Contacts of the helix formed by residues 134 - 145 (chain A) in PDB entry 2BME
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 THR 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A TYR* 5.8 0.2 - - - -
131A ARG* 3.9 10.5 - - - +
132A GLU 5.8 0.9 - - - +
133A VAL* 1.3 75.3 - - - +
135A PHE* 1.3 64.9 + - - +
136A LEU* 3.9 7.1 + - - +
137A GLU* 2.9 43.0 + - - +
138A ALA* 3.1 25.1 + - - +
151A GLU* 4.6 0.4 - - - -
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Residues in contact with PHE 135 (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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131A ARG* 3.5 10.6 - - - +
134A THR* 1.3 73.3 - - - +
136A LEU* 1.3 74.5 + - + +
138A ALA 3.5 0.2 + - - -
139A SER* 2.6 49.4 + - - -
149A PHE* 3.5 32.1 - + - -
151A GLU* 3.7 26.7 - - - +
1181A TRS 4.0 32.5 - - - -
10C LEU 3.9 19.1 - - - -
11C PHE* 4.2 20.2 - + - -
82C GLY 6.1 0.9 - - - -
84C ALA* 4.4 17.5 - - + -
171C ILE* 5.1 1.3 - - + -
175C ILE* 5.1 0.4 - - + -
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Residues in contact with LEU 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 THR* 3.3 6.9 + - - +
135A PHE* 1.3 97.2 - - + +
137A GLU* 1.3 57.9 + - - +
139A SER* 3.2 6.5 + - - -
140A ARG* 3.0 27.9 + - - +
84C ALA* 5.8 2.2 - - + -
115C ASN* 4.5 24.9 - - + +
171C ILE* 4.7 10.3 - - + -
174C LYS* 3.9 41.1 - - + +
175C ILE* 4.4 21.9 - - + +
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Residues in contact with GLU 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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95A ARG* 2.7 41.9 + - - -
98A TYR* 3.3 19.3 + - - +
133A VAL* 4.1 5.8 - - + -
134A THR* 2.9 46.4 + - - +
136A LEU* 1.3 74.3 - - - +
138A ALA* 1.3 66.6 + - - +
140A ARG* 3.3 10.7 + - - +
141A PHE* 3.1 17.7 + - - +
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Residues in contact with ALA 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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90A TYR* 3.1 29.4 - - + +
98A TYR* 3.6 21.8 - - + -
120A LEU* 4.4 4.4 - - + +
133A VAL* 4.2 1.1 - - + -
134A THR 3.1 15.5 + - - +
137A GLU* 1.3 78.0 - - - +
139A SER* 1.3 57.7 + - - +
141A PHE* 3.3 2.4 + - - +
142A ALA* 2.9 30.1 + - - +
149A PHE* 3.5 18.9 - - + -
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Residues in contact with SER 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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135A PHE* 2.6 39.6 + - - -
136A LEU* 3.2 8.5 - - - -
138A ALA* 1.3 74.0 - - - +
140A ARG* 1.3 57.6 + - - +
142A ALA* 3.5 3.8 + - - +
143A GLN* 3.0 28.9 + - - +
149A PHE* 3.5 20.7 - - - -
9C PHE* 4.9 5.5 - - - -
11C PHE* 5.6 0.2 - - - -
175C ILE* 3.7 30.1 - - - +
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Residues in contact with ARG 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 LEU 3.0 12.0 + - - +
137A GLU* 3.5 11.6 - - - +
139A SER* 1.3 72.3 - - - +
141A PHE* 1.3 61.7 + - - +
143A GLN* 3.3 3.9 + - - +
144A GLU* 2.9 55.1 + - + +
174C LYS 3.2 13.5 + - - -
175C ILE* 2.8 27.6 + - - +
176C GLU 4.0 7.7 + - - +
177C SER* 2.5 36.1 + - - +
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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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88A LEU* 6.1 0.2 - - + -
98A TYR* 3.5 28.5 - + - +
101A LEU* 3.9 38.1 - - + -
102A THR* 3.9 20.0 - - - -
105A LEU* 4.0 20.4 - - + -
120A LEU* 4.1 18.6 - - + -
137A GLU 3.1 2.8 + - - +
138A ALA* 3.3 5.1 + - - +
140A ARG* 1.3 78.6 - - - +
142A ALA* 1.3 69.1 + - - +
144A GLU* 3.3 15.3 + - - +
145A ASN* 3.0 53.2 + - - -
147A LEU* 4.8 3.4 - - + -
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Residues in contact with ALA 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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120A LEU* 4.1 8.7 - - + -
138A ALA 2.9 16.7 + - - +
139A SER* 3.7 5.4 - - - +
140A ARG 3.3 0.2 - - - -
141A PHE* 1.3 82.7 - - - +
143A GLN* 1.3 62.7 + - - +
145A ASN 3.0 3.3 + - - -
146A GLU 3.0 5.4 + - - -
147A LEU* 2.9 48.9 + - + +
149A PHE* 3.6 22.9 - - + -
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Residues in contact with GLN 143 (chain A).
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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139A SER 3.0 16.7 + - - +
140A ARG* 3.6 6.3 - - - +
142A ALA* 1.3 75.3 - - - +
144A GLU* 1.3 64.6 + - + +
146A GLU* 3.1 16.8 + - - +
147A LEU 4.3 0.4 + - - -
1183A BME 3.9 19.1 - - - -
9C PHE* 3.7 21.4 - - + -
57C LYS* 3.4 19.6 - - - +
172C LEU* 5.1 1.9 - - - +
175C ILE* 3.4 22.7 - - - +
176C GLU* 2.7 37.8 + - - +
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Residues in contact with GLU 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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140A ARG* 2.9 40.2 + - + +
141A PHE* 3.3 23.6 + - - +
143A GLN* 1.3 77.6 - - + +
145A ASN* 1.3 64.5 + - - +
146A GLU* 3.4 5.0 + - - +
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Residues in contact with ASN 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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105A LEU* 3.6 19.9 - - + +
109A ARG* 2.9 37.0 + - - +
141A PHE* 3.0 51.3 + - + +
142A ALA 3.0 4.6 + - - +
144A GLU* 1.3 85.5 + - - +
146A GLU* 1.3 70.9 - - - +
147A LEU* 3.3 19.4 + - + +
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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