Contacts of the helix formed by residues 135 - 155 (chain B) in PDB entry 2B92
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 ASN 135 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.7 26.8 - - + +
47A TYR* 4.4 4.3 - - + -
102A GLY* 3.6 14.6 - - - +
104A VAL* 3.8 3.1 - - - -
46B LEU* 6.3 0.4 - - - +
133B THR* 3.9 17.3 - - - +
134B ILE* 1.3 85.1 - - - +
136B GLN* 1.3 68.4 + - - +
137B GLN* 3.5 19.9 + - - +
138B ALA* 2.9 35.7 + - + +
139B MET* 3.1 5.5 + - - +
180B TRP* 4.7 2.2 - - + -
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Residues in contact with GLN 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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102A GLY* 2.9 28.3 + - - +
103A ASP 4.0 3.4 - - - +
104A VAL* 3.5 10.6 - - - +
107A GLY* 3.6 23.9 - - - -
108A ASP 5.0 0.7 - - - +
109A ASN* 3.8 20.4 - - - +
135B ASN* 1.3 75.3 + - - +
137B GLN* 1.3 51.7 + - + +
139B MET* 3.0 26.1 + - - +
140B ASP* 2.7 63.9 + - - +
222B PRO* 4.8 3.6 - - - +
223B ARG* 3.1 29.8 + - - +
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Residues in contact with GLN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.3 21.3 - - + +
101A LEU* 4.6 7.5 - - - +
102A GLY* 4.7 5.5 - - - -
109A ASN* 5.6 5.0 + - - +
112A ASP* 4.9 5.9 + - - -
137A GLN* 4.6 33.8 - - + +
138A ALA* 5.8 0.3 - - - -
141A GLN* 3.1 31.1 + - - +
135B ASN* 3.2 18.1 + - - +
136B GLN* 1.3 72.2 - - + +
138B ALA* 1.3 62.0 + - - +
140B ASP* 3.5 10.0 - - - +
141B GLN* 3.0 24.1 + - - +
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Residues in contact with ALA 138 (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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137A GLN* 5.6 0.9 - - - -
128B TYR* 3.6 26.7 + - + +
130B SER* 5.8 1.8 - - - -
135B ASN* 2.9 26.6 + - + +
137B GLN* 1.3 75.9 - - - +
139B MET* 1.3 58.2 + - - +
141B GLN* 3.0 7.7 + - - +
142B LEU* 2.9 29.7 + - - +
180B TRP* 3.9 24.0 - - + -
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Residues in contact with MET 139 (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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104A VAL* 5.2 3.8 - - - -
134B ILE* 5.2 3.1 - - + -
135B ASN 3.1 6.0 + - - +
136B GLN* 3.0 30.3 + - - +
138B ALA* 1.3 76.8 - - - +
140B ASP* 1.3 64.6 + - - +
142B LEU* 3.1 8.2 + - + +
143B TYR* 2.9 23.8 + - - +
180B TRP* 4.6 18.1 - - + -
205B SER* 4.1 19.7 - - - +
206B LEU* 3.6 24.9 - - + -
222B PRO* 4.2 16.2 - - + -
223B ARG* 3.6 35.7 - - + +
226B ILE* 4.0 15.5 - - + +
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Residues in contact with ASP 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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109A ASN* 3.1 31.6 + - - +
136B GLN* 2.7 47.0 + - - +
137B GLN* 3.5 10.8 - - - +
139B MET* 1.3 71.8 - - - +
141B GLN* 1.3 57.7 + - - +
143B TYR* 3.1 12.6 + - - +
144B TYR* 2.9 26.4 + - - +
222B PRO* 5.0 7.1 - - - +
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Residues in contact with GLN 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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137A GLN* 2.9 34.2 + - - +
46B LEU* 5.6 0.2 - - - +
101B LEU* 4.0 18.9 - - - +
109B ASN* 6.3 0.8 - - - +
112B ASP* 4.9 5.1 - - - +
113B SER* 4.6 13.9 + - - +
116B PHE* 3.6 32.0 - - + -
