Contacts of the helix formed by residues 103 - 113 (chain B) in PDB entry 1B06
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 GLY 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B GLY* 1.3 75.2 - - - +
104B ALA* 1.3 62.9 + - - -
106B ALA* 3.2 7.7 + - - +
107B ASP* 3.3 12.4 + - - +
201B GLU* 3.7 10.1 - - - -
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Residues in contact with ALA 104 (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* 1.3 72.1 - - - -
105B LEU* 1.3 63.6 + - - +
107B ASP* 3.2 10.0 + - - +
108B LEU* 2.9 28.8 + - + +
201B GLU* 3.1 6.4 + - - +
204B LEU* 3.8 5.8 - - + -
205B GLN* 3.5 14.0 - - - +
208B LEU* 3.5 32.8 - - + -
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Residues in contact with LEU 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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101B PRO* 4.0 5.4 - - + -
102B GLY 3.7 4.7 - - - +
104B ALA* 1.3 76.5 - - - +
106B ALA* 1.3 63.5 + - - +
108B LEU* 3.2 2.4 + - - +
109B ILE* 3.0 38.6 + - + +
138B LEU* 4.9 4.3 - - + -
147B LEU* 4.2 18.4 - - + -
166B ILE* 4.2 16.8 - - + -
197B TRP* 3.6 36.6 - - + +
200B ALA* 3.8 20.0 - - + -
201B GLU* 2.9 26.4 + - + +
204B LEU* 3.4 16.5 - - + +
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Residues in contact with ALA 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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100B LYS* 3.8 15.4 + - - +
101B PRO* 3.5 35.7 - - - +
102B GLY* 3.1 18.5 + - - +
103B GLY 3.7 2.2 - - - +
105B LEU* 1.3 77.7 - - - +
107B ASP* 1.3 61.8 + - - +
109B ILE* 3.5 5.1 + - - +
110B ASP* 3.2 29.7 + - - +
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Residues in contact with ASP 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 GLY 3.3 9.6 + - - +
104B ALA* 3.2 13.8 + - - +
105B LEU 3.1 0.2 - - - -
106B ALA* 1.3 78.4 - - - +
108B LEU* 1.3 70.4 + - - +
110B ASP* 3.4 8.7 + - - +
111B LYS* 3.1 62.1 + - - +
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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
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104B ALA* 2.9 19.9 + - + +
105B LEU* 3.8 2.2 - - - +
107B ASP* 1.3 83.1 - - - +
109B ILE* 1.3 60.9 + - - +
111B LYS* 3.3 13.6 + - + +
112B GLN* 2.9 49.5 + - - +
140B TYR* 4.2 24.5 - - + -
145B GLY 4.6 4.5 - - - +
147B LEU* 3.7 25.1 - - + -
204B LEU* 4.3 20.2 - - + -
208B LEU* 4.8 8.1 - - + -
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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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100B LYS* 5.9 0.9 - - - +
101B PRO* 4.0 19.1 - - + -
105B LEU* 3.0 39.8 + - + +
106B ALA* 3.8 5.8 - - - +
108B LEU* 1.3 74.9 - - - +
110B ASP* 1.3 57.3 + - - +
113B TYR* 2.7 37.8 + - - +
114B GLY 3.5 0.5 + - - -
115B SER 3.8 10.3 + - - +
116B PHE* 3.9 13.5 - - + +
119B PHE* 3.8 55.6 - - + -
138B LEU* 5.4 0.7 - - + -
147B LEU* 3.9 14.4 - - + -
197B TRP* 4.8 2.7 - - + -
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Residues in contact with ASP 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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100B LYS* 4.3 13.1 + - - -
106B ALA* 3.2 19.2 + - - +
107B ASP* 3.6 12.1 - - - +
108B LEU 3.2 0.2 - - - -
109B ILE* 1.3 78.8 - - - +
111B LYS* 1.3 60.3 + - + +
114B GLY* 2.8 36.9 + - - +
115B SER* 3.5 19.8 - - - -
116B PHE 4.0 4.9 + - - -
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Residues in contact with LYS 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 ASP* 3.1 47.1 + - - +
108B LEU* 3.3 15.3 + - + +
110B ASP* 1.3 79.8 - - + +
112B GLN* 1.3 62.9 + - + +
114B GLY 4.8 0.5 + - - -
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Residues in contact with GLN 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 LEU* 2.9 34.8 + - - +
111B LYS* 1.3 84.7 - - + +
113B TYR* 1.3 77.3 + - + +
114B GLY 3.7 0.7 - - - -
145B GLY 3.0 27.1 + - - -
146B ASN* 3.6 14.1 + - - +
147B LEU* 2.8 35.6 + - - +
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Residues in contact with TYR 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* 2.7 24.8 + - - +
112B GLN* 1.3 94.9 - - + +
114B GLY* 1.3 58.0 + - - +
115B SER 3.1 8.9 + - - +
118B ARG* 3.3 24.6 - - + +
119B PHE* 3.8 57.2 - + + +
122B VAL* 4.5 17.7 - - + -
138B LEU* 4.5 0.3 - - - +
147B LEU* 2.9 34.0 + - + -
149B ILE* 3.7 29.0 + - + +
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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