Contacts of the helix formed by residues 129 - 137 (chain B) in PDB entry 1QNB
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 ARG 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B ILE* 1.3 70.9 - - - +
130B LEU* 1.3 64.0 + - - +
131B GLU* 3.3 2.7 - - + -
132B GLY* 3.1 13.9 + - - +
133B LEU* 3.1 20.4 + - - +
194B GLU 2.9 27.5 + - - -
195B PHE* 2.6 39.7 + - + +
196B ARG 3.3 17.4 + - - +
197B LYS* 3.5 24.5 - - + +
198B ILE* 5.3 6.0 - - - +
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Residues in contact with LEU 130 (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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128B ILE* 3.1 23.8 + - + +
129B ARG* 1.3 68.4 - - - +
131B GLU* 1.3 60.2 + - - +
133B LEU* 3.3 3.9 + - + -
134B ALA* 2.9 27.0 + - - +
143B TYR* 3.8 34.3 - - + +
149B PRO 3.9 6.3 - - - +
151B LEU* 3.2 24.8 - - + +
164B ILE* 3.5 49.4 - - + +
165B PHE 4.3 1.1 - - - -
166B VAL* 3.6 29.8 - - + +
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Residues in contact with GLU 131 (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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129B ARG 3.3 0.8 - - - -
130B LEU* 1.3 77.2 - - - +
132B GLY* 1.3 59.0 + - - +
134B ALA* 3.7 2.7 + - - +
135B TYR* 3.0 32.4 + - + +
143B TYR* 3.9 21.0 - - + -
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Residues in contact with GLY 132 (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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129B ARG* 3.1 20.2 + - - +
131B GLU* 1.3 79.1 + - - +
133B LEU* 1.3 62.3 + - - +
135B TYR* 3.4 7.6 + - - +
136B SER* 2.9 27.0 + - - -
195B PHE* 3.5 18.1 - - - -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ILE* 4.7 2.0 - - + -
129B ARG 3.1 12.8 + - - +
130B LEU* 3.3 9.8 + - + +
132B GLY* 1.3 74.1 - - - +
134B ALA* 1.3 60.6 + - - +
136B SER* 3.2 4.2 + - - -
137B HIS* 2.8 64.2 + - + +
141B SER* 4.6 2.0 - - - +
151B LEU* 4.0 18.8 - - + -
153B TYR* 4.2 8.7 - - + -
164B ILE* 4.0 33.7 - - + -
188B ILE* 5.3 0.7 - - + -
191B VAL* 3.6 22.2 - - + -
192B LEU* 4.0 15.7 - - + -
195B PHE* 3.7 15.3 - - + -
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Residues in contact with ALA 134 (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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130B LEU 2.9 18.7 + - - +
131B GLU* 3.9 5.6 - - - +
133B LEU* 1.3 75.7 - - - +
135B TYR* 1.3 57.7 + - - +
137B HIS 3.1 0.3 - - - -
138B ALA* 2.8 34.8 + - - +
141B SER* 3.7 19.2 - - - -
143B TYR* 4.1 15.9 - - + +
151B LEU* 3.6 12.6 - - + -
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Residues in contact with TYR 135 (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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131B GLU* 3.0 23.3 + - + +
132B GLY* 3.6 8.3 - - - +
133B LEU 3.2 0.2 - - - -
134B ALA* 1.3 78.3 - - - +
136B SER* 1.3 63.4 + - - +
137B HIS 3.5 0.5 + - - -
138B ALA* 4.0 10.6 + - - +
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Residues in contact with SER 136 (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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132B GLY 2.9 10.6 + - - -
135B TYR* 1.3 80.4 - - - +
137B HIS* 1.3 82.1 + - - +
138B ALA 3.7 0.9 - - - -
195B PHE* 2.9 34.7 - - - -
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Residues in contact with HIS 137 (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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133B LEU* 2.8 30.1 + - + +
134B ALA 3.1 4.7 - - - -
136B SER* 1.3 111.9 + - - +
138B ALA* 1.3 58.3 + - - +
139B ALA 3.2 2.9 - - - -
140B PHE* 3.0 17.9 + - + -
141B SER* 2.7 38.3 + - - +
153B TYR* 3.3 25.3 + - + -
191B VAL* 3.5 29.8 - - + +
194B GLU* 5.6 2.0 + - - -
195B PHE* 4.1 4.4 - + - -
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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