Contacts of the helix formed by residues 106 - 116 (chain B) in PDB entry 3ECS
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 106 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ARG* 3.0 33.2 - - + +
103B ARG* 3.5 13.0 - - - +
105B SER* 1.3 85.3 - - - +
107B SER* 1.3 57.9 + - - +
108B ARG 3.5 1.6 - - - -
109B ASN* 3.3 13.0 + - + +
110B LYS* 2.9 50.8 + - + +
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Residues in contact with SER 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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103B ARG* 3.9 3.5 + - - -
104B ILE* 3.6 27.0 + - - +
105B SER 3.4 0.6 - - - -
106B LEU* 1.3 77.6 - - - +
108B ARG* 1.3 66.1 + - - +
110B LYS* 2.9 4.4 + - - +
111B ILE* 2.8 28.6 + - - +
231B GLU* 3.7 26.0 - - - +
232B SER* 4.8 1.4 + - - -
233B PHE* 4.9 0.5 - - - -
287B ASP* 3.4 36.3 + - - +
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Residues in contact with ARG 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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19B ASP* 2.6 28.0 + - - +
20B MSE 4.4 1.2 - - - +
21B ALA* 3.6 25.9 - - - +
105B SER 5.0 2.5 + - - +
106B LEU 3.5 0.4 - - - -
107B SER* 1.3 78.0 - - - +
109B ASN* 1.3 57.7 + - - +
111B ILE* 3.2 8.9 + - - +
112B ALA* 2.9 29.7 + - - +
132B ARG* 3.3 33.6 - - - +
133B VAL* 3.8 22.7 - - + +
136B ARG* 3.5 52.5 - - + +
231B GLU* 3.2 24.2 + - + +
502B SO4 3.7 8.5 + - - -
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Residues in contact with ASN 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 SER 5.4 1.3 + - - +
106B LEU* 3.3 16.8 + - + +
107B SER 3.2 1.0 - - - -
108B ARG* 1.3 77.7 - - - +
110B LYS* 1.3 62.8 + - + +
112B ALA* 3.5 7.6 + - - +
113B ASP* 3.1 28.8 + - - +
136B ARG* 3.5 27.8 + - - +
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Residues in contact with LYS 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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103B ARG* 5.8 5.4 - - - +
106B LEU* 2.9 36.8 + - + +
107B SER 2.9 5.9 + - - +
109B ASN* 1.3 76.0 - - + +
111B ILE* 1.3 63.0 + - - +
113B ASP* 3.6 6.8 + - - +
114B LEU* 3.2 30.7 + - + +
287B ASP* 4.4 30.1 - - + +
117D THR* 5.4 0.2 - - - +
120D LYS* 5.9 0.4 - - - +
121D ASP* 5.3 7.1 - - - +
146D LYS* 3.4 29.4 - - - +
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Residues in contact with ILE 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 SER 2.8 18.7 + - - +
108B ARG* 3.5 6.7 - - - +
110B LYS* 1.3 74.7 - - - +
112B ALA* 1.3 67.9 + - - +
114B LEU* 2.9 18.7 + - - +
115B CYS* 2.9 13.0 + - - +
133B VAL* 3.9 16.8 - - + -
137B VAL* 4.2 2.0 - - + -
229B VAL* 3.3 33.7 - - + -
230B ALA* 3.4 37.5 - - - +
231B GLU* 3.6 14.8 - - + +
285B PHE* 3.8 8.7 - - + +
286B THR* 3.7 20.6 - - - -
287B ASP 3.8 1.6 - - - +
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Residues in contact with ALA 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 ARG 2.9 16.1 + - - +
109B ASN* 3.8 8.7 - - - +
111B ILE* 1.3 75.2 - - - +
113B ASP* 1.3 58.2 + - - +
116B HIS* 2.9 38.2 + - - +
136B ARG* 3.9 14.6 - - + +
137B VAL* 3.9 33.0 - - - +
140B ALA* 3.9 9.9 - - + -
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Residues in contact with ASP 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 ASN* 3.1 18.4 + - - +
110B LYS* 3.6 8.5 - - - +
111B ILE 3.1 0.4 - - - -
112B ALA* 1.3 81.4 - - - +
114B LEU* 1.3 59.7 + - + +
116B HIS* 3.2 26.4 + - - -
117B THR* 4.0 5.2 + - - -
140B ALA* 5.5 2.9 - - - +
113D ASP 4.8 1.6 - - - +
116D HIS* 2.4 40.1 + - - -
117D THR* 3.8 15.7 + - + +
144D ALA* 4.4 8.2 - - - +
146D LYS* 6.0 0.9 - - - -
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Residues in contact with LEU 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 LYS* 3.2 20.4 + - + +
111B ILE* 2.9 8.3 + - - +
113B ASP* 1.3 78.2 - - - +
115B CYS* 1.3 62.6 + - - +
117B THR* 4.3 4.3 + - - -
118B PHE* 3.7 21.8 - - - -
285B PHE* 3.8 12.6 - - + -
286B THR 3.1 30.1 - - - +
287B ASP* 5.0 2.7 - - - +
289B GLY* 3.8 16.8 - - - +
290B VAL* 3.6 22.1 - - + +
117D THR* 3.1 34.5 - - + -
118D PHE* 5.3 6.3 - - + -
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Residues in contact with CYS 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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111B ILE 2.9 13.9 + - - +
114B LEU* 1.3 75.2 - - - +
116B HIS* 1.3 63.5 + - - +
117B THR 3.1 2.9 - - - -
118B PHE* 3.0 19.1 + - - +
119B ILE* 4.2 4.2 + - - +
137B VAL* 3.7 22.0 - - + -
194B ILE* 4.3 19.7 - - - -
227B TYR* 5.1 5.8 - - - -
229B VAL* 4.1 11.2 - - + -
285B PHE* 3.5 42.8 - - + -
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Residues in contact with HIS 116 (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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112B ALA 2.9 22.8 + - - +
113B ASP* 3.2 36.1 + - - -
115B CYS* 1.3 72.4 - - - +
117B THR* 1.3 80.5 + - - +
118B PHE 3.1 4.7 + - - -
119B ILE* 3.3 23.1 + - - +
137B VAL* 3.9 23.6 - - - +
140B ALA* 4.0 25.4 + - + -
141B ALA* 4.1 3.1 - - - +
144B ALA* 4.7 12.5 - - + +
146B LYS* 3.9 13.2 - - - +
113D ASP* 3.2 29.0 + - - +
116D HIS* 5.1 4.2 - - - -
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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