Contacts of the helix formed by residues 249 - 254 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A TRP* 3.5 25.6 - - - -
245A TRP* 3.0 67.5 + - + +
246A THR 3.3 3.6 - - - +
248A PHE* 1.3 88.2 - - - +
250A GLN* 1.3 63.9 + - - +
251A GLU 3.6 1.6 - - - -
252A ARG* 3.3 39.7 + - + +
253A ILE* 3.5 10.3 - - + +
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Residues in contact with GLN 250 (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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246A THR* 3.0 11.2 + - + +
247A SER* 3.0 25.2 + - - +
248A PHE 3.3 2.0 + - - -
249A ASN* 1.3 74.1 - - - +
251A GLU* 1.3 72.7 + - + +
253A ILE* 2.8 15.4 + - - -
254A VAL* 2.9 30.5 + - + +
329A TYR* 3.2 13.2 - - - +
330A GLN* 2.8 53.4 + - - +
340A TRP* 5.3 0.5 - - - -
803A GLA 3.8 24.1 + - - +
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Residues in contact with GLU 251 (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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248A PHE 5.3 0.4 + - - -
249A ASN 3.6 0.4 - - - -
250A GLN* 1.3 82.5 - - + +
252A ARG* 1.3 60.9 + - - +
253A ILE 3.4 0.2 + - - -
254A VAL* 4.5 2.3 + - - -
255A ASP* 5.0 10.9 + - - +
803A GLA 2.6 44.5 + - - -
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Residues in contact with ARG 252 (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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209A TRP* 3.9 24.7 - - - -
210A PRO 4.9 6.1 + - - -
212A GLN 5.8 0.4 - - - -
213A LYS* 4.6 22.1 - - - +
214A PRO* 3.5 28.0 - - - +
216A TYR* 3.9 36.5 + - + +
245A TRP* 4.7 4.4 - - - -
249A ASN* 3.3 35.7 + - - +
250A GLN 3.0 0.4 - - - -
251A GLU* 1.3 80.2 - - - +
253A ILE* 1.3 61.9 + - - +
256A VAL* 4.3 4.6 - - - +
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Residues in contact with ILE 253 (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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216A TYR* 3.5 38.8 - - + +
228A ASN* 4.2 4.0 - - - +
245A TRP* 4.1 22.7 - - + -
246A THR* 4.1 27.1 - - + +
249A ASN* 3.5 17.5 - - + +
250A GLN* 2.8 16.3 + - - +
252A ARG* 1.3 81.4 - - - +
254A VAL* 1.3 65.3 + - + +
255A ASP 3.3 2.0 - - - -
256A VAL* 2.8 25.6 - - + +
263A ASN* 2.8 36.8 + - + +
327A GLN* 4.6 2.5 - - - +
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Residues in contact with VAL 254 (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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246A THR* 5.8 1.8 - - + -
250A GLN* 2.9 39.9 + - + +
251A GLU 4.5 0.2 + - - -
253A ILE* 1.3 80.7 - - + +
255A ASP* 1.3 66.1 + - - +
257A ALA* 3.3 19.8 + - - +
326A LYS* 6.1 1.1 - - + +
327A GLN* 3.2 48.2 + - + +
328A GLY 3.5 17.9 - - - +
329A TYR* 4.4 4.3 - - + -
803A GLA 3.3 26.2 - - - +
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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