Contacts of the helix formed by residues 135 - 150 (chain A) in PDB entry 3BU0
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 ILE 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A GLU* 3.7 41.1 - - + +
89A VAL* 4.6 4.3 - - + +
115A TYR* 4.3 15.9 - - + +
133A PRO 3.6 8.0 + - - +
134A TRP* 1.3 79.0 - - - +
136A PRO* 1.3 78.6 - - + +
137A VAL* 4.0 15.0 - - + -
138A LEU* 2.8 42.2 + - + +
139A GLU* 3.2 11.3 + - - +
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Residues in contact with PRO 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLU* 4.9 8.1 - - - +
134A TRP 4.7 0.9 - - - +
135A ILE* 1.3 87.9 - - + +
137A VAL* 1.3 57.8 + - - +
139A GLU* 3.3 14.1 + - + +
140A ARG* 2.9 31.2 + - - +
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ILE* 4.0 26.9 - - + -
84A GLU* 3.4 45.4 + - + +
85A LEU* 3.8 23.8 - - + +
88A GLU* 4.9 0.9 - - + -
135A ILE* 2.9 24.2 + - + +
136A PRO* 1.3 77.4 - - - +
138A LEU* 1.3 62.2 + - + +
140A ARG* 3.7 14.4 + - - +
141A ILE* 3.1 33.5 + - + +
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 3.8 19.1 - - + -
89A VAL* 5.0 0.7 - - + -
115A TYR* 3.3 48.7 - - + -
134A TRP* 3.9 17.0 - - + -
135A ILE* 2.8 28.8 + - + +
137A VAL* 1.3 75.7 - - + +
139A GLU* 1.3 56.8 + - - +
141A ILE* 3.4 2.8 + - - -
142A ARG* 2.8 35.2 + - - +
156A VAL* 4.1 6.1 - - + -
158A ILE* 3.9 12.6 - - + -
251A LEU* 3.8 27.6 - - + -
253A PHE* 3.8 5.1 - - + -
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Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A TRP* 3.7 35.1 - - + +
135A ILE* 3.2 19.5 + - - +
136A PRO* 3.6 11.6 - - + +
138A LEU* 1.3 74.9 - - - +
140A ARG* 1.3 56.1 + - - +
142A ARG* 3.7 31.4 + - - +
143A ASP* 2.8 44.7 + - - +
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PHE* 4.9 5.5 - - - -
77A GLU* 2.8 39.8 + - - +
80A GLU* 5.8 3.0 + - - +
81A ILE* 3.8 24.2 - - - +
84A GLU* 4.6 12.9 + - - -
136A PRO 2.9 18.6 + - - +
137A VAL* 3.9 8.7 - - - +
139A GLU* 1.3 76.7 - - - +
141A ILE* 1.3 74.2 + - - +
143A ASP* 4.1 5.1 - - - +
144A HIS* 3.2 25.4 + - - +
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Residues in contact with ILE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PHE* 4.8 12.6 - - + -
81A ILE* 3.6 28.5 - - + -
85A LEU* 4.6 3.8 - - + -
137A VAL* 3.1 25.3 + - + +
138A LEU 3.9 2.9 - - - +
140A ARG* 1.3 85.9 - - - +
142A ARG* 1.3 65.5 + - - +
144A HIS* 3.3 4.8 + - - +
145A VAL* 3.0 31.3 + - + +
187A VAL* 4.2 22.7 - - + -
189A PHE* 4.1 6.7 - - + -
251A LEU* 3.6 22.2 - - + -
253A PHE* 3.7 22.9 - - + -
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Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASP* 5.2 1.0 + - - -
134A TRP* 3.5 43.2 - - + +
138A LEU 2.8 22.6 + - - +
139A GLU* 3.6 27.2 + - - +
141A ILE* 1.3 73.7 - - - +
143A ASP* 1.3 88.9 + - - +
145A VAL* 3.2 5.0 + - - +
146A SER* 2.9 34.6 + - - +
153A PHE* 3.4 34.6 + - + +
253A PHE* 3.6 28.6 - - + -
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Residues in contact with ASP 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLU* 2.8 27.6 + - - +
140A ARG* 4.1 5.3 - - - +
142A ARG* 1.3 104.3 + - - +
144A HIS* 1.3 57.5 + - - +
146A SER* 3.3 8.6 + - - -
147A GLY* 2.9 25.1 + - - -
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Residues in contact with HIS 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 4.0 27.3 + - + +
73A PHE* 3.9 34.4 - + + -
140A ARG* 3.2 20.3 + - + +
141A ILE* 3.8 5.2 - - - +
142A ARG 3.3 0.2 - - - -
143A ASP* 1.3 72.7 - - - +
145A VAL* 1.3 65.9 - - - +
147A GLY* 3.2 3.3 + - - +
148A VAL* 3.0 42.1 + - + +
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 3.9 24.2 - - + -
141A ILE* 3.0 24.6 + - + +
142A ARG* 3.6 5.4 - - - +
144A HIS* 1.3 75.0 - - - +
146A SER* 1.3 58.7 + - - +
148A VAL* 3.2 5.4 + - - +
149A THR* 2.8 46.1 + - + +
153A PHE* 3.7 22.7 - - + -
185A ALA* 3.7 17.7 - - + -
187A VAL* 4.0 19.1 - - + -
223A LEU* 4.4 6.5 - - + -
253A PHE* 4.7 4.3 - - + -
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Residues in contact with SER 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ARG* 2.9 19.0 + - - +
143A ASP* 3.4 13.4 + - - -
145A VAL* 1.3 77.2 - - - +
147A GLY* 1.3 56.2 + - - +
149A THR* 4.0 0.2 - - - -
150A GLY* 2.8 31.4 + - - -
151A GLN 2.8 26.0 + - - -
152A THR* 4.0 9.7 - - - +
153A PHE* 3.7 11.5 + - - -
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Residues in contact with GLY 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ASP 2.9 14.9 + - - -
144A HIS* 3.2 5.1 + - - -
146A SER* 1.3 77.2 - - - +
148A VAL* 1.3 61.8 + - - +
150A GLY* 4.6 1.4 + - - -
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Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A TRP* 3.7 31.3 + - + +
70A THR* 5.5 0.7 - - + -
72A LEU* 4.1 21.1 - - + -
144A HIS* 3.0 43.2 + - + +
145A VAL* 3.2 4.5 + - - +
147A GLY* 1.3 80.9 - - - +
149A THR* 1.3 61.4 + - + +
223A LEU* 4.8 0.2 - - + -
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Residues in contact with THR 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A TRP* 4.3 14.4 - - + -
145A VAL* 2.8 33.4 + - + +
148A VAL* 1.3 78.7 - - + +
150A GLY* 1.3 58.8 + - - +
151A GLN* 3.0 39.8 + - - +
153A PHE* 4.4 0.3 - - - -
223A LEU* 4.3 4.0 - - + -
225A MET* 3.6 35.7 - - + -
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Residues in contact with GLY 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A SER* 2.8 20.2 + - - -
147A GLY 4.5 1.6 + - - -
148A VAL 3.7 1.0 - - - -
149A THR* 1.3 72.7 - - - +
151A GLN* 1.3 64.9 + - - +
152A THR* 4.2 4.7 + - - +
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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