Contacts of the strand formed by residues 245 - 251 (chain D) in PDB entry 5VQ9
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 ALA 245 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204D TYR* 3.5 7.8 - - - -
206D TYR* 3.2 44.2 - - + +
208D GLN* 4.3 12.1 - - + -
239D LEU 4.7 2.2 - - - +
242D ASP 3.3 8.7 + - - +
243D LYS 3.2 1.0 - - - +
244D ASP* 1.3 78.5 - - - +
246D LEU* 1.3 58.5 + - - +
247D VAL* 4.5 6.1 - - + -
292D ASN* 2.9 31.5 + - - +
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Residues in contact with LEU 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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157D LEU* 3.9 32.1 - - + -
196D LEU* 4.7 7.0 - - + +
197D THR* 5.1 3.8 - - + +
200D LEU* 4.2 10.1 - - + -
204D TYR* 3.7 40.9 - - + -
206D TYR 3.3 7.9 + - - +
207D GLY* 3.6 5.3 - - - -
208D GLN 3.1 21.3 + - - +
245D ALA* 1.3 71.5 - - - +
247D VAL* 1.3 60.8 + - - +
248D PHE* 3.5 37.3 + - + -
292D ASN 3.4 21.3 - - - +
294D VAL* 4.2 7.4 - - + -
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Residues in contact with VAL 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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208D GLN* 3.6 25.6 - - + -
210D ILE* 4.4 18.2 - - + -
236D ILE* 4.7 2.9 - - + -
239D LEU* 4.0 12.1 - - + +
240D ILE* 3.6 50.7 - - + +
245D ALA* 4.4 3.1 - - + +
246D LEU* 1.3 73.0 - - - +
248D PHE* 1.3 62.1 + - - +
249D VAL* 4.5 7.0 - - + -
292D ASN* 2.9 19.7 + - - +
293D VAL* 3.5 4.8 - - - +
294D VAL* 2.9 27.0 + - - +
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Residues in contact with PHE 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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127D LEU* 4.0 4.0 - - + -
157D LEU* 5.4 0.2 - - + -
193D ALA* 3.6 34.5 - - + -
196D LEU* 3.5 35.0 - - + -
197D THR* 3.9 6.3 - - - -
208D GLN 2.7 19.9 + - - +
209D LEU* 3.4 18.4 - - + +
210D ILE* 2.9 29.5 + - - +
246D LEU* 3.5 39.9 - - + -
247D VAL* 1.3 72.2 - - - +
249D VAL* 1.3 60.0 + - - +
250D LEU 4.2 0.2 - - - -
294D VAL* 3.2 40.6 - - + -
296D LEU* 4.2 14.1 - - + -
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Residues in contact with VAL 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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210D ILE* 3.5 15.0 - - + +
212D ILE* 4.2 23.1 - - + -
233D PHE* 5.2 2.0 - - + -
236D ILE* 4.4 20.9 - - + -
240D ILE* 5.3 0.2 - - + -
247D VAL* 4.5 9.9 - - + -
248D PHE* 1.3 77.9 - - - +
250D LEU* 1.3 58.2 + - - +
251D ILE* 5.0 7.6 - - + -
284D ILE* 6.2 1.1 - - + -
287D ILE* 3.9 29.4 - - + -
293D VAL* 4.8 6.3 - - + -
294D VAL 3.0 9.6 + - - +
295D ILE* 3.4 9.8 - - + +
296D LEU* 2.6 34.9 + - - +
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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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186D THR* 3.9 24.7 - - + +
189D CYS* 3.7 39.3 - - + -
190D LYS* 4.3 12.3 - - + -
209D LEU* 4.1 17.5 - - + -
210D ILE 2.9 15.1 + - - +
211D GLU* 4.2 17.7 - - + -
212D ILE* 2.9 31.0 + - - +
249D VAL* 1.3 72.5 - - - +
251D ILE* 1.3 78.3 + - - +
252D ASP* 4.4 3.4 - - + +
296D LEU* 3.1 20.2 - - + +
298D THR* 4.4 7.6 - - + -
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Residues in contact with ILE 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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212D ILE* 4.0 25.6 - - + +
214D SER* 5.4 6.1 - - - +
249D VAL* 5.0 9.2 - - + +
250D LEU* 1.3 81.7 - - - +
252D ASP* 1.3 67.3 + - - +
254D VAL* 3.6 28.6 - - + +
257D LEU* 5.1 10.3 - - + -
280D VAL* 5.1 6.3 - - + -
284D ILE* 3.5 35.2 - - + -
295D ILE* 5.4 5.4 - - + -
296D LEU 2.7 15.1 + - - +
297D THR* 3.5 10.4 - - + -
298D THR 3.2 23.0 + - - -
312D ARG* 4.8 2.0 - - - +
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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