Contacts of the helix formed by residues 46 - 51 (chain A) in PDB entry 3LX9
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 HIS 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A TRP* 3.3 33.8 - - + -
45A LEU* 1.3 72.6 - - - +
47A TRP* 1.3 66.1 + - - +
48A GLU 3.5 0.3 + - - -
49A ARG 3.5 1.4 + - - -
50A PHE* 2.9 33.6 + - + +
51A MET 2.9 29.6 + - - -
64A ILE* 3.5 28.4 - - + +
68A LEU* 4.7 1.8 - - + -
69A PHE* 3.4 18.3 - + + -
90A CYS 3.6 6.5 + - - -
91A ILE* 4.5 0.2 - - + -
92A ASP* 3.1 36.3 + - + -
93A ASP 3.3 21.0 + - - -
297A SER* 3.5 2.4 + - - -
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Residues in contact with TRP 47 (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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45A LEU* 3.2 4.4 + - + -
46A HIS* 1.3 85.1 + - - +
48A GLU* 1.3 65.4 + - - +
51A MET* 2.7 84.1 + - + +
52A CYS* 3.7 21.1 - - + -
92A ASP* 3.6 34.7 - - - +
93A ASP* 3.8 12.3 - - + -
94A CYS* 4.2 2.9 - - - -
143A ALA* 4.8 2.9 - - + -
231A ASP* 4.6 8.2 + - + +
232A ILE 6.0 0.9 - - - -
267A MET* 4.2 19.1 - - + -
1000A A2G 3.3 50.6 - - - -
359B ILE* 4.9 8.6 - - + +
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Residues in contact with GLU 48 (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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47A TRP* 1.3 86.1 - - + +
49A ARG* 1.3 61.1 + - - +
51A MET* 3.6 2.4 - - - +
232A ILE* 4.2 17.3 - - + +
233A ASP* 4.3 1.1 - - - -
234A ASP* 3.4 26.8 + - - +
267A MET* 3.8 13.2 - - + -
269A VAL* 3.6 23.3 - - + -
272A ASN* 3.2 26.7 + - - +
297A SER* 3.0 18.3 + - - +
359B ILE* 3.4 10.6 - - + +
360B GLY* 2.9 44.5 + - - +
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Residues in contact with ARG 49 (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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48A GLU* 1.3 84.1 - - - +
50A PHE* 1.3 88.7 + - + +
271A GLY 4.2 9.1 + - - -
272A ASN* 2.9 24.5 + - - +
273A PHE* 3.4 32.8 - - - -
297A SER* 3.1 6.8 + - - +
298A ASN* 3.8 26.5 - - - +
299A ASP* 3.5 35.4 + - - +
302A HIS* 4.6 11.1 + - - +
360B GLY* 3.3 14.1 - - - -
361B GLY* 3.2 30.5 + - - -
362B PRO* 4.5 6.9 - - - +
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Residues in contact with PHE 50 (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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44A TRP* 3.8 20.2 - + - -
46A HIS* 2.9 16.3 + - + +
49A ARG* 1.3 100.2 - - + +
51A MET* 1.3 73.5 + - - +
52A CYS 3.4 1.0 + - - -
53A ASN* 3.6 19.6 + - - +
62A SER* 3.3 32.3 - - - +
64A ILE* 3.6 17.6 - - + +
68A LEU* 3.9 13.2 - - + -
72A MET* 3.9 7.6 - - + -
298A ASN 3.6 15.0 - - - -
299A ASP* 3.7 18.2 - - + -
301A ARG* 3.5 29.4 - - - -
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Residues in contact with MET 51 (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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46A HIS* 2.9 27.3 + - - -
47A TRP* 2.7 63.2 + - + +
48A GLU 3.6 9.0 - - - +
50A PHE* 1.3 75.0 - - - +
52A CYS* 1.3 60.0 + - - +
53A ASN 4.9 0.2 - - - +
64A ILE* 3.4 5.4 - - - +
93A ASP 4.3 0.3 - - - +
357B GLN* 4.2 9.2 - - - +
359B ILE* 3.7 38.8 - - + +
360B GLY* 3.6 24.5 - - - -
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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