Contacts of the helix formed by residues 107 - 115 (chain B) in PDB entry 4QYJ
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 LEU 107 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B THR* 4.0 0.2 - - - -
105B GLY 3.9 0.4 + - - -
106B LYS* 1.3 75.2 - - - +
108B LEU* 1.3 66.9 + - - +
109B ILE* 4.5 11.4 - - + +
110B TYR* 2.9 46.8 + - + +
111B SER 3.2 8.0 + - - -
297B HIS* 4.8 5.1 + - - +
332B SER 4.3 0.2 - - - +
333B GLY* 3.8 20.6 - - - +
335B GLU 5.0 3.4 - - - +
338B VAL* 3.6 45.1 - - + +
339B HIS* 3.7 18.2 - - - +
340B MET* 5.1 5.8 - - - -
341B GLY 5.2 1.1 - - - +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ASP 5.2 0.9 - - - +
97B ALA* 3.8 30.7 - - + +
98B ARG* 4.1 6.7 - - + +
101B THR* 3.3 10.3 - - - +
106B LYS 3.5 1.8 + - - -
107B LEU* 1.3 71.7 - - - +
109B ILE* 1.3 66.8 + - + +
111B SER* 3.1 12.7 + - - -
112B LYS* 3.2 12.3 + - + +
333B GLY 3.1 19.6 + - - +
334B LEU* 3.4 30.7 - - + +
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Residues in contact with ILE 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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107B LEU* 4.6 11.4 - - + -
108B LEU* 1.3 80.6 - - + +
110B TYR* 1.3 89.5 + - + +
112B LYS* 3.3 6.2 + - - +
113B LEU* 3.1 45.2 + - + +
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Residues in contact with TYR 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 LYS* 4.1 18.4 - - + +
107B LEU* 2.9 43.6 + - + +
109B ILE* 1.3 90.6 - - + +
111B SER* 1.3 59.5 + - - +
112B LYS 3.2 0.2 - - - -
113B LEU* 4.4 7.0 - - + +
114B MET* 3.0 67.5 + - + +
115B GLU 3.7 1.0 + - - -
295B PHE* 5.8 4.3 - + - -
339B HIS 4.9 5.2 - - - -
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Residues in contact with SER 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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97B ALA* 3.5 26.6 - - - -
100B GLU* 3.6 14.1 - - - +
101B THR* 3.4 15.9 + - - -
106B LYS* 3.3 22.2 - - - +
107B LEU 3.2 3.7 + - - -
108B LEU 3.1 11.8 + - - -
110B TYR* 1.3 77.1 - - - +
112B LYS* 1.3 58.4 + - - +
115B GLU* 3.3 8.0 - - - +
116B VAL* 2.9 30.7 + - - +
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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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93B GLY 5.3 1.8 - - - +
97B ALA* 4.2 13.2 - - + -
108B LEU* 3.2 10.8 + - + +
109B ILE* 3.6 11.4 - - - +
110B TYR 3.2 0.2 - - - -
111B SER* 1.3 81.1 - - - +
113B LEU* 1.3 63.9 + - + +
116B VAL* 3.8 9.1 - - - +
117B GLY* 3.5 17.7 + - - -
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Residues in contact with LEU 113 (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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109B ILE* 3.1 35.1 + - + +
110B TYR* 4.5 6.5 - - + +
112B LYS* 1.3 88.0 - - + +
114B MET* 1.3 68.9 - - + +
115B GLU 3.5 1.1 - - - -
117B GLY* 3.7 6.2 - - - +
118B ALA* 3.4 18.4 + - - +
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Residues in contact with MET 114 (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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110B TYR* 3.0 49.1 + - + +
113B LEU* 1.3 87.3 - - + +
115B GLU* 1.3 61.7 + - - +
118B ALA* 3.9 12.2 - - + +
170B PHE* 4.3 19.0 - - + -
173B LEU* 3.7 24.3 - - - +
295B PHE* 3.6 34.3 - - + -
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Residues in contact with GLU 115 (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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100B GLU* 4.6 14.4 - - + +
106B LYS* 5.0 7.2 - - - +
110B TYR 3.7 1.1 + - - +
111B SER* 3.3 20.0 + - - +
113B LEU 3.5 0.2 - - - -
114B MET* 1.3 80.7 - - - +
116B VAL* 1.3 63.9 + - + +
117B GLY 3.4 0.2 - - - -
119B SER* 2.7 30.8 + - - -
170B PHE* 5.2 3.8 - - + -
172B LEU* 3.3 25.5 - - + +
173B LEU* 4.6 6.3 - - + +
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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