Contacts of the helix formed by residues 243 - 253 (chain D) in PDB entry 3GV5
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 243 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237D LYS* 3.7 11.0 - - - -
241D GLY 3.8 2.0 + - - -
242D ILE* 1.3 73.6 - - - +
244D TYR* 1.3 67.1 + - - -
245D LYS 3.2 3.3 + - - -
246D THR 3.4 0.5 + - - -
247D ALA* 3.0 23.7 + - - +
871E G 3.1 21.6 + - - -
872E A 3.5 18.6 - - - -
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Residues in contact with TYR 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D LYS* 3.2 24.0 - - + +
243D GLY* 1.3 71.2 - - - +
245D LYS* 1.3 95.7 + - + +
247D ALA* 3.4 3.4 + - + +
248D LYS* 2.8 50.5 + - + +
871E G 3.7 4.8 + - - +
837F C 3.3 57.5 + - - -
838F A 3.7 17.3 - - - +
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Residues in contact with LYS 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D TYR* 1.3 113.1 - - + +
246D THR* 1.3 57.7 + - + +
248D LYS* 3.3 22.4 + - - +
249D CYS* 3.0 28.5 + - - +
870E T 3.1 52.9 + - + +
871E G 3.2 16.1 + - - +
838F A 4.9 7.1 + - - +
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Residues in contact with THR 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D GLY 4.8 3.6 - - - +
242D ILE* 3.3 19.6 - - - +
243D GLY 4.4 4.3 - - - +
245D LYS* 1.3 73.8 - - + +
247D ALA* 1.3 60.4 + - - +
249D CYS* 3.2 11.4 + - - +
250D LEU* 2.8 41.4 + - - +
273D LEU* 5.9 3.8 - - - -
277D VAL* 6.2 5.6 - - + -
281D ILE* 4.4 14.1 - - + +
870E T 4.0 7.0 - - - +
871E G 2.6 33.9 + - - +
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Residues in contact with ALA 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D ILE* 4.0 24.2 - - + -
237D LYS* 4.5 14.1 - - + +
242D ILE* 4.1 1.0 - - + +
243D GLY 3.0 20.1 + - - +
244D TYR* 3.6 5.8 - - + +
246D THR* 1.3 74.9 + - - +
248D LYS* 1.3 59.7 + - - +
250D LEU* 3.5 7.0 + - - +
251D GLU* 2.9 30.7 + - - +
255D ILE 4.8 0.7 - - - +
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Residues in contact with LYS 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D TYR* 2.8 42.7 + - + +
245D LYS* 3.5 26.7 - - - +
246D THR 3.3 0.2 - - - -
247D ALA* 1.3 76.4 - - - +
249D CYS* 1.3 62.5 + - - +
251D GLU* 3.3 19.1 + - - +
252D ALA* 3.2 21.7 + - - +
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Residues in contact with CYS 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D LYS 3.0 16.9 + - - +
246D THR* 3.3 15.3 - - - +
248D LYS* 1.3 76.1 - - - +
250D LEU* 1.3 60.9 + - - +
252D ALA* 3.4 16.0 + - - +
253D LEU* 3.5 18.3 + - - +
273D LEU* 4.4 20.4 - - + -
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Residues in contact with LEU 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D ILE* 4.1 33.4 - - + -
242D ILE* 4.3 2.2 - - + -
246D THR* 2.8 33.0 + - - +
247D ALA* 3.8 4.0 - - - +
249D CYS* 1.3 71.5 - - + +
251D GLU* 1.3 60.3 + - - +
253D LEU* 3.0 15.9 + - + +
255D ILE* 2.8 58.6 + - + +
261D LEU* 4.3 11.4 - - + -
269D LEU* 4.1 13.5 - - + -
273D LEU* 4.4 9.4 - - + -
281D ILE* 3.9 31.2 - - + -
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Residues in contact with GLU 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D ALA 2.9 18.6 + - - +
248D LYS* 3.3 20.2 + - - +
250D LEU* 1.3 75.3 - - - +
252D ALA* 1.3 56.5 + - - +
254D GLY* 3.2 18.2 + - - -
255D ILE 3.4 10.7 + - - +
256D ASN* 3.2 25.4 + - - +
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Residues in contact with ALA 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D LYS 3.2 11.5 + - - +
249D CYS* 3.5 12.6 - - - +
250D LEU 3.2 0.6 - - - -
251D GLU* 1.3 73.1 - - - +
253D LEU* 1.3 63.2 + - + +
254D GLY 3.2 5.6 + - - -
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Residues in contact with LEU 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D CYS 3.6 14.4 - - - +
250D LEU* 3.0 11.4 + - + +
252D ALA* 1.3 80.9 - - + +
254D GLY* 1.3 58.3 + - - +
255D ILE* 3.4 12.8 - - + -
264D PHE* 3.7 29.7 - - + -
269D LEU* 3.8 28.0 - - + -
272D GLU* 3.3 43.7 - - + +
273D LEU* 4.6 7.9 - - + -
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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