Contacts of the helix formed by residues 133 - 143 (chain B) in PDB entry 3BIL
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 CYS 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ALA* 4.0 30.5 - - - -
110B MET* 4.0 25.6 - - - -
111B SER* 4.3 10.3 - - - -
114B LEU* 4.5 7.6 - - + -
130B ASN* 2.8 17.0 + - - +
132B GLU* 1.3 77.5 - - - +
134B ALA* 1.3 57.3 + - - +
135B ASN 3.3 2.9 - - - +
136B GLN* 3.2 10.7 + - + +
137B LEU* 2.7 48.5 + - + +
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Residues in contact with ALA 134 (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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130B ASN 4.1 1.6 + - - -
131B GLU 3.7 13.5 + - - +
132B GLU 3.7 0.4 - - - -
133B CYS* 1.3 75.8 - - - +
135B ASN* 1.3 62.6 + - - +
137B LEU* 3.4 2.7 + - - +
138B GLU* 2.9 34.3 + - - +
154B LEU* 3.6 38.1 - - + +
155B PRO* 5.4 4.9 - - + -
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Residues in contact with ASN 135 (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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132B GLU 5.4 0.8 - - - -
133B CYS* 3.3 1.0 - - - -
134B ALA* 1.3 82.6 - - - +
136B GLN* 1.3 62.5 + - - +
138B GLU* 3.0 24.7 + - - +
139B ASP* 3.3 13.4 + - - +
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Residues in contact with GLN 136 (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 SER* 2.9 41.0 + - - -
114B LEU* 3.5 31.3 - - + +
115B GLU* 3.7 13.1 - - - +
133B CYS* 3.2 15.1 + - + +
135B ASN* 1.3 78.4 - - - +
137B LEU* 1.3 61.7 + - - +
139B ASP* 3.5 14.2 + - + +
140B LEU* 3.4 25.6 + - + +
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Residues in contact with LEU 137 (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 MET* 5.3 0.2 - - - -
114B LEU* 3.6 36.1 - - + -
125B ILE* 5.9 0.2 - - + -
127B CYS* 4.4 15.0 - - + -
129B PRO* 3.9 29.8 - - + -
133B CYS* 2.7 34.9 + - + +
134B ALA* 3.7 5.6 - - - +
136B GLN* 1.3 70.4 - - - +
138B GLU* 1.3 66.0 + - - +
140B LEU* 3.1 16.9 + - + +
141B GLN* 3.2 12.0 + - - +
147B VAL* 4.5 19.8 - - + +
149B LEU* 4.0 15.5 - - + -
154B LEU* 4.6 6.1 - - + -
160B ILE* 4.8 11.2 - - + -
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Residues in contact with GLU 138 (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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134B ALA 2.9 16.8 + - - +
135B ASN* 3.0 18.8 - - - +
137B LEU* 1.3 76.4 - - - +
139B ASP* 1.3 61.6 + - - +
141B GLN* 3.0 41.3 + - - +
142B LYS* 3.2 32.1 + - - +
154B LEU* 4.0 6.4 - - - +
157B ASP* 5.9 4.0 - - - +
159B THR* 3.7 21.4 + - - +
160B ILE* 3.3 20.0 - - - +
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Residues in contact with ASP 139 (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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135B ASN* 3.3 16.7 + - - +
136B GLN* 3.8 14.0 - - + +
137B LEU 3.3 0.2 - - - -
138B GLU* 1.3 75.2 - - - +
140B LEU* 1.3 64.0 + - + +
142B LYS* 3.2 33.4 + - - +
143B GLN* 2.9 27.1 + - - +
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Residues in contact with LEU 140 (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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114B LEU* 3.8 44.0 - - + +
118B THR* 3.5 35.7 - - + +
125B ILE* 4.7 8.3 - - + -
136B GLN* 3.4 15.0 + - + +
137B LEU* 3.1 12.5 + - - +
139B ASP* 1.3 79.3 - - + +
141B GLN* 1.3 56.1 + - - +
143B GLN* 3.5 17.8 + - - +
145B MET* 2.6 51.1 + - + -
147B VAL* 4.2 10.8 - - + -
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Residues in contact with GLN 141 (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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137B LEU 3.2 7.4 + - - +
138B GLU* 3.0 28.7 + - - +
140B LEU* 1.3 77.9 - - - +
142B LYS* 1.3 66.1 + - - +
143B GLN 3.0 8.8 + - - -
145B MET 3.6 13.3 + - - +
147B VAL* 4.1 16.2 - - + +
159B THR* 3.4 34.7 + - - +
160B ILE* 3.6 18.4 - - + +
161B PRO* 4.3 7.5 - - + +
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Residues in contact with LYS 142 (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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138B GLU* 3.2 32.8 + - - +
139B ASP* 3.2 29.4 + - - +
141B GLN* 1.3 80.3 - - + +
143B GLN* 1.3 60.1 + - + +
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Residues in contact with GLN 143 (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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118B THR* 4.8 4.7 + - - -
139B ASP* 2.9 31.8 + - - +
140B LEU* 3.8 19.0 - - - +
141B GLN 3.0 8.4 + - - -
142B LYS* 1.3 82.0 - - + +
145B MET* 2.3 37.1 + - - +
146B PRO* 5.1 1.2 - - - +
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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