Contacts of the helix formed by residues 145 - 155 (chain A) in PDB entry 1BSG
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 PRO 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A LEU* 4.1 7.6 - - + -
144A GLY* 1.3 82.1 - - - +
146A ALA* 1.3 57.9 + - + +
148A VAL* 3.0 26.5 + - - +
149A THR 3.5 0.9 + - - -
162A LEU* 3.4 28.0 - - + +
163A ASP* 3.4 29.8 - - - +
164A ARG 3.5 20.6 - - - +
165A TRP* 3.3 33.9 - - + +
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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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143A GLY 5.9 1.6 - - - +
144A GLY 3.1 1.9 + - - -
145A PRO* 1.3 77.5 - - + +
147A ALA* 1.3 60.5 + - - +
148A VAL 3.1 0.4 - - - -
149A THR* 3.1 8.5 + - - -
150A ARG* 2.9 29.0 + - - +
162A LEU 4.0 7.1 + - - -
163A ASP* 5.5 0.2 - - - +
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Residues in contact with ALA 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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79A ALA* 5.2 3.5 - - - +
142A LEU* 3.5 39.5 - - + +
143A GLY 4.7 2.6 + - - -
144A GLY 3.0 16.3 + - - +
146A ALA* 1.3 78.7 - - - +
148A VAL* 1.3 56.6 + - - +
150A ARG* 3.6 27.5 + - - +
151A PHE* 3.0 26.7 + - - +
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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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68A MET* 5.8 0.9 - - + -
72A PHE* 5.0 3.8 - - + +
75A LEU* 4.0 35.4 - - + -
76A SER* 4.2 18.2 - - - +
79A ALA* 5.6 2.0 - - + -
139A LEU* 3.6 30.3 - - + -
142A LEU* 4.6 6.7 - - + -
144A GLY 4.8 0.4 - - - +
145A PRO 3.0 11.9 + - - +
147A ALA* 1.3 76.4 - - - +
149A THR* 1.3 65.3 + - - +
151A PHE* 3.2 7.5 + - + +
152A VAL* 3.0 24.2 + - + +
160A THR* 5.9 0.9 - - + -
162A LEU* 3.8 21.5 - - + +
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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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145A PRO 3.5 0.8 + - - -
146A ALA* 3.1 11.9 + - - -
148A VAL* 1.3 79.0 - - - +
150A ARG* 1.3 57.0 + - - +
152A VAL* 3.3 8.0 - - - +
153A ARG* 2.9 67.6 + - + +
160A THR 4.2 3.6 - - - +
161A ARG* 3.7 5.1 - - + +
162A LEU 3.0 36.8 + - - +
163A ASP* 5.4 0.7 + - - -
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Residues in contact with ARG 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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83A ASP* 5.5 5.9 + - - +
142A LEU* 4.1 10.5 + - - +
146A ALA 2.9 15.7 + - - +
147A ALA* 3.7 30.3 + - - +
149A THR* 1.3 77.1 - - - +
151A PHE* 1.3 55.1 + - - +
153A ARG* 3.4 9.2 + - - +
154A SER* 3.0 28.5 + - - -
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Residues in contact with PHE 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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75A LEU* 3.8 26.7 - - + -
78A ALA* 3.9 24.5 - - + -
79A ALA* 3.9 20.6 - - + -
82A ARG* 3.4 50.5 - - + +
83A ASP* 3.9 10.8 - - - +
147A ALA 3.0 19.2 + - - +
148A VAL* 3.2 8.3 + - - +
150A ARG* 1.3 77.4 - - - +
152A VAL* 1.3 73.9 + - + +
154A SER* 2.5 26.2 + - - -
155A LEU* 3.4 23.0 + - + +
193A LEU* 4.0 15.9 - - + -
198A ALA* 5.9 0.2 - - + -
199A LEU* 5.0 1.3 - - + -
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Residues in contact with VAL 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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75A LEU* 3.8 30.1 - - + -
148A VAL 3.0 18.7 + - - +
149A THR* 3.3 16.8 - - - +
151A PHE* 1.3 85.5 - - + +
153A ARG* 1.3 65.4 + - - +
155A LEU* 2.9 23.6 + - - +
157A ASP* 3.1 29.2 + - + +
160A THR* 3.6 32.8 - - + +
189A THR* 4.2 16.4 - - + -
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Residues in contact with ARG 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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149A THR* 2.9 47.0 + - + +
150A ARG* 3.5 8.7 - - - +
152A VAL* 1.3 80.9 - - - +
154A SER* 1.3 61.8 + - - +
155A LEU 3.1 0.2 - - - -
156A GLY* 3.1 13.3 + - - -
157A ASP 2.8 32.5 + - - -
158A ARG* 3.4 36.8 + - - +
159A VAL 4.1 2.0 + - - -
160A THR 2.7 29.0 + - - -
161A ARG* 4.1 11.1 - - - +
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Residues in contact with SER 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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82A ARG* 2.9 35.6 + - - -
150A ARG* 3.0 13.8 + - - -
151A PHE 2.5 19.6 + - - -
153A ARG* 1.3 76.3 - - - +
155A LEU* 1.3 59.7 + - - +
156A GLY 3.3 1.6 + - - -
192A ARG* 4.9 1.4 + - - -
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Residues in contact with LEU 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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82A ARG* 3.6 24.0 - - - +
151A PHE* 3.7 25.4 - - + +
152A VAL* 2.9 10.3 + - - +
154A SER* 1.3 79.6 - - - +
156A GLY* 1.3 56.0 + - - +
157A ASP* 3.3 2.2 - - + +
188A ARG* 3.0 25.4 + - - +
189A THR* 4.2 22.4 - - + +
192A ARG* 3.1 28.7 + - + +
193A LEU* 4.0 26.2 - - + -
198A ALA* 3.7 26.5 - - + +
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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