Contacts of the helix formed by residues 135 - 150 (chain A) in PDB entry 3C6Q
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 ALA 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A SER* 3.2 14.6 + - - +
133A LEU 3.9 0.2 - - - -
134A THR* 1.3 81.6 + - - +
136A MET* 1.3 59.6 + - - +
137A ASN* 3.4 19.1 - - - +
138A SER* 3.4 3.0 + - - -
139A LEU* 3.0 26.5 + - - +
190A TYR* 3.5 14.4 - - - +
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Residues in contact with MET 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 3.5 3.8 + - - +
135A ALA* 1.3 69.7 - - - +
137A ASN* 1.3 68.0 + - - +
139A LEU* 3.1 8.2 + - + -
140A GLN* 2.8 50.6 + - + +
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Residues in contact with ASN 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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105A ASN* 3.6 31.2 - - - +
135A ALA* 3.4 9.6 - - - +
136A MET* 1.3 74.7 - - - +
138A SER* 1.3 76.4 + - - +
140A GLN* 4.0 0.4 + - - -
141A ARG* 2.9 45.0 + - - +
190A TYR* 2.8 36.3 + - - -
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Residues in contact with SER 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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130A THR* 2.7 20.5 + - - +
132A SER 2.6 29.4 + - - -
133A LEU* 5.5 0.3 - - - +
135A ALA* 3.6 7.6 - - - -
136A MET 3.1 0.4 - - - -
137A ASN* 1.3 82.4 + - - +
139A LEU* 1.3 65.2 + - - +
141A ARG* 3.5 1.6 + - - +
142A ILE* 3.1 29.6 + - - +
189A VAL* 3.9 10.4 - - - +
190A TYR* 3.5 21.1 - - - -
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Residues in contact with LEU 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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133A LEU* 3.9 31.0 - - + +
134A THR* 3.3 27.4 - - - +
135A ALA 3.0 14.1 + - - +
136A MET* 3.7 8.3 - - + +
138A SER* 1.3 78.1 - - - +
140A GLN* 1.3 53.5 + - + +
142A ILE* 3.3 10.5 + - + +
143A GLN* 2.7 36.8 + - - +
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Residues in contact with GLN 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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104A ASP* 5.6 1.4 + - - -
105A ASN* 3.8 23.1 + - + +
106A TYR* 3.3 37.4 - - + +
136A MET* 2.8 48.6 + - + +
139A LEU* 1.3 75.4 - - + +
141A ARG* 1.3 59.7 + - - +
142A ILE 3.1 1.6 - - - -
143A GLN* 3.7 6.9 - - + +
144A GLY* 2.8 25.8 + - - -
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Residues in contact with ARG 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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103A THR* 5.5 0.2 - - - +
105A ASN* 3.0 41.7 + - + +
109A GLY* 3.4 8.4 - - - -
137A ASN* 2.9 35.8 + - - +
138A SER 4.0 4.0 - - - +
140A GLN* 1.3 75.0 - - - +
142A ILE* 1.3 57.9 + - - +
145A PHE* 3.1 26.3 + - - +
187A PHE* 4.1 5.3 - - + -
189A VAL* 2.9 36.7 + - + -
190A TYR* 4.0 15.9 - - - +
215A PHE* 3.2 46.0 - - + +
216A ASP* 4.5 6.1 + - - -
236A GLN* 3.6 25.3 + - - +
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Residues in contact with ILE 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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128A ILE* 4.1 26.0 - - + -
130A THR* 4.0 26.0 - - + -
133A LEU* 4.9 7.4 - - + -
138A SER* 3.1 23.4 + - - +
139A LEU* 3.6 10.3 - - + +
141A ARG* 1.3 76.0 - - - +
143A GLN* 1.3 61.2 + - - +
145A PHE* 3.5 5.3 + - - +
146A LYS* 2.8 57.3 + - + +
159A ILE* 4.4 12.6 - - + -
187A PHE* 4.6 0.9 - - + -
189A VAL* 3.9 16.2 - - + -
