Contacts of the helix formed by residues 140 - 155 (chain B) in PDB entry 2QNC
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 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B SER 3.5 4.0 + - - -
139B ASP* 1.3 77.6 - - - +
141B LYS* 1.3 67.8 + - - +
142B THR* 3.7 13.0 + - + +
143B GLN* 2.9 49.4 + - + +
144B LEU* 3.1 8.0 + - - +
1D G 3.8 12.9 + - - -
2D G 3.0 21.9 + - - -
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Residues in contact with LYS 141 (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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117B SER 4.9 6.9 + - - +
119B LEU 3.2 19.4 + - - -
121B LYS* 5.0 3.8 - - + +
124B MET* 3.5 23.7 - - + +
139B ASP 3.8 0.4 + - - -
140B THR* 1.3 73.9 + - - +
142B THR* 1.3 61.2 + - - +
144B LEU* 2.7 20.2 + - + +
145B ILE* 2.6 41.6 + - + +
2D G 3.0 43.8 + - + +
3D A 3.1 29.9 + - - -
4D T 6.4 0.2 - - - +
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Residues in contact with THR 142 (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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140B THR* 3.2 12.6 + - + -
141B LYS* 1.3 85.0 - - - +
143B GLN* 1.3 60.4 + - + +
145B ILE* 3.4 10.5 + - - +
146B ALA* 2.9 29.7 + - + +
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Residues in contact with GLN 143 (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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138B SER 4.8 0.3 - - - +
139B ASP* 3.3 25.5 + - + +
140B THR* 2.9 46.3 + - + +
142B THR* 1.3 77.4 - - + +
144B LEU* 1.3 56.8 - - - +
146B ALA* 3.6 7.3 - - - +
147B SER* 2.7 35.7 + - - -
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Residues in contact with LEU 144 (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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116B PHE* 4.2 2.8 - - + -
121B LYS* 3.9 26.5 - - + +
124B MET* 4.3 17.5 - - + -
125B MET* 4.7 7.4 - - + -
128B MET* 4.3 22.1 - - - +
135B TYR* 4.4 24.2 - - + -
136B ASN 4.6 1.6 - - - +
139B ASP* 3.6 28.3 - - + +
140B THR 3.1 5.8 + - - +
141B LYS* 2.7 32.4 + - + +
143B GLN* 1.3 68.9 - - - +
145B ILE* 1.3 67.3 + - - +
147B SER* 3.1 4.5 + - - -
148B PHE* 2.7 27.0 + - - +
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Residues in contact with ILE 145 (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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113B SER* 4.1 14.8 - - - +
116B PHE* 3.5 15.3 - - + -
117B SER* 3.9 34.1 - - - +
124B MET* 3.4 34.3 - - + -
141B LYS* 2.6 34.0 + - + +
142B THR* 3.4 9.6 - - - +
144B LEU* 1.3 77.4 - - - +
146B ALA* 1.3 64.0 + - - +
148B PHE* 3.0 3.1 + - - +
149B LYS* 2.9 26.6 + - - +
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Residues in contact with ALA 146 (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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142B THR* 2.9 20.9 + - + +
143B GLN* 3.6 8.5 - - - +
145B ILE* 1.3 77.2 - - - +
147B SER* 1.3 60.5 + - - +
149B LYS* 3.4 12.6 + - - +
150B LYS* 3.1 22.9 + - - +
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Residues in contact with SER 147 (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 MET* 4.4 6.0 - - - +
134B GLU 3.9 3.8 + - - -
135B TYR* 5.2 3.8 - - - +
143B GLN 2.7 22.5 + - - -
144B LEU* 3.6 5.6 - - - -
146B ALA* 1.3 70.6 - - - +
148B PHE* 1.3 67.8 + - - +
150B LYS* 3.0 6.0 + - - +
151B GLN* 2.8 52.2 + - - +
