Contacts of the helix formed by residues 105 - 111 (chain B) in PDB entry 1LL9
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 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A THR 4.8 4.9 + - - +
85B LEU 3.4 10.6 + - - -
86B SER* 3.5 20.4 - - - +
87B ASP 3.3 14.1 - - - +
88B PRO* 4.6 3.6 - - + -
89B THR* 3.7 8.2 + - - -
103B GLY* 4.2 8.5 - - - +
104B ILE* 1.3 77.7 - - - +
106B LEU* 1.3 65.1 - - - +
107B LEU* 3.3 15.6 + - - +
108B HIS* 3.0 36.2 + - + +
109B LEU* 3.2 10.6 + - - +
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Residues in contact with LEU 106 (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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83B ILE* 4.0 25.8 - - + -
84B LYS 3.5 14.4 - - - +
85B LEU* 3.5 10.5 + - - +
87B ASP 3.1 15.8 + - - +
89B THR* 4.3 13.9 - - - -
92B TYR* 3.5 39.5 - - + -
105B THR* 1.3 72.5 - - - +
107B LEU* 1.3 66.5 + - - +
109B LEU* 3.2 16.6 + - + +
110B ALA* 2.9 25.1 + - - +
158B PHE* 3.5 19.9 - - + -
161B LEU* 4.4 15.9 - - + -
162B ALA* 5.4 3.1 - - - -
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Residues in contact with LEU 107 (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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302A THR* 4.6 12.3 - - + +
303A PRO* 3.7 27.1 - - + -
85B LEU* 3.0 34.3 + - + +
105B THR* 3.1 6.7 - - - +
106B LEU* 1.3 77.5 - - - +
108B HIS* 1.3 59.2 + - + +
110B ALA* 3.3 1.0 + - - -
111B THR* 2.7 49.0 + - + +
259B TYR* 3.7 32.8 - - + +
260B TRP* 4.0 28.5 - - + +
269B LEU* 4.9 1.8 - - + -
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Residues in contact with HIS 108 (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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103B GLY 3.3 20.8 + - - -
104B ILE* 3.6 5.5 - - + -
105B THR* 3.0 38.2 + - + +
107B LEU* 1.3 82.2 - - + +
109B LEU* 1.3 62.6 + - - +
112B TYR 3.1 4.7 + - - -
113B THR* 2.9 43.5 + - - -
114B ALA* 3.6 20.3 + - - -
144B PRO* 3.8 11.5 - - + +
145B GLY* 3.6 26.9 + - - -
154B SER* 3.7 0.7 + - - -
260B TRP* 4.1 12.2 - + - -
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Residues in contact with LEU 109 (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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89B THR* 3.6 33.0 - - + +
101B TRP* 4.1 15.3 - - + -
104B ILE* 4.5 0.9 - - + -
105B THR 3.2 8.0 + - - +
106B LEU* 3.2 15.3 + - + +
108B HIS* 1.3 79.4 - - - +
110B ALA* 1.3 63.4 + - - +
111B THR 3.3 0.7 + - - -
112B TYR 3.6 1.2 + - - -
114B ALA* 4.4 4.5 - - + -
117B LEU* 3.6 30.1 - - + -
154B SER* 2.6 45.1 + - - +
155B ILE* 3.2 2.3 + - - -
157B LEU* 3.9 22.0 - - + -
158B PHE* 3.9 12.6 - - + +
161B LEU* 4.0 6.7 - - + -
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Residues in contact with ALA 110 (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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85B LEU* 4.8 0.2 - - + -
106B LEU 2.9 16.5 + - - +
107B LEU* 3.8 5.4 - - - +
109B LEU* 1.3 76.4 - - - +
111B THR* 1.3 60.9 + - - +
112B TYR* 3.6 5.2 + - - -
155B ILE* 4.0 21.6 - - + +
158B PHE* 3.6 38.3 - - + +
268B GLY 4.5 5.7 - - - +
269B LEU* 4.0 19.9 - - + -
270B GLY 4.5 4.2 + - - -
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Residues in contact with THR 111 (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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107B LEU* 2.7 38.0 + - + +
109B LEU 3.2 0.2 - - - -
110B ALA* 1.3 79.7 - - - +
112B TYR* 1.3 78.7 + - - +
113B THR* 2.9 19.1 + - - +
148B ARG* 4.0 3.8 - - - +
259B TYR* 4.4 4.7 - - + -
260B TRP* 2.9 34.1 + - + -
267B GLN* 3.8 15.0 - - + +
268B GLY 3.8 19.1 - - - +
269B LEU* 4.4 7.9 - - + -
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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