Contacts of the helix formed by residues 135 - 149 (chain A) in PDB entry 2BZN
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 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ASN* 3.7 17.5 + - - +
133A GLY 3.4 0.8 - - - +
134A TYR* 1.3 78.3 - - - +
136A GLU* 1.3 64.4 + - - +
137A HIS* 4.0 10.7 + - - +
138A PHE* 3.2 29.3 + - - +
139A VAL* 3.2 16.9 + - - +
21B ARG* 5.1 0.2 - - - -
22B SER* 3.6 15.7 - - - -
24B LEU 6.0 2.2 - - - -
317B THR* 6.5 0.2 - - - -
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Residues in contact with GLU 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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134A TYR 3.8 0.2 + - - -
135A SER* 1.3 73.1 - - - +
137A HIS* 1.3 56.1 + - - +
139A VAL* 3.2 2.4 + - - +
140A GLU* 2.9 45.5 + - + +
21B ARG* 3.1 37.2 + - - +
22B SER 2.8 18.1 + - - +
23B THR* 3.1 27.2 + - - +
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Residues in contact with HIS 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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105A THR* 3.7 36.4 + - - +
135A SER* 3.2 9.8 - - - +
136A GLU* 1.3 78.3 - - - +
138A PHE* 1.3 58.2 + - - +
140A GLU* 3.5 7.0 + - - +
141A PHE* 3.0 30.0 + + + +
24B LEU 6.4 1.8 - - - -
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Residues in contact with PHE 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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104A GLY 6.2 0.2 - - - -
105A THR* 3.8 12.6 - - + -
128A LEU* 3.7 29.2 - - + -
129A ASP 4.4 0.4 - - - -
130A VAL* 3.6 34.3 - - + -
132A ASN 4.5 2.0 - - - +
133A GLY* 3.8 22.0 - - - +
135A SER* 3.2 20.1 + - - +
137A HIS* 1.3 77.1 + - - +
139A VAL* 1.3 59.3 + - - +
141A PHE* 3.2 10.9 + + - +
142A VAL* 2.8 50.3 + - + +
156A ALA* 4.0 2.7 - - + -
157A GLY* 3.6 35.4 - - - -
168A LEU* 4.0 14.6 - - + -
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Residues in contact with VAL 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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133A GLY 4.8 0.4 - - - +
135A SER 3.2 10.6 + - - +
136A GLU 3.2 7.6 + - - +
138A PHE* 1.3 77.2 - - - +
140A GLU* 1.3 76.1 + - - +
142A VAL* 3.2 5.4 + - - +
143A LYS* 3.1 26.6 + - - +
164A MET* 3.5 32.3 - - + -
167A GLU* 3.7 14.8 - - - +
168A LEU* 4.0 16.2 - - + -
171A SER* 3.4 25.6 - - - +
21B ARG* 3.9 14.8 - - - +
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Residues in contact with GLU 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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136A GLU* 2.9 35.8 + - + +
137A HIS* 3.9 6.3 - - + +
139A VAL* 1.3 80.7 - - - +
141A PHE* 1.3 61.1 - - - +
143A LYS* 2.7 43.5 + - - +
144A ASP* 3.1 31.0 + - - +
21B ARG* 5.3 0.5 + - - -
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Residues in contact with PHE 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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103A SER* 4.2 2.0 - - - -
104A GLY 3.2 28.3 - - - -
105A THR* 3.8 36.6 - - + -
110A PHE* 4.1 24.5 - + + -
128A LEU* 3.7 32.1 - - + -
137A HIS* 3.0 20.4 + + + +
138A PHE* 3.2 14.6 + + - +
140A GLU* 1.3 73.5 - - - +
142A VAL* 1.3 65.7 + - - +
144A ASP* 3.3 12.5 + - + +
145A VAL* 3.1 39.8 + - + +
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Residues in contact with VAL 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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128A LEU* 4.1 16.6 - - + -
