Contacts of the helix formed by residues 52 - 62 (chain A) in PDB entry 2LI6
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 PHE 52 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASN* 5.7 6.5 - - - -
20A TYR* 5.2 20.2 - + + -
50A ASN* 3.1 16.8 + - - +
51A LEU* 1.3 84.7 - - + +
53A TYR* 1.3 59.8 + - - +
55A TYR* 3.9 8.3 - + + +
56A MET* 3.0 43.7 + - + +
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Residues in contact with TYR 53 (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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13A THR* 5.0 21.4 - - + -
17A ASN* 5.7 6.3 - - + -
21A GLU* 2.9 40.2 - - + +
46A ASN* 3.8 20.2 + - - +
47A ARG 3.3 17.7 - - - -
48A LYS* 3.5 23.0 - - + -
50A ASN* 3.5 10.8 + - + +
52A PHE* 1.3 76.0 - - - +
54A LEU* 1.3 64.7 - - - +
55A TYR 3.1 1.6 - - - -
56A MET* 3.2 5.6 + - + +
57A LEU* 3.0 40.0 + - + +
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Residues in contact with LEU 54 (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 LYS* 2.9 24.8 + - + +
49A ILE* 4.3 9.4 - - + +
50A ASN 3.0 19.1 + - - +
51A LEU* 5.1 1.6 - - - +
53A TYR* 1.3 77.7 - - - +
55A TYR* 1.3 58.9 + - - +
57A LEU* 3.8 6.8 + - + +
58A VAL* 2.9 39.6 + - + +
80A LEU* 4.3 19.3 - - + -
82A ILE* 4.5 14.8 - - + -
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Residues in contact with TYR 55 (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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51A LEU 3.3 22.0 + - - +
52A PHE* 3.7 9.1 + + + +
53A TYR 3.1 0.4 - - - -
54A LEU* 1.3 79.6 - - - +
56A MET* 1.3 66.8 + - + +
58A VAL* 3.2 12.2 + - + +
59A GLN* 3.0 38.7 + - + +
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Residues in contact with MET 56 (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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52A PHE* 3.0 33.3 + - + +
53A TYR* 3.2 6.7 + - + +
55A TYR* 1.3 78.4 - - + +
57A LEU* 1.3 57.2 + - - +
59A GLN* 3.5 33.0 + - - +
60A LYS* 2.9 49.6 + - + +
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Residues in contact with LEU 57 (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 LYS* 4.6 21.8 - - + -
53A TYR* 3.0 36.4 + - + +
54A LEU* 3.9 8.5 - - + +
56A MET* 1.3 77.9 - - - +
58A VAL* 1.3 63.3 + - + +
60A LYS* 3.2 13.9 + - + +
61A PHE* 2.9 42.1 + - + -
76A VAL* 4.1 25.8 - - + -
80A LEU* 4.6 8.7 - - + -
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Residues in contact with VAL 58 (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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54A LEU* 2.9 30.5 - - + +
55A TYR* 3.2 13.4 + - + +
57A LEU* 1.3 77.8 - - + +
59A GLN* 1.3 56.0 + - - +
61A PHE* 3.1 14.3 + - - +
62A GLY 3.1 0.2 + - - -
63A GLY* 2.7 30.7 + - - -
64A ALA* 3.2 38.1 - - + +
67A VAL* 5.2 5.2 - - + -
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Residues in contact with GLN 59 (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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55A TYR* 3.0 31.5 + - + +
56A MET* 3.5 30.1 - - - +
58A VAL* 1.3 78.6 - - - +
60A LYS* 1.3 63.3 + - - +
62A GLY* 3.2 12.6 + - - -
63A GLY* 4.2 5.4 - - - +
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Residues in contact with LYS 60 (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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56A MET* 2.9 37.5 + - + +
57A LEU* 3.4 13.2 - - + +
58A VAL 3.1 0.2 - - - -
59A GLN* 1.3 75.9 - - - +
61A PHE* 1.3 65.7 + - + +
62A GLY* 3.1 6.0 + - - -
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Residues in contact with PHE 61 (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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57A LEU* 2.9 39.5 + - + +
58A VAL* 3.1 9.4 + - - +
60A LYS* 1.3 79.4 - - + +
62A GLY* 1.3 58.7 + - - +
66A GLN* 2.9 29.3 - - - +
67A VAL* 3.6 31.6 - - + -
72A GLN* 4.6 11.4 - - + -
76A VAL* 3.6 33.7 - - + -
79A ARG* 5.8 6.1 - - - -
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Residues in contact with GLY 62 (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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58A VAL 3.1 1.0 + - - -
59A GLN* 3.2 8.0 + - - -
60A LYS 3.1 6.4 + - - -
61A PHE* 1.3 78.8 - - - +
63A GLY* 1.3 61.1 + - - +
65A ASP* 5.0 2.4 + - - +
66A GLN* 3.3 34.4 + - - +
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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