Contacts of the helix formed by residues 234 - 244 (chain Z) in PDB entry 5V04
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 GLY 234 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A C 3.3 34.9 + - - -
4A T 4.1 3.4 - - - -
222Z SER* 3.8 7.6 - - - -
233Z ILE* 1.3 76.4 - - - +
235Z LEU* 1.3 65.9 + - - -
236Z ALA 3.3 2.2 - - - -
237Z LYS* 4.7 0.4 - - - +
238Z ALA* 3.3 23.7 + - - +
401Z NA 4.1 2.5 - - - -
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Residues in contact with LEU 235 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A C 4.0 3.0 + - - +
3Z ILE* 4.0 14.6 - - + -
4Z GLN 3.9 11.0 - - - +
5Z GLY 3.2 35.2 - - - +
6Z LEU* 3.9 14.8 - - + -
9Z PHE* 3.7 31.8 - - + -
218Z MET* 3.9 18.5 - - + +
219Z CYS* 4.9 1.8 - - - -
222Z SER* 3.5 26.9 - - - +
234Z GLY* 1.3 72.2 - - - +
236Z ALA* 1.3 57.1 + - - +
238Z ALA* 3.8 2.2 - - - +
239Z CYS* 2.9 31.7 + - - +
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Residues in contact with ALA 236 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A G 3.7 27.6 - - - +
3A C 3.3 20.7 + - - +
9Z PHE* 3.9 18.5 - - + -
205Z GLN* 5.9 0.7 - - - +
235Z LEU* 1.3 78.3 - - - +
237Z LYS* 1.3 58.3 - - + +
239Z CYS* 3.2 4.7 + - - +
240Z LYS* 2.9 27.1 + - - +
243Z ARG* 4.6 3.8 + - - -
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Residues in contact with LYS 237 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A G 4.0 23.6 - - - +
3A C 2.6 25.3 + - - +
10B G 6.1 1.6 - - - +
232Z GLY* 3.6 24.0 + - - +
233Z ILE* 4.7 3.1 - - + -
234Z GLY 4.7 4.5 - - - +
236Z ALA* 1.3 71.5 - - + +
238Z ALA* 1.3 60.6 + - - +
240Z LYS* 3.3 12.4 + - + +
241Z VAL* 2.9 33.2 + - - +
261Z LEU* 3.6 23.3 - - + +
263Z MET* 3.4 35.7 - - + +
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Residues in contact with ALA 238 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218Z MET* 4.1 15.9 - - + +
221Z LEU* 3.8 30.5 - - + +
222Z SER 4.4 0.4 - - - +
233Z ILE* 4.2 9.5 - - + +
234Z GLY 3.3 18.9 + - - +
235Z LEU 3.8 2.9 - - - +
236Z ALA 3.3 0.4 - - - -
237Z LYS* 1.3 76.1 - - - +
239Z CYS* 1.3 64.3 + - - +
241Z VAL* 3.1 10.7 + - - +
242Z LEU* 3.0 27.3 + - - +
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Residues in contact with CYS 239 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Z PHE* 4.2 6.3 - - + -
205Z GLN 3.5 17.9 - - - -
206Z LEU* 3.2 33.7 - - - -
209Z VAL* 4.1 6.7 - - - -
218Z MET* 3.7 21.6 - - - +
235Z LEU 2.9 19.1 + - - +
236Z ALA* 3.4 5.8 - - - +
238Z ALA* 1.3 77.0 - - - +
240Z LYS* 1.3 57.1 + - - +
242Z LEU* 3.3 6.4 + - - +
243Z ARG* 2.9 40.3 + - - +
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Residues in contact with LYS 240 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236Z ALA 2.9 13.8 + - - +
237Z LYS* 3.4 14.1 - - + +
238Z ALA 3.1 0.2 - - - -
239Z CYS* 1.3 73.9 - - - +
241Z VAL* 1.3 59.6 + - - +
243Z ARG* 3.2 24.8 + - - +
244Z LEU* 2.9 66.7 + - + +
260Z TYR 4.6 4.7 - - - -
261Z LEU* 3.9 20.2 - - + +
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Residues in contact with VAL 241 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221Z LEU* 5.0 10.3 - - + -
233Z ILE* 6.0 0.2 - - + -
237Z LYS 2.9 20.4 + - - +
238Z ALA* 3.1 11.6 + - - +
240Z LYS* 1.3 76.4 - - - +
242Z LEU* 1.3 67.0 + - + +
244Z LEU* 3.5 2.6 + - - +
245Z ALA* 3.2 22.0 + - - +
253Z VAL* 4.0 25.1 - - + +
254Z ILE* 6.0 0.9 - - - -
257Z ILE* 4.0 21.1 - - + -
260Z TYR* 4.3 21.6 - - + -
261Z LEU* 3.6 27.4 - - + -
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Residues in contact with LEU 242 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208Z ASP* 4.8 4.5 - - - +
209Z VAL* 3.7 21.4 - - + +
214Z LYS* 3.1 44.8 + - + +
217Z TYR* 3.9 10.3 - - + -
218Z MET* 3.5 27.8 - - + +
221Z LEU* 4.6 9.6 - - + -
238Z ALA 3.0 17.0 + - - +
239Z CYS 3.8 0.7 - - - +
241Z VAL* 1.3 79.9 - - + +
243Z ARG* 1.3 64.4 + - - +
245Z ALA* 3.6 19.6 + - + +
250Z ILE* 4.2 24.9 - - + -
253Z VAL* 5.1 4.0 - - + -
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Residues in contact with ARG 243 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204Z ARG 5.0 1.4 + - - -
205Z GLN* 3.7 23.7 + - - +
206Z LEU 4.1 4.5 - - - +
207Z GLY* 4.0 19.5 - - - +
208Z ASP* 3.6 24.8 - - - +
209Z VAL* 4.0 8.5 - - + -
236Z ALA 4.6 3.8 + - - -
239Z CYS* 2.9 21.9 + - - +
240Z LYS* 3.2 35.5 + - - +
242Z LEU* 1.3 78.9 - - - +
244Z LEU* 1.3 67.5 + - + +
245Z ALA 3.1 5.7 + - - +
246Z ASN* 6.0 0.3 - - - -
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Residues in contact with LEU 244 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240Z LYS* 2.9 48.9 + - + +
241Z VAL 3.8 1.6 - - - +
242Z LEU 3.4 0.2 - - - -
243Z ARG* 1.3 84.8 - - + +
245Z ALA* 1.3 58.7 + - - +
246Z ASN* 3.6 14.0 + - - -
260Z TYR* 3.3 51.1 - - + +
262Z LYS* 6.2 1.3 - - + -
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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