP* 3.6 28.9 - - + -
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Residues in contact with ASN 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E ARG* 3.7 15.4 + - - +
332E GLU* 3.7 21.3 + - - +
336E ARG* 4.0 13.0 + - - +
233G SER 2.8 16.5 + - - -
234G ARG* 3.4 11.8 - - - +
235G ALA 3.0 5.9 - - - +
236G LEU* 1.3 80.6 - - - +
238G ARG* 1.3 58.4 + - + +
679M THR* 6.2 1.6 - - - +
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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