Contacts of the helix formed by residues 137 - 146 (chain A) in PDB entry 2BBM
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 ASN 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A PHE* 4.4 6.1 - - - -
98A GLY 4.9 0.4 - - - -
99A PHE* 3.3 38.0 - - - +
133A ASP* 6.4 1.3 - - - -
135A GLN* 4.9 3.6 + - - +
136A VAL* 1.3 77.1 - - - +
138A TYR* 1.3 62.5 + - - +
139A GLU* 3.4 7.6 - - + +
140A GLU* 3.4 19.2 + - + +
141A PHE* 3.1 27.6 + - - +
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Residues in contact with TYR 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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82A GLU* 5.5 8.2 + - - +
85A ILE* 5.2 5.8 - - + +
86A ARG* 3.7 43.6 + - + +
89A PHE* 3.3 37.7 - + + -
98A GLY* 4.9 3.6 + - - +
137A ASN* 1.3 75.1 - - - +
139A GLU* 1.3 69.1 + - - +
141A PHE* 3.5 6.0 - + - +
142A VAL* 2.9 43.6 + - + +
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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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137A ASN* 3.4 4.8 - - + +
138A TYR* 1.3 81.3 - - - +
140A GLU* 1.3 62.6 + - + +
142A VAL* 3.2 4.4 + - - +
143A THR* 2.8 36.3 + - - +
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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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128A ALA* 4.5 10.6 - - + +
129A ASP* 2.6 22.9 - - - +
130A ILE* 3.6 3.5 + - - +
131A ASP* 2.9 22.5 - - - +
133A ASP* 3.5 2.0 - - - +
135A GLN 3.4 0.7 - - - +
136A VAL* 4.0 6.2 - - + -
137A ASN* 3.4 30.6 + - + +
138A TYR 3.3 0.2 - - - -
139A GLU* 1.3 80.2 - - + +
141A PHE* 1.3 62.9 + - - +
143A THR* 4.2 7.1 - - - +
144A MET* 3.0 27.9 + - - +
184A CA 2.1 31.3 - - - -
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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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85A ILE* 3.9 27.8 - - + -
89A PHE* 4.1 45.3 - + + -
92A PHE* 5.7 7.9 - + - -
100A ILE* 5.0 7.4 - - + -
136A VAL* 4.4 13.2 - - + +
137A ASN 3.1 21.7 + - - +
138A TYR* 3.5 9.4 - + - +
140A GLU* 1.3 78.8 - - - +
142A VAL* 1.3 71.0 + - + +
144A MET* 4.1 2.2 - - - +
145A MET* 3.0 71.0 + - + +
4B TRP* 5.4 5.6 - + - -
8B PHE* 4.7 11.9 - + + -
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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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82A GLU* 5.5 6.5 - - - +
85A ILE* 5.9 4.9 - - + -
138A TYR* 2.9 43.7 + - + +
139A GLU* 3.8 4.3 - - - +
141A PHE* 1.3 83.0 - - + +
143A THR* 1.3 62.7 + - - +
144A MET 3.0 1.6 - - - -
145A MET* 5.1 1.1 - - - -
146A THR* 2.7 51.5 + - + +
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Residues in contact with THR 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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130A ILE* 5.5 11.7 - - + -
139A GLU* 2.8 25.0 + - - +
140A GLU* 4.2 6.5 - - - +
142A VAL* 1.3 77.6 - - - +
144A MET* 1.3 61.2 + - - +
146A THR* 3.5 17.6 - - - +
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Residues in contact with MET 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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128A ALA* 4.1 30.3 - - + +
136A VAL* 6.1 2.9 - - + -
140A GLU 3.0 20.9 + - - +
141A PHE* 4.1 2.9 - - - +
142A VAL 3.0 0.6 - - - -
143A THR* 1.3 82.5 - - + +
145A MET* 1.3 84.4 + - + +
146A THR 3.4 2.8 - - - +
147A SER* 5.1 4.3 - - - -
2B ARG 5.4 2.9 - - - +
3B ARG* 6.3 0.4 - - - -
4B TRP* 3.8 33.0 - - + +
5B LYS* 5.2 11.3 + - - -
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Residues in contact with MET 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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85A ILE* 6.3 0.7 - - + -
141A PHE* 3.0 69.0 + - + +
142A VAL* 4.5 0.9 - - - +
144A MET* 1.3 97.8 - - + +
146A THR* 1.3 63.8 + - - +
147A SER* 3.5 5.7 + - - -
4B TRP* 3.7 30.3 - - + -
5B LYS* 4.9 23.9 + - + +
8B PHE* 4.6 25.8 - - + -
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Residues in contact with THR 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 VAL* 2.7 42.3 + - + +
143A THR* 3.5 18.6 - - - +
144A MET 4.2 1.0 - - - +
145A MET* 1.3 74.2 - - - +
147A SER* 1.3 59.6 + - - +
148A LYS* 3.0 26.2 + - - +
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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