Contacts of the helix formed by residues 135 - 150 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B SER* 3.1 14.9 + - - +
133B LEU 3.9 0.2 - - - -
134B THR* 1.3 81.7 + - - +
136B MET* 1.3 64.4 + - - +
137B ASN* 3.4 18.8 - - - +
138B SER* 3.3 3.2 + - - -
139B LEU* 3.0 21.3 + - - +
190B TYR* 3.5 14.4 - - - +
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Residues in contact with MET 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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134B THR 3.5 4.1 + - - +
135B ALA* 1.3 69.9 - - - +
137B ASN* 1.3 68.0 + - - +
139B LEU* 3.1 8.0 + - + -
140B GLN* 2.8 50.3 + - + +
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASN* 3.7 30.8 - - - +
135B ALA* 3.4 9.4 - - - +
136B MET* 1.3 75.1 - - - +
138B SER* 1.3 77.3 + - - +
140B GLN* 4.0 0.2 + - - -
141B ARG* 2.9 45.7 + - - +
190B TYR* 2.8 36.7 + - - -
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Residues in contact with SER 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B THR* 2.7 19.9 + - - +
132B SER 2.7 29.3 + - - -
135B ALA* 3.6 7.9 - - - -
136B MET 3.2 0.4 - - - -
137B ASN* 1.3 82.2 + - - +
139B LEU* 1.3 65.7 + - - +
141B ARG* 3.5 1.7 + - - +
142B ILE* 3.1 29.5 + - - +
189B VAL* 3.9 10.2 - - - +
190B TYR* 3.5 20.9 - - - -
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 3.9 31.0 - - + +
134B THR* 3.3 28.7 - - - +
135B ALA 3.0 13.4 + - - +
136B MET* 3.7 8.3 - - + +
138B SER* 1.3 78.1 - - - +
140B GLN* 1.3 54.0 + - + +
142B ILE* 3.2 10.8 + - + +
143B GLN* 2.7 37.2 + - - +
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Residues in contact with GLN 140 (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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104B ASP* 5.6 1.6 + - - -
105B ASN* 3.7 21.1 + - + +
106B TYR* 3.3 39.2 - - + +
136B MET* 2.8 48.2 + - + +
139B LEU* 1.3 75.2 - - + +
141B ARG* 1.3 59.7 + - - +
142B ILE 3.1 1.6 - - - -
143B GLN* 3.7 6.9 - - + +
144B GLY* 2.8 25.8 + - - -
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Residues in contact with ARG 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASN* 3.0 41.1 + - + +
109B GLY* 3.3 8.8 - - - -
137B ASN* 2.9 36.5 + - - +
138B SER 3.9 4.0 - - - +
140B GLN* 1.3 75.7 - - - +
142B ILE* 1.3 58.4 + - - +
145B PHE* 3.1 26.3 + - - +
187B PHE* 4.0 5.7 - - + -
189B VAL* 2.9 37.8 + - + -
190B TYR* 3.9 16.1 - - - +
215B PHE* 3.2 45.9 - - + +
216B ASP* 4.5 5.5 + - - -
236B GLN* 3.7 25.3 + - - +
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Residues in contact with ILE 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ILE* 4.1 25.4 - - + -
130B THR* 4.0 26.0 - - + -
133B LEU* 4.9 7.6 - - + -
138B SER* 3.1 23.0 + - - +
139B LEU* 3.6 10.1 - - + +
140B GLN 3.1 0.4 - - - -
141B ARG* 1.3 76.5 - - - +
143B GLN* 1.3 61.1 + - - +
145B PHE* 3.7 4.7 - - - +
146B LYS* 2.8 58.6 + - + +
159B ILE* 4.4 12.8 - - + -
187B PHE* 4.6 1.1 - - + -
189B VAL* 3.9 16.2 - - + -
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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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106B TYR* 3.9 12.1 - - + -
139B LEU 2.7 21.0 + - - +
140B GLN* 3.7 8.1 - - + +
142B ILE* 1.3 75.8 - - - +
