Contacts of the strand formed by residues 289 - 293 (chain D) in PDB entry 1L9X
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 GLN 289 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C GLU* 5.4 0.2 + - - -
273C ILE* 5.0 1.7 - - - +
274C TYR* 3.6 38.0 - - + +
276C PHE 5.0 4.0 - - - +
291C TYR* 5.2 5.2 + - - -
33D ALA* 3.9 1.0 - - - -
34D ALA* 2.9 32.9 + - + +
35D SER 4.7 0.3 + - - -
38D LYS* 2.8 39.4 - - - +
227D GLU* 4.9 1.3 + - - +
278D PRO* 4.5 20.1 - - + +
279D ILE 3.3 13.0 - - - +
280D TYR* 4.6 5.4 - - - -
281D THR* 3.6 4.3 - - - -
287D PHE* 4.0 3.6 - - - +
288D GLN* 1.3 84.0 - - - +
290D CYS* 1.3 67.4 + - - +
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Residues in contact with CYS 290 (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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24D MET* 3.5 33.7 - - + -
31D TYR* 3.8 11.0 - - + -
32D ILE 3.6 5.2 - - - +
33D ALA* 4.1 3.1 - - - -
34D ALA 4.2 0.9 - - - +
278D PRO* 3.3 5.1 - - - +
279D ILE* 2.8 34.0 + - - +
281D THR* 3.5 21.3 + - + -
287D PHE* 3.7 25.6 - - - -
289D GLN* 1.3 79.6 - - - +
291D TYR* 1.3 62.0 + - - +
292D ILE* 3.7 6.2 + - + +
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Residues in contact with TYR 291 (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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289C GLN* 5.3 6.1 + - - -
31D TYR* 3.0 6.6 - - - +
32D ILE* 2.9 43.3 + - + +
34D ALA* 3.9 21.5 - - + -
37D VAL* 3.9 22.6 - - + +
273D ILE* 3.6 34.4 + - + +
276D PHE* 3.5 24.4 + - + -
277D SER 4.0 4.7 - - - -
278D PRO* 3.5 45.6 - - + +
290D CYS* 1.3 72.7 - - - +
292D ILE* 1.3 59.5 + - - +
293D PHE* 3.5 20.9 - - + -
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Residues in contact with ILE 292 (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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19D CYS* 4.4 1.6 - - - -
24D MET* 4.2 35.7 - - + +
27D TYR* 3.4 34.8 - - + +
28D GLY* 3.3 37.5 - - - +
30D TYR 3.3 9.2 - - - +
31D TYR* 4.3 1.8 - - + -
277D SER 4.9 6.4 + - - +
279D ILE* 4.8 19.3 - - + +
281D THR* 5.0 4.0 - - + -
290D CYS* 3.7 9.5 + - + +
291D TYR* 1.3 77.2 - - - +
293D PHE* 1.3 69.3 + - - +
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Residues in contact with PHE 293 (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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16D MET* 3.4 38.4 - - + -
28D GLY* 4.5 0.9 - - - -
29D ARG 3.1 6.2 + - - -
30D TYR* 2.8 40.0 + - - +
31D TYR* 4.2 1.3 - - - -
32D ILE* 3.9 20.4 - - + -
49D PRO* 3.7 21.5 - - + -
51D ARG* 4.2 2.7 - - - +
273D ILE* 4.4 4.3 - - + -
276D PHE* 3.5 44.2 - + + -
291D TYR* 3.5 38.6 - - + -
292D ILE* 1.3 77.2 - - - +
294D ASP* 1.3 68.8 + - - +
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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