Contacts of the helix formed by residues 159 - 169 (chain B) in PDB entry 2BAM
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 PHE 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B LYS* 3.6 30.5 - - + -
6B GLU* 3.6 24.7 - - - -
7B PHE* 3.8 5.6 - - + -
143B MET* 3.7 22.2 - - + -
144B PRO 2.9 14.5 + - - +
145B ILE* 4.2 5.6 - - + -
158B ASN* 1.3 71.7 - - - +
160B GLU* 1.3 66.8 + - - +
162B LEU* 3.3 0.5 + - - -
163B GLU* 3.0 45.9 + - - +
166B PHE* 3.4 32.4 - + - -
176B PHE* 3.6 25.4 - - + -
178B GLY* 3.5 25.1 - - - -
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Residues in contact with GLU 160 (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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89A LYS* 3.8 16.8 - - - +
5B LYS* 3.0 40.3 + - + -
145B ILE* 3.7 7.1 - - - +
146B LYS* 2.7 54.7 + - + +
147B GLN 4.9 0.7 + - - -
158B ASN* 4.1 4.4 - - - +
159B PHE* 1.3 74.2 + - - +
161B GLU* 1.3 59.9 - - - +
163B GLU* 3.3 31.3 - - - +
164B PRO* 3.4 6.6 - - - +
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Residues in contact with GLU 161 (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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89A LYS* 3.9 16.7 - - + +
90A GLY* 6.0 3.8 - - - +
117B ILE* 3.6 24.8 - - + +
121B HIS* 5.0 0.3 - - - -
155B ARG* 3.0 38.8 + - - -
158B ASN* 3.0 39.4 + - - +
160B GLU* 1.3 74.9 - - - +
162B LEU* 1.3 61.7 + - - +
164B PRO* 3.5 10.2 - - - +
165B TYR* 4.1 11.3 - - - -
3D T 3.5 24.8 + - - +
4D G 3.9 5.9 + - - -
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Residues in contact with LEU 162 (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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117B ILE* 3.8 7.8 - - + +
120B ALA* 3.9 34.3 - - + +
121B HIS* 3.7 39.9 - - + +
124B MET* 5.0 7.4 - - + -
141B ILE* 4.6 8.5 - - + -
143B MET* 4.0 23.1 - - + -
158B ASN 3.3 11.9 + - - +
159B PHE 4.1 1.3 - - - +
161B GLU* 1.3 75.3 - - - +
163B GLU* 1.3 54.7 + - - +
164B PRO* 3.3 2.0 - - - -
165B TYR* 2.8 35.3 + - + +
166B PHE* 3.4 18.9 - - + -
176B PHE* 4.2 11.9 - - + -
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Residues in contact with GLU 163 (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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87A LYS* 5.0 0.9 + - - -
5B LYS* 5.2 2.1 - - - +
159B PHE* 3.0 33.1 + - - +
160B GLU* 3.3 29.1 - - - +
162B LEU* 1.3 76.4 - - - +
164B PRO* 1.4 64.0 - - + +
165B TYR 3.0 1.2 + - - -
166B PHE* 3.1 36.1 + - + +
167B GLU 4.7 0.2 + - - -
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Residues in contact with PRO 164 (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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83A LEU* 3.9 23.8 - - + -
87A LYS* 2.6 43.8 + - + -
89A LYS* 3.6 34.3 - - + +
90A GLY* 5.0 0.9 - - - +
129A LEU* 3.9 6.1 - - - +
160B GLU 3.4 13.5 - - - +
161B GLU 3.5 9.4 - - - +
162B LEU 3.3 5.6 - - - +
163B GLU* 1.4 91.3 - - + +
165B TYR* 1.3 66.7 + - + +
166B PHE 3.7 0.3 + - - -
167B GLU* 4.0 3.5 + - - +
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Residues in contact with TYR 165 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A LEU* 3.7 10.4 - - + +
90A GLY* 5.2 4.1 - - - -
122A ARG* 4.3 7.3 - - + +
125A ASN* 3.9 15.0 - - + -
126A LYS* 3.2 50.5 - - + +
129A LEU* 3.6 27.6 - - + -
121B HIS* 3.2 32.8 - + + +
124B MET* 3.7 23.8 - - + +
161B GLU 4.1 10.3 - - - -
162B LEU* 2.8 18.6 + - + +
164B PRO* 1.3 88.6 - - + +
166B PHE* 1.3 63.7 + - - +
167B GLU 3.1 2.7 - - - -
168B LEU* 3.1 26.7 + - + +
4D G 4.5 3.1 + - - -
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Residues in contact with PHE 166 (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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7B PHE* 3.6 40.8 - + + -
143B MET* 3.7 14.4 - - + -
159B PHE* 3.4 41.1 - + - -
162B LEU* 3.4 29.4 - - + -
163B GLU* 3.1 33.6 + - + +
165B TYR* 1.3 77.9 - - - +
167B GLU* 1.3 59.2 + - - +
168B LEU 3.1 0.7 - - - -
169B THR* 2.7 28.1 + - - -
176B PHE* 3.4 39.9 - + + -
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Residues in contact with GLU 167 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A LYS* 2.7 33.2 + - - +
129A LEU* 3.6 19.7 - - + +
132A LYS* 3.0 38.4 + - - +
133A HIS* 2.9 35.0 + - - -
7B PHE* 5.7 2.2 - - - -
163B GLU 4.7 0.6 + - - -
164B PRO 4.0 1.7 + - - +
165B TYR 3.1 1.0 - - - -
166B PHE* 1.3 75.5 - - - +
168B LEU* 1.3 60.1 + - - +
169B THR 3.1 6.9 + - - -
170B GLU* 3.4 19.5 + - - +
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Residues in contact with LEU 168 (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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125A ASN* 3.6 50.3 - - + +
128A LEU* 4.3 17.7 - - + -
129A LEU* 3.8 17.5 - - + -
132A LYS* 3.6 30.7 - - + +
124B MET* 4.4 8.1 - - + -
125B ASN* 6.0 0.2 - - - +
128B LEU* 3.6 18.4 - - + +
132B LYS* 6.1 0.3 - - - -
165B TYR* 3.1 23.1 + - + +
166B PHE 3.1 1.4 - - - -
167B GLU* 1.3 74.3 - - - +
169B THR* 1.3 58.1 + - - +
170B GLU* 3.2 6.7 + - - +
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Residues in contact with THR 169 (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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9B THR* 3.5 18.7 - - - +
124B MET* 3.5 33.7 - - + -
128B LEU* 3.9 10.8 - - + -
166B PHE 2.7 17.2 + - - +
167B GLU 3.1 0.2 - - - -
168B LEU* 1.3 78.0 - - - +
170B GLU* 1.3 63.3 + - - +
171B GLY 3.7 0.2 + - - -
172B GLN* 3.1 24.8 + - - +
174B PHE* 3.6 27.6 - - + -
176B PHE* 3.6 18.9 - - + -
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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