Contacts of the strand formed by residues 242 - 249 (chain I) in PDB entry 1LWU
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 TYR 242 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153I ASP* 2.4 39.1 + - + +
192I THR* 4.7 2.2 - - + -
236I LEU* 2.9 33.3 - - + +
237I THR* 3.7 15.3 - - - -
239I GLN* 3.0 18.4 + - - -
240I GLN* 3.5 26.1 + - + -
241I ALA* 1.3 77.2 - - - +
243I ARG* 1.3 60.1 + - - +
244I LEU 3.8 0.2 - - - -
262I HIS* 3.0 8.1 + - - +
263I PHE* 2.8 43.4 + - + +
384I LEU* 4.0 27.1 - - + -
385I LEU* 3.3 25.1 - - - -
386I PRO* 3.6 13.7 - - + -
387I MET* 4.0 1.6 - - - -
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Residues in contact with ARG 243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191I TRP* 3.7 21.5 - - - -
242I TYR* 1.3 69.9 - - - +
244I LEU* 1.3 68.4 + - - +
245I ARG* 4.5 1.2 - - - +
259I ASP* 3.1 26.1 + - + +
260I TYR 3.4 9.4 - - - +
280I LEU* 3.9 27.5 + - - +
281I ASP* 5.4 3.8 - - - +
384I LEU* 3.6 2.1 - - - -
385I LEU* 2.6 41.3 + - - +
386I PRO 4.9 1.1 - - - +
387I MET* 3.1 52.9 + - + +
389I ARG 4.7 0.8 + - - -
390I ASP* 4.4 31.9 + - - +
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Residues in contact with LEU 244 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194I ILE* 5.8 0.4 - - + -
242I TYR 3.7 2.4 + - - -
243I ARG* 1.3 74.0 - - - +
245I ARG* 1.3 75.9 + - - +
246I ILE* 4.2 12.8 - - + -
259I ASP* 3.3 7.3 - - - +
260I TYR* 2.8 42.0 + - + +
263I PHE* 3.3 47.5 - - + +
288I PHE* 4.2 21.8 - - + -
382I MET* 4.0 27.4 - - + -
383I LYS 3.4 11.7 - - - +
384I LEU* 3.5 15.9 - - + -
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Residues in contact with ARG 245 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186I GLU* 4.6 11.1 + - - -
191I TRP* 3.6 41.4 - - + -
243I ARG* 3.8 5.1 + - - +
244I LEU* 1.3 74.7 - - - +
246I ILE* 1.3 68.9 + - - +
247I ASP* 3.4 26.5 - - - +
257I TYR* 3.7 19.0 + - + -
258I ALA 3.4 2.9 - - - +
259I ASP* 3.0 33.1 + - - +
381I THR 3.4 1.2 - - - +
382I MET* 3.3 4.9 - - - -
383I LYS* 2.7 55.0 + - + +
390I ASP* 4.5 8.5 + - - -
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Residues in contact with ILE 246 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244I LEU* 4.2 17.3 - - + -
245I ARG* 1.3 78.7 - - - +
247I ASP* 1.3 62.0 + - - +
248I LEU* 3.3 35.1 - - + +
257I TYR* 3.1 9.2 - - - +
258I ALA* 2.9 33.9 + - + +
260I TYR* 4.4 6.3 - - + -
288I PHE* 3.9 20.2 - - + -
342I LEU* 3.6 20.2 - - + -
367I TRP* 3.6 35.0 - - + -
381I THR 3.3 6.3 - - - +
382I MET* 4.5 5.8 - - + -
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Residues in contact with ASP 247 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184I GLU* 4.9 0.7 - - - +
245I ARG* 3.4 22.5 - - - +
246I ILE* 1.3 73.4 - - - +
248I LEU* 1.3 62.0 + - - +
249I THR* 4.9 1.9 + - - +
255I HIS* 6.3 2.2 - - + -
256I ARG 3.8 4.4 - - - +
257I TYR* 3.6 10.9 - - - +
379I MET* 4.3 0.5 - - - +
380I THR* 3.3 6.6 + - - -
381I THR* 3.0 45.6 + - + +
383I LYS* 3.1 34.0 + - - +
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Residues in contact with LEU 248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246I ILE* 3.3 43.1 - - + +
247I ASP* 1.3 79.7 - - - +
249I THR* 1.3 69.9 + - - +
254I THR 3.5 0.8 - - - +
255I HIS* 3.5 19.9 - - - +
256I ARG 3.2 13.5 + - - +
258I ALA 5.0 0.2 - - - +
284I ALA* 4.3 17.9 - - + -
342I LEU* 3.5 22.7 - - + -
367I TRP* 4.3 15.7 - - + +
370I TRP* 3.9 14.8 - - + -
377I LEU* 3.5 22.9 - - + -
379I MET 3.8 2.9 - - - -
380I THR* 3.8 11.2 - - + +
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Residues in contact with THR 249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247I ASP* 4.9 2.3 + - - +
248I LEU* 1.3 82.5 + - - +
250I ASP* 1.3 67.4 + - - +
253I ASN* 4.0 7.4 - - - +
254I THR 3.1 10.8 - - - +
255I HIS* 3.2 31.7 - - - +
377I LEU* 3.5 6.6 - - - +
378I LYS* 2.7 48.1 + - - +
379I MET* 3.3 34.0 + - + +
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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