Contacts of the helix formed by residues 104 - 112 (chain B) in PDB entry 3T3Q
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 GLN 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B GLU* 1.3 73.6 - - - +
105B ALA* 1.3 59.9 + - - +
106B THR* 3.0 16.0 + - - -
107B PHE* 3.1 27.5 + - + +
108B ASP* 2.8 28.5 + - - +
118B PHE* 3.7 26.7 - - + -
212B THR* 3.9 21.6 - - - +
217B GLY 5.4 0.2 + - - -
218B GLN* 4.6 2.0 - - - +
221B GLU* 2.9 31.2 + - - +
370B LEU* 4.0 6.5 - - + -
480B PHE* 3.9 28.8 - - + +
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Residues in contact with ALA 105 (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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76B ARG* 4.6 2.6 - - - +
103B GLU* 4.1 13.3 + - - +
104B GLN* 1.3 67.7 - - - +
106B THR* 1.3 66.3 + - - +
108B ASP* 3.3 9.8 + - - +
109B TRP* 3.1 19.1 + - - +
220B TYR* 3.5 28.8 + - + +
221B GLU* 2.8 27.6 + - - +
224B SER* 3.8 17.7 - - - +
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Residues in contact with THR 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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104B GLN* 3.0 10.5 + - - -
105B ALA* 1.3 79.0 - - - +
107B PHE* 1.3 67.8 + - + +
109B TRP* 3.2 18.6 - - - +
208B SER* 4.8 2.9 - - - +
211B PHE* 3.4 33.1 - - + -
212B THR* 3.6 25.4 - - + +
217B GLY 4.5 3.3 + - - -
220B TYR* 3.6 15.5 - - - -
221B GLU* 3.3 6.0 + - - -
237B ALA* 5.0 4.5 - - + -
238B PHE* 4.9 6.7 - - + -
241B LEU* 3.4 19.8 - - + +
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Residues in contact with PHE 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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104B GLN* 3.1 29.0 + - + +
106B THR* 1.3 74.0 - - + +
108B ASP* 1.3 65.2 + - - +
110B VAL* 3.1 6.6 + - - +
111B PHE* 3.1 37.5 + + + -
118B PHE* 3.7 21.5 - - + -
208B SER* 4.7 5.6 - - - -
209B PHE* 4.7 5.2 - + - -
212B THR* 3.8 22.7 - - + -
241B LEU* 4.3 19.7 - - + -
300B PHE* 3.9 17.9 - + - -
480B PHE* 3.7 33.9 - + - -
501B 9PL 3.4 42.2 - + + -
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Residues in contact with ASP 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 GLU* 4.8 15.5 - - + +
104B GLN 2.8 24.2 + - - +
105B ALA* 3.3 11.5 + - - +
107B PHE* 1.3 68.4 - - - +
109B TRP* 1.3 64.0 + - - +
111B PHE* 4.3 3.1 - - - +
112B LYS* 2.8 48.6 + - - +
113B GLY* 3.8 6.2 + - - -
118B PHE* 4.9 8.6 - - + +
228B LYS* 5.5 4.9 + - - -
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Residues in contact with TRP 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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105B ALA 3.1 11.2 + - - +
106B THR 3.2 15.5 - - - +
107B PHE 3.2 0.4 - - - -
108B ASP* 1.3 77.7 + - - +
110B VAL* 1.3 71.8 + - + +
112B LYS* 3.6 21.2 - - - +
220B TYR* 4.0 7.4 - - - +
228B LYS* 4.5 22.5 + - + +
235B GLN* 5.9 0.2 - - - -
238B PHE* 3.4 81.8 - + + -
239B GLN* 5.4 4.9 - - - -
241B LEU* 4.4 2.7 - - + -
242B GLN* 3.9 31.0 - - + -
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Residues in contact with VAL 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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106B THR 4.3 0.6 + - - -
107B PHE 3.1 12.8 + - - +
109B TRP* 1.3 88.5 - - + +
111B PHE* 1.3 95.6 + - + +
112B LYS* 3.5 9.6 + - - +
241B LEU* 4.0 37.5 - - + +
242B GLN 4.7 0.7 - - - +
245B GLU* 3.3 40.8 - - + +
289B LYS* 4.7 0.2 + - - -
293B MET* 3.2 22.1 - - + +
296B LEU* 4.4 5.8 - - + -
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Residues in contact with PHE 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 PHE* 3.1 33.2 + + + +
108B ASP* 4.7 0.9 - - - -
110B VAL* 1.3 88.8 - - + +
112B LYS* 1.3 69.2 + - - +
113B GLY 4.4 2.2 - - - +
114B TYR* 2.9 35.7 + - - +
118B PHE* 3.5 26.2 - + + -
241B LEU* 6.0 0.9 - - + -
289B LYS* 4.6 1.0 - - - -
293B MET* 3.6 30.5 - - + +
296B LEU* 3.7 35.4 - - + -
297B ASN* 3.2 25.6 - - - -
300B PHE* 5.3 4.3 - + - -
501B 9PL 3.3 26.0 - + - -
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Residues in contact with LYS 112 (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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108B ASP* 2.8 38.1 + - - +
109B TRP* 3.6 17.7 - - - +
110B VAL 3.9 8.2 + - - +
111B PHE* 1.3 72.1 - - - +
113B GLY* 1.3 56.6 + - - +
114B TYR* 3.2 24.2 - - + -
123B ARG* 4.8 0.5 + - - -
289B LYS* 4.4 20.0 - - - +
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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