Contacts of the helix formed by residues 245 - 250 (chain D) in PDB entry 1RG9
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 LYS 245 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259C GLY* 5.6 2.0 - - - -
8D GLU* 5.3 5.2 - - - -
10D VAL* 3.9 32.3 - - + -
14D HIS* 4.2 0.9 - - + -
16D ASP* 2.9 28.9 + - + +
17D LYS* 3.8 18.6 - - + +
20D ASP* 4.5 4.7 + - - +
165D LYS* 5.4 0.7 - - - +
243D GLY* 3.4 1.2 - - - -
244D ARG* 1.3 82.7 + - - +
246D ILE* 1.3 64.9 + - - +
247D ILE 3.0 3.6 + - - -
248D VAL* 3.2 34.8 + - + -
249D ASP* 2.9 29.6 + - - +
684D PPK 2.8 52.9 + - - -
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Residues in contact with ILE 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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244C ARG* 5.6 4.9 - - - +
246C ILE* 4.7 29.8 - - + -
259C GLY* 5.8 0.6 - - - -
243D GLY* 4.5 12.9 - - - +
244D ARG* 3.4 3.2 + - - +
245D LYS* 1.3 77.4 - - - +
247D ILE* 1.3 77.5 + - + +
249D ASP* 3.3 16.9 + - - +
250D THR* 3.2 13.3 + - - +
257D HIS* 3.4 34.6 - - + +
259D GLY* 3.4 43.1 - - - +
260D GLY 3.9 10.3 - - - +
261D ALA* 4.2 9.9 - - - +
262D PHE* 5.6 0.2 - - - -
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Residues in contact with ILE 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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121C LEU* 5.9 0.7 - - + -
247C ILE* 5.7 0.2 - - + -
257C HIS* 3.3 33.4 - - + +
258C GLY 3.6 15.3 - - - +
259C GLY* 3.6 20.2 - - - +
8D GLU* 6.4 0.9 - - + -
245D LYS 3.2 0.8 - - - -
246D ILE* 1.3 93.0 - - + +
248D VAL* 1.3 67.5 + - + +
249D ASP 3.0 1.8 - - - -
250D THR* 3.0 18.0 + - - +
252D GLY* 3.2 18.7 + - - +
253D GLY* 3.3 29.4 - - - +
255D ALA 5.7 2.5 - - - +
256D ARG 5.8 0.4 - - - -
257D HIS* 3.9 22.7 - - + +
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Residues in contact with VAL 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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258C GLY 5.5 0.7 - - - +
259C GLY* 6.4 0.7 - - - -
8D GLU* 3.5 43.1 - - + +
9D SER* 4.1 8.1 - - - +
10D VAL* 4.4 11.7 - - + -
17D LYS* 4.4 7.2 - - - +
138D ILE* 3.8 13.1 - - + +
142D HIS* 3.1 41.6 + - + -
245D LYS* 3.2 41.5 + - + +
247D ILE* 1.3 77.9 - - + +
249D ASP* 1.3 63.5 + - - +
250D THR 3.4 0.5 + - - -
252D GLY* 4.9 0.4 - - - -
357D TYR 6.1 0.2 - - - +
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Residues in contact with ASP 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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17D LYS* 2.5 32.5 + - - -
20D ASP* 3.7 14.8 - - - +
243D GLY* 5.6 2.6 - - - -
245D LYS* 2.9 24.6 + - - +
246D ILE* 3.3 10.6 + - - +
248D VAL* 1.3 80.7 - - - +
250D THR* 1.3 58.0 + - + +
261D ALA* 6.0 0.5 - - - +
262D PHE* 4.5 13.5 + - + +
263D SER* 5.2 0.9 + - - -
358D GLY* 3.7 3.7 + - - -
359D HIS* 2.8 62.0 + - + +
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Residues in contact with THR 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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123D PHE 5.9 1.3 - - - +
134D MET* 3.3 21.5 - - - +
138D ILE* 4.6 3.6 - - - +
142D HIS* 5.5 1.0 + - - -
246D ILE 3.2 14.3 + - - +
247D ILE* 3.0 14.6 + - - +
248D VAL 4.6 2.0 - - - +
249D ASP* 1.3 78.9 - - - +
251D TYR* 1.3 84.7 + - + -
252D GLY 3.8 0.4 - - - -
256D ARG 5.5 0.3 + - - -
257D HIS* 3.6 23.0 + - + +
262D PHE* 3.7 32.1 - - + -
358D GLY* 5.7 0.7 - - - -
360D PHE* 3.6 17.1 + - + +
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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