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Residues in contact with GLN 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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106A TYR* 4.0 12.3 - - + -
139A LEU 2.7 21.6 + - - +
140A GLN* 3.7 8.3 - - + +
142A ILE* 1.3 74.2 - - - +
144A GLY* 1.3 62.6 + - - +
146A LYS* 3.2 19.9 + - - +
147A ASP* 3.0 59.5 + - - +
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Residues in contact with GLY 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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106A TYR* 3.6 23.0 - - - -
109A GLY 4.0 0.2 - - - -
110A TYR* 3.6 22.5 - - - -
140A GLN 2.8 20.3 + - - -
143A GLN* 1.3 72.0 - - - +
145A PHE* 1.3 62.8 + - - +
147A ASP* 3.1 5.2 + - - +
148A ALA* 3.0 22.5 + - - +
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Residues in contact with PHE 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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109A GLY 3.3 11.2 + - - +
112A ALA 4.2 2.0 - - - -
113A GLY* 3.7 19.3 - - - -
116A MET* 3.8 47.1 - - + -
126A VAL* 4.2 15.0 - - + -
128A ILE* 4.4 4.0 - - + -
141A ARG 3.1 19.9 + - - +
142A ILE* 3.7 4.3 - - - +
144A GLY* 1.3 73.7 - - - +
146A LYS* 1.3 65.1 + - - +
148A ALA* 3.1 11.8 + - - +
149A ILE* 3.4 34.8 + - + +
156A ILE* 4.1 18.8 - - + -
187A PHE* 3.7 47.3 - + + -
213A VAL* 5.5 0.2 - - + -
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Residues in contact with LYS 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 ILE* 2.8 42.5 + - + +
143A GLN* 3.4 24.2 + - - +
145A PHE* 1.3 74.9 - - - +
147A ASP* 1.3 63.7 + - - +
149A ILE* 3.4 10.0 + - - +
150A LYS* 3.2 23.4 + - - +
156A ILE* 3.8 21.8 - - + -
159A ILE* 4.4 19.2 - - - +
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Residues in contact with ASP 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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106A TYR* 2.6 41.4 + - - +
110A TYR* 4.1 10.6 + - + -
143A GLN* 3.0 32.3 + - - +
144A GLY 3.1 3.6 + - - +
146A LYS* 1.3 78.2 - - - +
148A ALA* 1.3 63.9 + - - +
149A ILE 3.4 0.5 + - - -
150A LYS* 3.5 21.9 + - - +
151A ASP* 5.0 1.6 + - - +
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Residues in contact with ALA 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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110A TYR* 3.5 42.2 + - + +
113A GLY* 3.5 17.7 - - - -
114A LEU* 3.7 15.2 - - + +
117A LYS* 3.8 17.7 + - - +
144A GLY 3.0 10.4 + - - +
145A PHE 3.1 4.2 + - - +
147A ASP* 1.3 78.0 - - - +
149A ILE* 1.3 60.0 + - - +
150A LYS 3.5 0.2 - - - -
151A ASP* 3.8 6.9 - - - +
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Residues in contact with ILE 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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113A GLY* 4.1 20.0 - - - +
116A MET* 5.0 0.4 - - + -
117A LYS* 4.6 6.3 - - + +
145A PHE* 3.7 35.9 - - + +
146A LYS* 3.4 13.2 - - - +
148A ALA* 1.3 79.2 - - - +
150A LYS* 1.3 68.5 + - - +
151A ASP* 3.2 2.9 - - - -
152A SER* 2.7 36.5 + - - +
154A ILE* 3.7 45.7 - - + +
156A ILE* 4.1 20.4 - - + +
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Residues in contact with LYS 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 LYS 3.2 13.3 + - - +
147A ASP* 3.6 20.6 - - - +
148A ALA 3.5 1.2 - - - -
149A ILE* 1.3 77.6 - - - +
151A ASP* 1.3 63.8 + - - +
152A SER 2.9 14.2 + - - +
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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