144B GLY* 1.3 62.6 + - - +
146B LYS* 3.2 18.3 + - - +
147B ASP* 3.0 58.6 + - - +
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Residues in contact with GLY 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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106B TYR* 3.6 23.0 - - - -
109B GLY 4.0 0.2 - - - -
110B TYR* 3.6 22.3 - - - -
140B GLN 2.8 19.8 + - - -
143B GLN* 1.3 72.9 - - - +
145B PHE* 1.3 62.8 + - - +
147B ASP* 3.1 4.5 + - - +
148B ALA* 3.0 22.7 + - - +
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Residues in contact with PHE 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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109B GLY 3.3 11.7 + - - +
112B ALA 4.2 2.0 - - - -
113B GLY* 3.7 19.1 - - - -
116B MET* 3.8 46.9 - - + -
126B VAL* 4.2 15.0 - - + -
128B ILE* 4.4 4.0 - - + -
141B ARG 3.1 20.1 + - - +
142B ILE* 3.7 4.0 - - - +
144B GLY* 1.3 73.1 - - - +
146B LYS* 1.3 65.3 + - - +
148B ALA* 3.1 12.1 + - - +
149B ILE* 3.4 34.4 + - + +
156B ILE* 4.1 18.8 - - + -
187B PHE* 3.7 47.3 - + + -
213B VAL* 5.5 0.2 - - + -
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Residues in contact with LYS 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 ILE* 2.8 41.9 + - + +
143B GLN* 3.5 24.0 + - - +
144B GLY 3.2 0.2 - - - -
145B PHE* 1.3 74.0 - - - +
147B ASP* 1.3 63.4 + - - +
149B ILE* 3.4 10.2 + - - +
150B LYS* 3.2 23.6 + - - +
156B ILE* 3.8 22.7 - - + -
159B ILE* 4.3 19.0 - - - +
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Residues in contact with ASP 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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106B TYR* 2.6 41.2 + - - +
110B TYR* 4.1 10.7 + - + -
143B GLN* 3.0 33.3 + - - +
144B GLY 3.1 3.6 + - - +
146B LYS* 1.3 77.6 - - - +
148B ALA* 1.3 62.7 + - - +
149B ILE 3.4 0.5 + - - -
150B LYS* 3.6 22.1 + - - +
151B ASP* 5.1 1.4 + - - +
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Residues in contact with ALA 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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110B TYR* 3.5 39.8 + - + +
113B GLY* 3.5 17.7 - - - -
114B LEU* 3.7 17.6 - - + +
117B LYS* 3.7 18.0 + - - +
144B GLY 3.0 10.2 + - - +
145B PHE 3.1 4.2 + - - +
147B ASP* 1.3 78.4 - - - +
149B ILE* 1.3 60.4 + - - +
150B LYS 3.5 0.2 - - - -
151B ASP* 3.8 6.8 - - - +
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Residues in contact with ILE 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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113B GLY* 4.0 20.9 - - - +
116B MET* 5.0 0.4 - - + -
117B LYS* 4.6 11.0 - - + +
145B PHE* 3.7 35.9 - - + +
146B LYS* 3.4 13.0 - - - +
148B ALA* 1.3 78.8 - - - +
150B LYS* 1.3 67.8 + - - +
151B ASP* 3.3 2.7 - - - -
152B SER* 2.7 36.5 + - - +
154B ILE* 3.7 40.4 - - + +
156B ILE* 4.1 20.6 - - + +
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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 LYS 3.2 12.3 + - - +
147B ASP* 3.6 20.4 - - - +
148B ALA 3.5 1.2 - - - -
149B ILE* 1.3 78.3 - - - +
151B ASP* 1.3 63.4 + - - +
152B SER 2.9 13.3 + - - +
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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