Contacts of the helix formed by residues 143 - 158 (chain A) in PDB entry 3BRS
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 SER 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LYS* 3.8 23.1 - - - -
74A ALA 3.8 19.1 - - - -
75A ASP 5.0 0.2 - - - -
76A TYR 4.4 2.0 - - - +
98A SER* 4.1 2.5 - - - -
139A PHE* 3.8 4.3 - - - -
140A VAL* 2.9 23.6 + - - +
142A ASN* 1.3 78.2 - - - +
144A LYS* 1.3 62.1 + - - +
145A THR* 3.6 3.0 + - - -
146A ALA* 3.2 19.2 + - - +
147A MET* 3.1 15.6 + - - +
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Residues in contact with LYS 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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73A ALA 5.3 0.2 + - - -
76A TYR* 3.3 41.2 - - + +
98A SER* 3.5 7.0 + - - +
99A GLY* 3.4 39.4 + - - +
100A MET 4.4 4.9 - - - +
142A ASN 3.8 1.6 + - - -
143A SER* 1.3 71.4 - - - +
145A THR* 1.3 58.7 + - - +
147A MET* 3.3 12.2 + - + +
148A ASP* 2.9 56.7 + - - +
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Residues in contact with THR 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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13A LYS* 3.1 21.0 + - - -
97A ASP* 3.2 41.9 + - - +
98A SER* 3.3 10.6 + - - +
113A ASN* 3.7 20.0 - - - +
139A PHE* 3.3 12.6 - - - -
143A SER* 3.6 0.3 + - - -
144A LYS* 1.3 78.0 - - - +
146A ALA* 1.3 64.1 + - - +
148A ASP* 4.0 1.0 - - - +
149A ARG* 3.1 45.9 + - - +
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Residues in contact with ALA 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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138A SER* 3.9 13.0 + - - +
139A PHE* 3.3 25.5 - - + -
140A VAL 3.1 31.0 - - - +
141A LYS* 4.4 5.4 - - - +
143A SER* 3.2 6.8 + - - +
145A THR* 1.3 81.6 + - - +
147A MET* 1.4 63.1 + - - +
149A ARG* 3.7 1.9 - - - +
150A GLU* 3.1 27.2 + - - +
169A TYR* 5.7 1.3 - - + -
197A LEU* 4.3 2.6 - - - +
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Residues in contact with MET 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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76A TYR* 3.7 53.4 - - + -
141A LYS 3.4 15.3 - - - +
142A ASN* 3.9 9.0 - - - +
143A SER 3.1 16.4 + - - +
144A LYS* 3.6 7.0 - - + +
146A ALA* 1.4 75.9 - - - +
148A ASP* 1.3 65.3 + - - +
150A GLU* 3.6 5.3 + - - +
151A GLU* 3.2 26.5 + - - +
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Residues in contact with ASP 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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113A ASN* 3.5 29.8 + - + +
114A ILE* 3.6 37.7 + - + +
144A LYS* 2.9 51.2 + - - +
145A THR* 4.1 0.4 - - - +
147A MET* 1.3 80.6 - - - +
149A ARG* 1.3 57.7 + - - +
151A GLU* 3.5 8.7 + - - +
152A GLY 2.8 25.8 + - - -
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Residues in contact with ARG 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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21A PHE* 5.6 0.2 - - - -
97A ASP* 4.4 4.9 + - - -
113A ASN* 2.8 41.7 + - + +
116A ALA* 5.2 0.4 - - + +
117A GLY* 3.5 7.1 - - - -
139A PHE* 3.4 22.8 - - - -
145A THR* 3.1 29.1 + - - +
146A ALA 3.7 3.8 - - - +
148A ASP* 1.3 77.1 - - - +
150A GLU* 1.3 53.4 + - - +
153A LEU* 2.8 33.6 + - - +
197A LEU* 2.8 50.6 + - + +
198A ASN* 3.6 11.1 - - - +
223A ILE* 3.4 36.9 - - + +
244A GLN* 3.4 27.0 + - - +
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Residues in contact with GLU 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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138A SER* 4.6 2.1 + - - -
141A LYS* 5.5 0.3 + - - -
146A ALA 3.1 17.8 + - - +
147A MET* 4.1 5.6 - - - +
149A ARG* 1.3 74.2 - - - +
151A GLU* 1.3 64.1 + - - +
153A LEU* 3.4 7.8 - - + +
154A LYS* 3.0 53.7 + - + +
167A ILE* 3.6 22.5 - - + +
