Contacts of the strand formed by residues 289 - 293 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA* 3.9 0.7 - - - -
34A ALA* 2.9 33.7 + - + +
35A SER 4.7 0.7 + - - -
38A LYS* 2.9 33.5 + - - +
227A GLU* 4.9 1.6 + - - +
278A PRO* 4.3 21.9 - - + +
279A ILE 3.4 12.8 - - - +
280A TYR* 4.6 2.0 - - - -
281A THR* 3.6 0.9 - - - -
287A PHE* 3.4 4.0 - - - +
288A GLN* 1.3 87.1 - - + +
290A CYS* 1.3 70.4 + - - +
273B ILE* 4.9 2.8 + - - +
274B TYR* 3.4 45.1 + - + +
276B PHE 5.0 4.8 + - - -
291B TYR* 5.2 6.5 + - - -
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Residues in contact with CYS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A MET* 3.9 12.1 - - - -
31A TYR* 3.8 19.3 - - + -
32A ILE 3.6 6.3 - - - +
33A ALA* 4.1 3.1 - - - -
34A ALA 4.1 0.4 - - - +
278A PRO* 3.2 5.1 - - - +
279A ILE* 2.9 29.9 + - - +
281A THR* 3.6 20.8 + - + -
287A PHE* 3.7 28.5 - - - -
289A GLN* 1.3 80.8 - - - +
291A TYR* 1.3 60.7 + - - +
292A ILE* 3.0 24.8 - - + +
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Residues in contact with TYR 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TYR* 3.0 6.4 - - - +
32A ILE* 2.8 42.3 + - + +
34A ALA* 3.9 25.5 - - + +
37A VAL* 3.9 27.5 - - + +
273A ILE* 3.7 30.5 + - + +
276A PHE* 3.5 24.4 + - + -
277A SER 3.9 4.7 - - - -
278A PRO* 3.4 41.3 - - + +
290A CYS* 1.3 72.6 - - - +
292A ILE* 1.3 60.1 + - - +
293A PHE* 3.4 21.1 - - + -
289B GLN* 5.2 6.8 + - - -
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Residues in contact with ILE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A CYS* 4.5 0.7 - - - -
24A MET* 4.0 17.0 - - + +
27A TYR* 3.5 16.5 - - + +
28A GLY* 3.2 38.4 - - - +
30A TYR 3.3 7.9 - - - +
31A TYR* 4.3 8.7 - - + -
276A PHE* 5.6 1.9 - - - +
277A SER 4.9 6.7 + - - +
278A PRO* 5.2 0.2 - - - +
279A ILE* 3.5 30.2 - - + +
290A CYS* 3.0 36.3 + - + +
291A TYR* 1.3 77.4 - - - +
293A PHE* 1.3 69.4 + - - +
294A ASP* 5.4 0.7 - - - +
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Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A MET* 3.4 37.9 - - + -
27A TYR 5.1 0.4 - - - -
28A GLY* 3.4 4.8 - - - -
29A ARG 3.0 22.5 + - - -
30A TYR* 2.8 22.2 + - + +
31A TYR* 4.1 1.1 - - - -
32A ILE* 3.9 21.5 - - + -
49A PRO* 3.6 26.0 - - + -
51A ARG* 3.9 8.3 - - - +
273A ILE* 4.4 4.0 - - + -
276A PHE* 3.4 46.0 - + + -
291A TYR* 3.4 39.0 - - + -
292A ILE* 1.3 76.0 - - - +
294A ASP* 1.3 64.6 + - - +
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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