Contacts of the helix formed by residues 224 - 237 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183E PRO 3.1 19.0 + - - -
184E ASP* 3.5 26.4 - - - -
185E ILE 3.3 6.7 - - - -
186E PRO* 3.7 2.4 - - - +
223E LEU* 1.3 69.8 - - - +
225E PRO* 1.3 69.3 - - - +
226E VAL* 3.5 4.0 + - - +
227E GLN* 2.4 59.7 + - - +
228E VAL* 2.9 10.0 + - - +
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Residues in contact with PRO 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E TRP* 4.0 12.5 - - + -
181E PHE* 3.8 20.2 - - + -
182E ASP 3.1 27.1 - - - +
183E PRO 3.2 7.0 - - - +
185E ILE 3.2 9.4 - - - +
187E LEU* 4.2 11.4 - - + -
189E TRP* 5.5 0.2 - - + -
224E SER* 1.3 80.1 - - - +
226E VAL* 1.3 62.1 + - - +
228E VAL* 3.1 8.3 + - + +
229E CYS* 3.0 26.3 + - - -
242E TYR* 3.3 37.2 - - + -
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Residues in contact with VAL 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E PRO* 3.0 37.9 - - + +
184E ASP* 3.8 11.4 - - - +
224E SER* 3.0 4.7 - - - +
225E PRO* 1.3 75.3 - - - +
227E GLN* 1.3 53.1 + - + +
229E CYS* 3.2 6.4 + - - +
230E ALA* 2.8 33.2 + - + +
242E TYR* 4.4 13.4 - - + +
239G ARG* 4.5 18.6 - - - +
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Residues in contact with GLN 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E PRO* 4.3 7.6 - - - +
222E THR 4.6 2.9 + - - +
223E LEU* 3.4 23.8 - - + +
224E SER* 2.4 53.1 + - - +
226E VAL* 1.3 73.0 - - + +
228E VAL* 1.3 54.8 + - - +
230E ALA* 3.4 9.4 - - - +
231E ALA* 2.7 36.4 + - - +
234E ARG* 5.4 0.2 + - - -
239G ARG* 4.7 16.8 - - - +
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Residues in contact with VAL 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157E PHE* 3.5 39.7 - - + -
177E TRP* 3.9 6.5 - - + -
189E TRP* 3.3 34.5 - - + +
223E LEU* 3.7 14.6 - - + -
224E SER 2.9 18.4 + - - +
225E PRO* 3.3 9.9 - - + +
227E GLN* 1.3 77.0 - - - +
229E CYS* 1.3 59.1 + - - +
231E ALA* 3.3 7.0 + - - +
232E PHE* 3.0 38.4 + - + -
331E MET* 3.9 9.4 - - + -
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Residues in contact with CYS 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E MET* 4.7 3.1 - - - -
177E TRP* 4.0 20.4 - - - -
225E PRO 3.0 16.0 + - - -
226E VAL* 3.4 9.0 - - - +
228E VAL* 1.3 74.9 - - - +
230E ALA* 1.3 53.9 + - - +
232E PHE* 3.0 3.1 + - - -
233E SER* 2.6 33.3 + - - -
240E VAL* 3.3 45.0 - - + +
241E THR 4.0 1.6 - - - -
242E TYR* 3.5 31.9 - - + +
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Residues in contact with ALA 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E VAL* 2.8 19.3 + - + +
227E GLN* 3.1 12.8 + - - +
229E CYS* 1.3 71.1 - - - +
231E ALA* 1.3 60.3 + - - +
233E SER* 2.9 25.2 + - - -
234E ARG* 3.0 27.9 + - + +
240E VAL 4.8 1.3 + - - -
239G ARG* 4.7 23.3 - - + +
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Residues in contact with ALA 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223E LEU* 5.4 4.3 - - + -
227E GLN 2.7 20.1 + - - +
228E VAL* 3.4 6.5 - - - +
230E ALA* 1.3 74.0 - - - +
232E PHE* 1.3 60.9 + - - +
234E ARG* 3.5 21.4 + - - +
235E ALA* 3.1 26.2 + - - +
331E MET* 4.0 25.6 - - + -
332E GLU* 4.2 14.2 - - + +
335E ALA* 4.9 0.2 - - - -
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Residues in contact with PHE 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E PHE* 3.7 38.1 - + + -
167E MET* 3.8 28.5 - - + -
228E VAL* 3.0 25.5 + - + +
229E CYS 3.0 7.6 + - - +
231E ALA* 1.3 73.8 - - - +
233E SER* 1.3 66.2 + - - +
236E LEU* 3.1 44.2 + - + +
240E VAL* 3.7 17.5 - - + +
331E MET* 3.8 19.5 - - + -
334E TYR* 4.0 14.6 - + - -
335E ALA* 3.8 26.2 - - + -
339E PHE* 3.8 24.9 - + - -
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Residues in contact with SER 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E CYS 2.6 17.0 + - - -
230E ALA* 2.9 16.0 + - - -
232E PHE* 1.3 73.4 - - - +
234E ARG* 1.3 58.4 + - - +
237E ASN* 2.9 27.9 + - - -
238E ARG 3.1 25.8 + - - +
239E ARG* 4.4 1.7 - - - -
240E VAL* 3.6 14.9 + - - -
230G ALA* 6.0 1.7 - - - +
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Residues in contact with ARG 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E GLN 5.4 0.2 + - - -
230E ALA* 3.0 19.8 + - - +
231E ALA* 3.9 24.7 - - - +
233E SER* 1.3 79.2 + - - +
235E ALA* 1.3 62.7 + - - +
236E LEU 3.2 1.0 + - - -
330E ASP* 5.5 0.4 + - - -
332E GLU* 2.8 46.4 + - - +
336E ARG* 3.4 4.6 + - - +
233G SER* 3.3 20.2 - - - +
234G ARG* 3.2 38.6 + - - +
237G ASN 3.7 10.3 + - - -
238G ARG 3.1 29.2 - - - -
239G ARG* 4.9 12.8 - - + +
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Residues in contact with ALA 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E ALA 3.1 15.8 + - - +
232E PHE 4.1 0.7 - - - +
234E ARG* 1.3 79.4 - - - +
236E LEU* 1.3 61.6 + - - +
332E GLU* 3.4 29.6 - - + +
335E ALA* 3.7 8.7 - - + -
336E ARG* 3.4 40.9 - - + +
234G ARG* 3.5 16.0 + - - -
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Residues in contact with LEU 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E PHE* 4.0 24.2 - - + -
232E PHE* 3.1 34.4 + - + +
233E SER 4.4 0.2 - - - +
235E ALA* 1.3 85.7 - - + +
237E ASN* 1.3 72.8 + - - +
238E ARG* 3.7 17.7 + - + +
240E VAL* 5.2 1.3 - - + -
335E ALA 3.5 25.4 - - - +
336E ARG* 4.4 0.7 - - - -
339E PHE* 4.0 26.5 - - + -
340E PRO* 4.1 15.0 - - + -
350E TRP* 4.4 10.7 - - + -
234G ARG* 4.3 2.2 + - - -
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Residues in contact with ASN 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E SER 2.9 10.7 + - - -
234E ARG 3.6 3.0 + - - -
236E LEU* 1.3 81.0 - - - +
238E ARG* 1.3 67.1 + - - +
231G ALA* 6.0 1.4 - - - +
234G ARG* 3.3 27.7 - - - +
332G GLU* 3.4 24.0 + - - -
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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