128B TYR* 5.0 4.5 + - + +
137B GLN 3.0 12.9 + - - +
138B ALA* 3.0 5.4 + - - +
140B ASP* 1.3 76.2 - - - +
142B LEU* 1.3 66.4 + - - +
144B TYR* 3.1 10.3 + - + +
145B VAL* 3.0 26.2 + - + +
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Residues in contact with LEU 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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116B PHE* 4.1 29.3 - - + -
120B VAL* 5.3 1.8 - - + -
126B PHE* 4.4 7.2 - - + -
128B TYR* 5.1 5.6 - - + -
138B ALA 2.9 12.4 + - - +
139B MET* 3.3 9.4 - - - +
141B GLN* 1.3 76.3 - - - +
143B TYR* 1.3 63.3 + - - +
145B VAL* 3.6 0.9 + - + +
146B THR* 3.1 21.9 + - - +
178B PHE* 3.8 30.5 - - + -
180B TRP* 4.6 11.9 - - + -
226B ILE* 3.8 28.3 - - + -
230B PHE* 3.9 26.0 - - + -
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Residues in contact with TYR 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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139B MET 2.9 12.2 + - - +
140B ASP* 3.3 11.2 - - - +
142B LEU* 1.3 73.2 - - - +
144B TYR* 1.3 72.8 + - - +
146B THR* 2.9 16.9 + - + -
147B GLU* 3.0 41.0 + - + +
221B LEU* 3.4 34.5 - - + +
222B PRO* 3.7 34.3 - - + +
225B CYS* 3.4 31.2 - - + -
226B ILE* 4.3 6.5 - - + +
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Residues in contact with TYR 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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113B SER* 3.7 24.6 - - - -
140B ASP 2.9 12.4 + - - +
141B GLN* 3.5 12.8 - - + +
143B TYR* 1.3 84.1 - - + +
145B VAL* 1.3 66.2 + - + +
147B GLU* 3.4 5.6 + - - +
148B LEU* 3.0 42.5 + - + +
151B ARG* 4.5 20.1 + - - -
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Residues in contact with VAL 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* 4.7 7.9 - - - +
116B PHE* 3.6 43.7 - - + -
117B ALA* 3.7 33.4 - - + -
120B VAL* 4.3 10.3 - - + -
141B GLN* 3.0 19.3 + - + +
142B LEU* 4.0 3.4 - - + +
144B TYR* 1.3 84.2 - - + +
146B THR* 1.3 58.0 + - - +
148B LEU* 2.9 7.6 + - + +
149B THR* 2.7 34.2 + - - +
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Residues in contact with THR 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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120B VAL* 5.5 2.7 - - - +
142B LEU* 3.1 13.2 + - - +
143B TYR* 2.9 12.3 + - - +
145B VAL* 1.3 80.3 - - - +
147B GLU* 1.3 70.3 + - + +
149B THR* 3.0 29.2 - - - +
150B HIS* 3.4 13.9 + - - +
225B CYS* 4.4 16.2 - - + +
226B ILE* 5.1 2.1 - - - +
229B PHE* 3.8 31.4 - - + +
230B PHE* 3.7 26.0 - - - -
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Residues in contact with GLU 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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143B TYR* 3.0 44.2 + - + +
144B TYR* 3.7 7.4 - - - +
146B THR* 1.3 79.8 - - + +
148B LEU* 1.3 56.4 + - - +
150B HIS* 3.7 28.5 + - - +
151B ARG* 3.2 35.6 + - - +
225B CYS* 3.1 27.9 - - - +
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Residues in contact with LEU 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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113B SER* 4.2 13.2 - - - +
114B TRP* 3.8 32.5 - - + -
117B ALA* 4.3 11.0 - - + -
144B TYR* 3.0 37.4 + - + +
145B VAL* 2.9 12.0 + - + +
147B GLU* 1.3 75.6 - - - +
149B THR* 1.3 65.2 + - - +
150B HIS 3.2 1.3 - - - -