138A PHE* 2.8 51.7 + - + +
139A VAL* 3.5 8.7 - - - +
141A PHE* 1.3 74.7 - - - +
143A LYS* 1.3 62.0 + - - +
145A VAL* 3.3 1.7 + - - +
146A ARG* 3.0 22.0 + - - +
154A ILE* 4.5 3.1 - - + +
156A ALA* 4.0 10.8 - - + -
168A LEU* 4.2 10.1 - - + +
171A SER* 4.0 11.2 - - - +
172A GLY 4.2 1.3 - - - -
173A ALA* 3.8 34.1 - - + +
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Residues in contact with LYS 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 VAL* 3.1 19.1 + - - +
140A GLU* 2.7 44.5 + - - +
141A PHE 3.3 0.2 - - - -
142A VAL* 1.3 75.2 - - - +
144A ASP* 1.3 60.1 + - - +
146A ARG* 3.2 4.7 + - - +
147A LYS* 2.9 42.2 + - - +
167A GLU* 5.4 1.8 + - - -
171A SER* 3.5 44.2 - - - +
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Residues in contact with ASP 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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110A PHE* 5.5 3.5 - - + -
140A GLU* 3.1 17.9 + - - +
141A PHE* 3.3 14.6 + - + +
143A LYS* 1.3 74.8 - - - +
145A VAL* 1.3 60.6 + - + +
147A LYS* 3.2 26.9 + - - +
148A ARG* 3.0 28.8 + - - +
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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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110A PHE* 3.9 16.8 - - + -
113A LEU* 4.9 1.6 - - + -
126A ILE* 3.8 31.9 - - + -
128A LEU* 3.8 21.1 - - + -
141A PHE* 3.1 44.0 + - + +
142A VAL 3.9 3.8 - - - +
144A ASP* 1.3 74.9 - - + +
146A ARG* 1.3 57.3 + - - +
148A ARG* 3.2 5.2 + - - +
149A PHE* 2.9 39.0 + - + +
154A ILE* 3.9 10.3 - - + +
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Residues in contact with ARG 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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40A ASN* 3.7 14.0 - - - +
41A SER 3.7 7.6 - - - +
142A VAL 3.0 13.1 + - - +
143A LYS 3.2 10.8 - - - +
145A VAL* 1.3 78.2 - - - +
147A LYS* 1.3 63.5 + - + +
148A ARG 3.4 0.2 + - - -
149A PHE 3.0 25.1 + - - -
150A PRO* 3.5 34.0 + - - +
152A HIS 3.0 15.2 + - - -
154A ILE* 3.7 22.1 - - + +
171A SER 4.3 2.2 - - - +
172A GLY* 2.8 40.9 + - - -
174A ASP* 2.6 33.5 + - - -
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Residues in contact with LYS 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 LYS* 2.9 28.7 + - - +
144A ASP* 3.2 28.8 + - - +
146A ARG* 1.3 78.7 - - + +
148A ARG* 1.3 61.9 + - - +
150A PRO* 3.7 11.3 - - - +
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Residues in contact with ARG 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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110A PHE* 4.2 11.7 - - + -
114A GLU* 2.9 20.2 + - - +
118A GLU* 3.5 31.3 + - - +
144A ASP 3.0 16.8 + - - +
145A VAL 3.2 3.3 + - - +
147A LYS* 1.3 78.9 - - - +
149A PHE* 1.3 98.3 + - + +
150A PRO* 3.4 6.8 - - - +
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Residues in contact with PHE 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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110A PHE* 4.1 17.7 - + - -
113A LEU* 4.8 2.5 - - + -
114A GLU* 4.1 21.3 - - + -
117A LEU* 3.7 28.7 - - + -
118A GLU* 5.6 0.7 - - + -
126A ILE* 3.8 16.8 - - + -
145A VAL* 2.9 20.5 + - + +
146A ARG* 3.0 22.2 + - - +
148A ARG* 1.3 126.5 - - + +
150A PRO* 1.4 61.7 - - - +
151A GLN 3.3 2.7 - - - -
152A HIS* 3.2 43.4 + + + +
154A ILE* 5.0 0.7 - - - +
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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