Contacts of the helix formed by residues 140 - 150 (chain A) in PDB entry 2B4M
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 LYS 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A GLY* 3.8 16.6 - - - +
139A GLU* 1.3 74.7 - - - +
141A PRO* 1.3 77.9 - - + +
142A ALA* 3.2 5.2 - - + +
143A LYS* 2.9 34.4 + - + +
144A VAL* 3.0 11.6 + - - +
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Residues in contact with PRO 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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131A ILE* 5.4 2.1 - - + +
135A VAL* 3.9 26.0 - - + -
139A GLU 3.5 6.5 - - - +
140A LYS* 1.3 93.8 - - + +
142A ALA* 1.3 56.5 + - - +
144A VAL* 3.3 2.1 + - - +
145A ALA* 2.8 30.3 + - - +
182A ILE* 4.0 22.9 - - + +
186A ASN* 3.3 27.2 + - + +
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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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140A LYS* 3.2 3.6 - - + +
141A PRO* 1.3 77.8 - - - +
143A LYS* 1.3 58.3 + - + +
145A ALA* 3.7 5.1 - - - +
146A ALA* 3.1 26.7 + - - +
186A ASN* 3.6 12.4 - - - +
190A LYS* 4.5 6.4 - - + +
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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 GLU* 5.3 6.1 - - + -
140A LYS* 2.9 26.6 + - + +
142A ALA* 1.3 77.2 - - + +
144A VAL* 1.3 60.7 + - + +
146A ALA* 3.2 7.1 + - - +
147A GLU* 2.9 45.0 + - - +
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Residues in contact with VAL 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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130A GLU 4.5 2.0 - - - +
131A ILE* 3.8 35.7 - - + +
134A LYS* 3.8 22.7 - - + -
135A VAL* 4.0 14.1 - - + -
139A GLU* 3.6 31.4 - - + -
140A LYS 3.0 14.1 + - - +
141A PRO 3.8 4.7 - - - +
143A LYS* 1.3 71.5 - - - +
145A ALA* 1.3 59.7 + - - +
147A GLU* 3.4 12.6 + - + +
148A TYR* 2.9 29.4 + - + +
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Residues in contact with ALA 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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131A ILE* 4.9 6.6 - - + +
141A PRO 2.8 17.4 + - - +
142A ALA* 3.7 7.0 - - - +
144A VAL* 1.3 76.1 - - - +
146A ALA* 1.3 62.1 + - - +
148A TYR* 3.2 7.0 + - - +
149A VAL* 3.1 28.2 + - - +
186A ASN* 3.6 36.1 - - + +
187A VAL* 3.9 8.3 - - - +
190A LYS* 4.1 9.0 - - + -
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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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142A ALA 3.1 11.7 + - - +
143A LYS* 3.2 10.3 + - - +
145A ALA* 1.3 76.9 - - - +
147A GLU* 1.3 62.6 + - + +
149A VAL* 3.2 10.6 + - - +
150A ASN* 2.8 39.2 + - - +
190A LYS* 3.7 24.3 - - - +
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Residues in contact with GLU 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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134A LYS* 4.4 18.9 + - - +
139A GLU* 4.3 15.7 - - - +
143A LYS* 2.9 40.7 + - + +
144A VAL* 3.6 16.0 - - + +
146A ALA* 1.3 75.1 - - + +
148A TYR* 1.3 59.8 + - - +
150A ASN* 3.6 6.2 + - - +
151A LYS* 3.2 26.2 + - - +
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Residues in contact with TYR 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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123A TRP* 3.3 21.0 - + - -
127A GLU* 3.3 27.8 - - - +
130A GLU* 3.0 32.5 - - + -
131A ILE* 3.7 23.1 - - + -
144A VAL* 2.9 18.4 + - + +
145A ALA* 3.4 6.3 - - - +
147A GLU* 1.3 77.4 - - - +
149A VAL* 1.3 61.2 + - + +
151A LYS* 3.1 6.3 + - - +
152A HIS* 2.8 46.4 + + + +
155A GLN* 2.7 28.6 + - - -
156A ILE* 4.7 2.7 - - + -
159A TRP* 4.5 4.9 - + - -
187A VAL* 3.8 21.8 - - + -
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Residues in contact with VAL 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 ALA 3.1 15.2 + - - +
146A ALA* 3.2 19.5 - - - +
148A TYR* 1.3 70.8 - - - +
150A ASN* 1.3 67.5 + - - +
151A LYS 3.1 7.4 + - - -
152A HIS 4.1 1.6 - - - -
153A LYS* 4.1 18.4 + - - +
156A ILE* 3.8 24.3 - - + +
187A VAL* 3.9 25.6 - - + +
190A LYS* 4.4 7.2 - - + -
191A VAL* 4.1 19.7 - - + +
194A ASP* 3.8 21.8 - - - +
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Residues in contact with ASN 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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146A ALA* 2.8 34.7 + - - +
147A GLU* 3.8 5.5 - - - +
148A TYR 3.3 0.2 - - - -
149A VAL* 1.3 85.8 - - - +
151A LYS* 1.3 56.6 + - - +
153A LYS* 4.1 23.0 - - - +
190A LYS* 5.5 3.0 - - - +
194A ASP* 5.0 3.1 + - - +
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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