Contacts of the helix formed by residues 55 - 66 (chain B) in PDB entry 1L9X
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 THR 55 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B ASP 5.6 0.7 - - - +
54B LEU* 1.3 75.8 - - - +
56B GLU* 1.3 65.9 + - - +
57B LYS* 3.5 12.1 + - - +
58B ASP* 2.7 48.2 + - - +
59B TYR* 3.0 18.1 + - - -
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Residues in contact with GLU 56 (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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55B THR* 1.3 72.5 - - - +
57B LYS* 1.3 57.9 + - - +
59B TYR* 3.2 6.4 + - - +
60B GLU* 2.9 59.9 + - - +
89B ILE* 3.2 41.0 - - + +
93B LEU* 4.9 6.4 - - - +
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Residues in contact with LYS 57 (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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55B THR* 3.6 9.8 - - - +
56B GLU* 1.3 79.9 - - - +
58B ASP* 1.3 68.9 + - - +
60B GLU* 3.2 13.6 + - - +
61B ILE* 3.1 48.2 + - + +
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Residues in contact with ASP 58 (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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54B LEU* 3.7 29.8 - - + +
55B THR* 2.7 39.5 + - - +
57B LYS* 1.3 85.1 - - - +
59B TYR* 1.3 58.2 + - - +
61B ILE* 3.2 12.0 + - - +
62B LEU* 2.9 28.9 + - - +
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Residues in contact with TYR 59 (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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50B VAL* 4.1 5.4 - - + -
51B ARG 2.6 29.9 + - - -
52B LEU* 3.0 24.7 - - - -
54B LEU* 3.1 44.3 + - + -
55B THR 3.0 19.3 + - - -
56B GLU 3.2 6.0 + - - +
58B ASP* 1.3 73.6 - - - +
60B GLU* 1.3 61.2 + - - +
62B LEU* 3.7 5.1 - - + +
63B PHE* 2.8 30.9 + - - +
85B LYS* 5.3 3.4 - - - -
86B VAL* 3.5 23.2 - - + +
89B ILE* 3.8 38.8 - - + -
90B PHE* 3.8 23.2 - + + -
93B LEU* 4.2 2.1 - - - +
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Residues in contact with GLU 60 (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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56B GLU* 2.9 50.7 + - - +
57B LYS* 3.2 11.3 + - - +
59B TYR* 1.3 75.5 - - - +
61B ILE* 1.3 64.1 + - + +
63B PHE* 3.5 2.9 + - - +
64B LYS* 3.1 43.8 + - - +
93B LEU* 4.1 23.6 - - + +
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Residues in contact with ILE 61 (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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57B LYS* 3.1 42.3 + - + +
58B ASP* 3.5 12.3 - - - +
60B GLU* 1.3 75.7 - - + +
62B LEU* 1.3 66.4 + - - +
64B LYS* 3.2 12.8 + - + +
65B SER* 2.9 31.6 + - - +
263B LYS* 5.9 11.4 - - + +
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Residues in contact with LEU 62 (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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48B VAL* 4.4 11.7 - - + -
49B PRO 5.4 0.2 - - - +
50B VAL* 3.9 39.3 - - + -
54B LEU* 4.9 9.9 - - + -
58B ASP 2.9 17.2 + - - +
59B TYR* 3.7 11.4 - - + +
61B ILE* 1.3 79.1 - - - +
63B PHE* 1.3 62.7 + - - +
65B SER* 2.9 14.7 + - - -
66B ILE* 3.0 38.2 + - + +
90B PHE* 4.1 9.6 - - + -
262B PHE* 4.2 19.3 - - + -
271B ALA* 5.5 2.0 - - + -
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Residues in contact with PHE 63 (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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59B TYR 2.8 18.5 + - - +
60B GLU* 3.5 4.9 - - - +
62B LEU* 1.3 76.0 - - - +
64B LYS* 1.3 69.0 + - + +
66B ILE* 3.2 11.1 - - - +
90B PHE* 3.9 20.4 - + + -
93B LEU* 3.4 57.2 - - + -
94B SER 3.7 5.2 - - - -
97B SER* 3.7 20.2 - - - -
102B ASP* 4.5 1.3 - - - -
104B PHE* 3.4 50.6 - + + -
260B HIS* 2.9 33.0 + + - -
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Residues in contact with LYS 64 (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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60B GLU* 3.1 29.8 + - - +
61B ILE* 3.2 11.6 + - + +
63B PHE* 1.3 84.0 - - + +
65B SER* 1.3 58.3 + - - +
260B HIS* 3.3 28.9 - - + +
261B HIS 3.6 8.6 + - - +
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Residues in contact with SER 65 (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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11B ILE* 5.4 1.7 - - - +
61B ILE* 2.9 19.9 + - - +
62B LEU* 2.9 10.5 + - - -
64B LYS* 1.3 80.3 - - - +
66B ILE* 1.3 62.1 - - - +
67B ASN* 4.7 1.6 - - - +
260B HIS 3.7 1.2 - - - +
261B HIS* 3.2 31.8 + - - -
262B PHE* 3.7 49.6 + - - -
263B LYS* 4.7 2.4 + - - +
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Residues in contact with ILE 66 (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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11B ILE* 3.6 20.0 - - + +
13B GLY* 4.0 14.8 - - - +
48B VAL* 4.4 8.5 - - + -
50B VAL* 4.9 1.8 - - + -
62B LEU* 3.0 30.9 + - + +
63B PHE 3.2 4.9 - - - +
65B SER* 1.3 79.5 - - - +
67B ASN* 1.3 63.2 + - - +
68B GLY 3.5 19.1 - - - +
69B ILE* 4.4 3.4 - - + -
90B PHE* 4.0 24.7 - - + -
104B PHE* 3.4 11.4 - - + -
260B HIS* 2.8 27.4 + - - +
262B PHE* 4.0 23.3 - - + -
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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