151B ARG* 3.1 33.4 + - + +
152B ILE* 3.1 39.4 + - + +
308B ASP* 4.7 4.7 - - - +
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Residues in contact with THR 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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117B ALA* 4.1 3.6 + - - +
120B VAL* 3.5 23.0 - - - +
121B LEU* 3.7 17.7 - - + +
145B VAL* 2.7 15.5 + - - +
146B THR* 3.0 12.1 - - - +
148B LEU* 1.3 72.8 - - - +
150B HIS* 1.3 71.6 + - - +
152B ILE* 3.1 19.1 + - - +
153B ARG* 2.9 51.0 + - - +
229B PHE* 3.7 10.1 - - + -
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Residues in contact with HIS 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 THR* 3.4 15.8 + - - +
147B GLU* 3.7 33.4 + - - +
148B LEU 3.2 0.8 - - - -
149B THR* 1.3 80.7 - - - +
151B ARG* 1.3 57.1 + - + +
153B ARG* 3.4 21.4 + - - +
154B SER* 2.7 32.1 + - - -
175B PHE* 4.3 11.2 - + - -
229B PHE* 3.5 33.6 - + - +
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Residues in contact with ARG 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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144B TYR* 4.5 17.8 + - - -
147B GLU* 3.2 29.5 + - - +
148B LEU* 3.1 32.7 + - + +
149B THR 3.1 0.2 + - - -
150B HIS* 1.3 77.9 - - + +
152B ILE* 1.3 62.0 + - - +
154B SER* 3.2 16.2 + - - -
155B LYS* 3.3 13.7 + - - +
308B ASP* 4.9 14.9 + - - +
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Residues in contact with ILE 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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114B TRP* 4.3 13.7 - - + -
117B ALA* 4.1 18.2 - - + -
121B LEU* 3.8 23.1 - - + -
148B LEU* 3.1 46.1 + - + +
149B THR* 3.7 5.8 - - - +
151B ARG* 1.3 74.1 - - - +
153B ARG* 1.3 67.0 + - - +
154B SER 3.2 0.7 + - - -
155B LYS* 3.3 20.0 + - - +
156B SER* 3.7 5.4 + - - -
300B TYR* 4.0 19.6 - - + +
303B ALA* 4.4 18.3 - - + +
304B ILE* 4.8 15.0 - - + -
308B ASP* 5.1 11.0 - - - +
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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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120B VAL* 5.7 0.4 + - - +
121B LEU* 3.8 16.4 - - + +
149B THR* 2.9 43.1 + - - +
150B HIS* 3.4 30.9 + - - +
152B ILE* 1.3 76.9 - - - +
154B SER* 1.3 59.2 + - - +
156B SER* 2.9 29.3 + - - +
174B PHE* 3.7 25.9 - - - -
175B PHE* 3.2 33.0 - - - -
176B PRO* 5.4 1.8 - - - +
229B PHE* 4.1 4.2 - - - -
300B TYR* 3.9 24.9 + - + +
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Residues in contact with SER 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 HIS 2.7 17.2 + - - -
151B ARG* 3.2 11.5 + - - -
152B ILE 3.2 0.2 - - - -
153B ARG* 1.3 71.9 - - - +
155B LYS* 1.3 51.0 + - - +
156B SER 2.2 27.1 + - - -
157B SER* 2.9 20.1 + - - +
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Residues in contact with LYS 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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151B ARG 3.3 8.7 + - - +
152B ILE* 3.3 14.4 + - - +
154B SER* 1.3 74.8 - - - +
156B SER* 1.4 57.2 + - - -
157B SER 4.0 1.8 - - - -
303B ALA* 3.7 24.9 + - + +
304B ILE 5.6 0.2 + - - -
306B SER* 3.5 19.9 - - - -
307B GLY 3.4 16.0 - - - +
308B ASP* 3.2 55.7 + - + +
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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