169A TYR* 2.9 37.8 + - - -
197A LEU* 3.8 15.0 - - + +
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Residues in contact with GLU 151 (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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114A ILE* 3.8 29.3 - - - +
147A MET* 3.2 17.8 + - - +
148A ASP* 3.6 11.3 - - - +
150A GLU* 1.3 74.5 - - - +
152A GLY* 1.3 66.2 + - - +
154A LYS* 3.3 8.1 + - - +
155A ILE* 3.0 47.3 + - + +
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Residues in contact with GLY 152 (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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114A ILE* 3.4 29.7 - - - +
118A ILE* 3.2 21.6 + - - +
148A ASP 2.8 18.1 + - - -
149A ARG 3.8 1.1 - - - -
151A GLU* 1.3 74.6 - - - +
153A LEU* 1.3 55.8 + - - +
155A ILE* 3.3 0.8 + - - -
156A GLY 2.8 26.5 + - - -
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Residues in contact with LEU 153 (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 GLY* 3.2 15.4 - - - +
120A ILE* 4.2 8.5 - - + -
121A GLY* 3.5 24.8 - - - +
124A THR* 4.5 3.1 - - - +
134A ILE* 5.7 0.2 - - + -
136A VAL* 3.9 37.5 - - + -
149A ARG 2.8 21.6 + - - +
150A GLU* 3.4 13.7 - - + +
151A GLU 3.4 0.2 - - - -
152A GLY* 1.3 73.3 - - - +
154A LYS* 1.3 56.1 + - + +
156A GLY 3.3 0.7 + - - -
157A LEU* 3.1 41.2 + - + +
164A ILE* 4.3 10.1 - - + -
167A ILE* 5.7 0.2 - - + -
195A VAL* 4.1 28.7 - - + -
197A LEU* 4.7 5.2 - - + -
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Residues in contact with LYS 154 (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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150A GLU* 3.0 48.5 + - + +
151A GLU* 3.7 6.7 - - - +
153A LEU* 1.3 70.2 - - + +
155A ILE* 1.3 65.8 + - - +
157A LEU* 3.0 15.2 + - - +
158A SER* 3.3 10.7 + - - +
161A SER* 3.7 21.2 - - - +
164A ILE* 4.0 20.9 - - + -
167A ILE* 4.1 14.8 - - - +
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Residues in contact with ILE 155 (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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114A ILE* 4.2 14.6 - - + -
118A ILE* 3.9 20.0 - - + -
151A GLU* 3.0 47.2 + - + +
152A GLY 3.5 5.4 - - - +
154A LYS* 1.3 75.5 - - + +
156A GLY* 1.3 64.1 + - - +
157A LEU 3.0 1.0 + - - -
158A SER* 3.2 15.8 + - - +
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Residues in contact with GLY 156 (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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118A ILE* 3.7 31.3 - - - +
121A GLY 3.6 16.1 - - - +
122A ALA* 3.6 11.4 + - - +
125A LYS* 3.7 9.7 + - - +
152A GLY 2.8 16.7 + - - -
153A LEU 3.3 4.7 + - - -
155A ILE* 1.3 73.2 - - - +
157A LEU* 1.3 58.6 + - - +
158A SER* 3.4 2.3 + - - -
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Residues in contact with LEU 157 (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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121A GLY* 3.6 17.9 - - - +
124A THR* 4.0 4.5 - - - -
125A LYS* 3.4 27.1 - - + +
128A VAL* 5.2 0.4 - - + -
134A ILE* 3.7 26.7 - - + -
153A LEU* 3.1 30.3 + - + +
154A LYS* 3.0 9.1 + - - +
156A GLY* 1.3 76.5 - - - +
158A SER* 1.4 73.0 + - - +
160A ASP* 3.0 27.8 + - + +
161A SER* 3.8 14.4 - - - +
164A ILE* 3.8 36.1 - - + -
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Residues in contact with SER 158 (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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125A LYS* 2.8 27.9 + - - -
154A LYS 3.3 4.7 + - - +
155A ILE 3.2 14.8 + - - -
156A GLY 4.6 1.0 + - - -
157A LEU* 1.4 77.8 - - - +
159A ASP* 1.4 73.1 + - - -
161A SER* 3.3 20.1 + - - -
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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