Contacts of the helix formed by residues 128 - 135 (chain B) in PDB entry 3QN3
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 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B GLY 4.2 4.5 - - - +
127B MET* 1.3 101.7 - - + +
129B LEU* 1.3 66.5 + - - +
130B TYR* 3.5 24.7 - - + -
131B ARG* 2.9 22.7 + - + +
132B TYR* 3.1 9.7 + - - +
398B ARG* 4.0 10.1 - - - +
405B GLU* 3.5 24.9 - - - +
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Residues in contact with LEU 129 (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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118B ALA* 4.1 10.5 - - + +
119B ARG* 4.0 44.2 - - + +
122B ALA* 4.1 10.2 - - + +
127B MET 3.6 1.4 + - - -
128B PRO* 1.3 73.5 - - - +
130B TYR* 1.3 64.1 + - - +
132B TYR* 3.0 4.3 + - + +
133B LEU* 2.9 43.3 + - + +
369B PHE* 3.4 38.8 - - + -
372B ASP* 3.5 29.1 + - + +
398B ARG* 4.3 2.9 - - - +
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Residues in contact with TYR 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 PRO* 3.5 16.4 - - + -
129B LEU* 1.3 76.1 - - - +
131B ARG* 1.3 82.6 + - + +
133B LEU* 4.7 0.2 - - - -
134B GLY 3.1 21.1 + - - -
138B ALA* 3.6 32.5 - - + +
372B ASP* 3.0 50.2 + - + +
375B VAL* 3.9 11.4 - - + -
376B ALA* 3.6 12.0 - - - +
398B ARG* 4.0 1.8 - - - -
402B ILE* 3.8 33.3 - - + +
405B GLU* 2.6 46.1 + - - +
406B SER* 4.5 5.4 + - - -
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Residues in contact with ARG 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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127B MET* 4.6 16.3 - - + -
128B PRO* 2.9 27.4 + - + +
130B TYR* 1.3 109.0 + - + +
132B TYR* 1.3 60.6 + - - +
135B GLY* 2.8 46.7 + - - +
136B ALA* 3.7 20.0 - - - +
138B ALA* 5.0 2.5 - - - -
84C PHE* 2.9 34.3 + - - +
85C ASN* 4.6 4.2 + - - +
86C GLN* 4.9 2.0 - - - +
131C ARG 5.0 0.9 - - - +
132C TYR* 3.0 33.7 + - - -
135C GLY* 4.2 1.0 - - - -
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Residues in contact with TYR 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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83B ALA 3.9 1.7 + - - -
84B PHE* 3.3 35.8 + + - -
86B GLN* 4.5 9.6 + - + +
118B ALA* 3.7 24.9 - - + -
121B ALA* 3.4 23.4 - - + +
122B ALA* 3.7 24.9 - - + -
125B LEU* 4.1 18.6 - - + -
127B MET* 5.0 5.3 - - + +
128B PRO 3.1 4.6 + - - +
129B LEU* 3.0 8.2 + - + +
131B ARG* 1.3 78.4 - - - +
133B LEU* 1.3 67.8 + - + +
127C MET* 4.8 7.9 - - + -
131C ARG* 3.0 31.6 + - - -
135C GLY* 3.4 4.5 - - - -
136C ALA* 3.0 27.6 + - + -
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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
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86B GLN* 5.5 0.9 - - + -
118B ALA* 4.3 11.9 - - + -
129B LEU* 2.9 32.0 + - + +
132B TYR* 1.3 93.1 - - + +
134B GLY* 1.3 56.7 + - - +
339B ILE* 4.2 22.4 - - + -
343B MET* 4.4 6.6 - - - +
369B PHE* 3.9 19.3 - - + -
373B PHE* 3.8 31.0 - - + +
376B ALA* 3.5 18.1 - - + +
136C ALA* 3.6 14.7 - - + +
137C ASN* 2.9 33.3 + - - +
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Residues in contact with GLY 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 TYR 3.1 10.3 + - - -
133B LEU* 1.3 79.4 - - - +
135B GLY* 1.3 67.2 + - - +
137B ASN* 3.7 4.9 + - - +
138B ALA* 3.2 14.5 + - - -
376B ALA* 3.4 21.9 - - - +
134C GLY* 3.4 22.5 - - - +
137C ASN* 4.7 2.0 - - - -
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Residues in contact with GLY 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 ARG* 2.8 40.1 + - - -
134B GLY* 1.3 77.5 - - - +
136B ALA* 1.3 58.4 + - - -
138B ALA* 3.0 18.5 + - - +
131C ARG 4.0 0.7 - - - -
132C TYR 3.3 13.9 - - - -
133C LEU 3.6 1.8 - - - -
135C GLY* 3.4 14.5 - - - +
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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