Contacts of the strand formed by residues 289 - 293 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ILE* 4.9 1.4 + - - +
274A TYR* 3.5 43.6 + - + +
276A PHE 4.9 5.9 + - - -
291A TYR* 5.2 6.1 + - - -
33B ALA* 3.9 1.2 - - - -
34B ALA* 3.0 34.2 + - + +
35B SER 4.7 0.5 + - - -
38B LYS* 2.8 34.0 + - - +
227B GLU* 4.9 1.7 + - - +
278B PRO* 4.3 21.6 - - + +
279B ILE 3.4 13.3 - - - +
280B TYR* 4.7 2.7 - - - -
281B THR* 3.5 3.8 - - - -
287B PHE* 3.4 4.4 - - - +
288B GLN* 1.3 84.2 - - + +
290B CYS* 1.3 65.4 + - - +
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Residues in contact with CYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B MET* 4.1 10.5 - - - -
31B TYR* 3.9 17.9 - - + -
32B ILE 3.6 6.1 - - - +
33B ALA* 4.1 2.7 - - - -
34B ALA 4.1 0.9 - - - +
278B PRO* 3.9 4.3 - - - -
279B ILE* 2.9 34.9 + - - +
281B THR* 3.6 24.0 + - + -
287B PHE* 3.7 28.0 - - - -
289B GLN* 1.3 79.3 - - - +
291B TYR* 1.3 61.2 + - - +
292B ILE* 3.5 15.8 + - + -
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Residues in contact with TYR 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLN* 5.2 6.4 + - - -
31B TYR* 3.0 7.1 - - - +
32B ILE* 2.8 42.5 + - + +
34B ALA* 3.9 23.6 - - + -
37B VAL* 3.9 31.5 - - + +
273B ILE* 3.7 31.8 + - + +
276B PHE* 3.5 22.8 + - + -
277B SER 4.0 5.4 - - - -
278B PRO* 3.4 42.0 - - + +
290B CYS* 1.3 72.5 - - - +
292B ILE* 1.3 60.1 + - - +
293B PHE* 3.5 22.2 - - + -
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Residues in contact with ILE 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B CYS* 4.2 7.4 - - - -
24B MET* 4.0 17.3 - - + +
27B TYR* 3.6 12.6 - - + +
28B GLY* 3.3 37.5 - - - +
30B TYR 3.3 6.7 - - - +
31B TYR* 3.5 24.9 - - + -
276B PHE* 5.7 1.6 - - - +
277B SER 4.8 7.8 + - - +
279B ILE* 3.5 34.3 - - + +
290B CYS* 3.5 14.0 + - + -
291B TYR* 1.3 75.8 - - - +
293B PHE* 1.3 69.0 + - - +
294B ASP* 5.3 0.5 - - - +
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Residues in contact with PHE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B MET* 3.3 40.6 - - + -
27B TYR 5.1 0.2 - - - -
28B GLY* 3.5 3.7 - - - -
29B ARG 3.0 22.3 + - - -
30B TYR* 2.8 21.5 + - + +
31B TYR* 4.2 1.1 - - - -
32B ILE* 3.9 22.2 - - + -
49B PRO* 3.6 22.2 - - + -
51B ARG* 3.9 9.0 - - - +
273B ILE* 4.3 4.3 - - + -
276B PHE* 3.5 46.0 - + + -
291B TYR* 3.5 37.5 - - + -
292B ILE* 1.3 76.2 - - - +
294B ASP* 1.3 64.3 + - - +
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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