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Residues in contact with PHE 148 (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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112B LYS* 4.0 7.6 - - + -
113B SER* 3.9 21.1 - - - -
116B PHE* 3.4 60.1 - + + -
127B GLU* 4.7 5.2 - - + -
128B MET* 4.4 13.4 - - + +
131B ARG* 3.1 34.8 - - - -
133B PHE* 3.9 25.4 - + - -
144B LEU 2.7 16.3 + - - +
145B ILE 3.4 7.2 - - - +
147B SER* 1.3 71.5 - - - +
149B LYS* 1.3 56.3 + - - +
151B GLN* 4.6 2.9 - - - +
152B LEU* 2.8 56.2 + - + +
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Residues in contact with LYS 149 (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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109B VAL* 4.0 8.5 - - + +
110B GLY* 4.7 10.7 - - - -
113B SER* 3.7 35.9 - - - +
145B ILE* 2.9 17.2 + - - +
146B ALA* 3.4 15.0 - - - +
147B SER 3.0 0.2 - - - -
148B PHE* 1.3 78.2 - - - +
150B LYS* 1.3 57.9 + - - +
152B LEU* 3.8 2.5 - - - +
153B ARG* 3.0 45.4 + - - +
8E A 3.5 29.7 + - - +
9E T 5.9 0.6 + - - -
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Residues in contact with LYS 150 (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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146B ALA 3.1 9.5 + - - +
147B SER* 3.0 9.4 + - - +
149B LYS* 1.3 80.9 - - - +
151B GLN* 1.3 67.5 + - + +
153B ARG* 3.5 16.5 - - - +
154B LYS* 3.3 29.4 + - + +
22D G 2.9 27.9 + - - -
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Residues in contact with GLN 151 (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 MET* 4.4 1.8 - - - +
133B PHE* 3.4 32.6 - - + +
134B GLU* 2.6 47.2 + - - +
147B SER* 2.8 39.6 + - - +
148B PHE* 4.1 1.1 - - - +
150B LYS* 1.3 75.1 - - + +
152B LEU* 1.3 68.0 + - - +
154B LYS* 3.3 12.4 + - - +
155B SER* 2.9 23.7 + - - -
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Residues in contact with LEU 152 (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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108B PHE* 4.8 6.3 - - + -
109B VAL* 4.5 17.0 - - + +
112B LYS* 3.7 35.4 - - + -
113B SER* 4.7 2.5 - - - +
131B ARG* 4.0 18.2 - - - +
133B PHE* 3.9 12.2 - - + -
148B PHE* 2.8 37.8 + - + +
149B LYS 3.8 2.0 - - - +
151B GLN* 1.3 72.5 - - - +
153B ARG* 1.3 66.1 + - - +
155B SER* 2.5 29.2 + - - +
156B LEU* 3.2 30.6 + - + +
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Residues in contact with ARG 153 (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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2A LEU* 4.0 12.7 - - + +
109B VAL* 4.1 35.2 - - + +
149B LYS* 3.0 35.1 + - - +
150B LYS* 3.5 16.6 - - - +
152B LEU* 1.3 76.2 - - - +
154B LYS* 1.3 63.7 + - - +
156B LEU* 2.9 16.1 + - - +
157B LYS* 3.5 7.1 + - - -
7E G 3.4 61.6 + - - +
8E A 3.5 14.6 + - - -
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Residues in contact with LYS 154 (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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150B LYS* 3.3 18.8 + - + +
151B GLN* 3.3 14.9 + - - +
153B ARG* 1.3 80.0 - - - +
155B SER* 1.3 59.6 + - - +
156B LEU 3.0 5.2 + - - -
157B LYS* 3.1 28.8 + - + +
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Residues in contact with SER 155 (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 PHE* 3.8 17.7 - - - -
151B GLN 2.9 15.8 + - - -
152B LEU* 2.5 32.4 + - - +
154B LYS* 1.3 76.7 - - - +
156B LEU* 1.3 67.2 + - - +
157B LYS 3.6 0.4 - - - -
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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