Contacts of the helix formed by residues 249 - 254 (chain B) in PDB entry 3LXA
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 ASN 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209B TRP* 3.7 10.2 - - + -
245B TRP* 3.0 68.9 + - + +
246B THR 2.9 6.3 + - - +
248B PHE* 1.3 92.7 - - - +
250B GLN* 1.3 63.4 + - - +
251B GLU* 3.0 5.3 + - - -
252B ARG* 3.0 44.1 + - - +
253B ILE* 3.5 14.9 + - + +
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Residues in contact with GLN 250 (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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246B THR* 2.8 13.5 + - + +
247B SER* 3.3 19.2 + - - +
248B PHE 3.4 1.4 - - - +
249B ASN* 1.3 77.4 - - - +
251B GLU* 1.3 61.7 + - + +
253B ILE* 3.8 4.3 - - - -
254B VAL* 2.9 44.2 + - + +
329B TYR* 3.5 9.3 - - - +
330B GLN* 2.9 53.3 + - - +
340B TRP* 5.2 1.4 - - - -
804B GLA 3.1 37.3 + - - +
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Residues in contact with GLU 251 (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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248B PHE 5.0 1.7 + - - +
249B ASN 3.1 1.8 - - - -
250B GLN* 1.3 81.6 - - + +
252B ARG* 1.3 60.6 + - - +
254B VAL 4.8 0.7 + - - -
255B ASP* 5.3 7.1 + - - +
804B GLA 3.1 38.6 + - - +
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Residues in contact with ARG 252 (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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209B TRP* 3.3 28.5 - - - -
213B LYS* 4.3 26.9 - - - +
214B PRO 4.6 8.5 - - - +
216B TYR* 4.1 23.0 - - + +
248B PHE* 6.0 1.0 - - - -
249B ASN* 3.0 37.7 + - - +
251B GLU* 1.3 80.0 - - - +
253B ILE* 1.3 62.2 + - + +
255B ASP 5.3 0.6 + - - -
256B VAL* 3.7 13.2 + - - +
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Residues in contact with ILE 253 (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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209B TRP* 5.4 1.1 - - + -
216B TYR* 3.5 39.5 - - + +
228B ASN* 3.7 17.0 - - - +
245B TRP* 4.2 15.3 - - + -
246B THR* 3.9 30.1 - - + +
249B ASN* 3.5 19.1 - - + +
250B GLN* 3.2 6.2 + - - -
252B ARG* 1.3 81.8 - - + +
254B VAL* 1.3 68.2 + - + +
255B ASP 3.3 2.5 - - - -
256B VAL* 2.8 19.2 - - + +
257B ALA 3.8 0.3 + - - -
263B ASN* 2.8 34.1 + - + +
327B GLN* 4.7 2.5 - - - +
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Residues in contact with VAL 254 (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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246B THR* 5.8 2.0 - - + -
250B GLN* 2.9 35.2 + - + +
253B ILE* 1.3 80.8 - - + +
255B ASP* 1.3 62.7 + - - +
257B ALA* 3.3 21.0 + - - +
326B LYS* 6.0 2.6 - - + +
327B GLN* 3.3 46.3 + - + +
328B GLY 3.6 19.7 - - - +
329B TYR* 4.3 4.9 - - + -
804B GLA 3.0 33.2 - - - +
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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