Contacts of the helix formed by residues 131 - 144 (chain B) in PDB entry 2W27
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 ASP 131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B PHE* 3.4 8.9 - - - -
130B GLY* 1.3 67.9 - - - -
132B ILE* 1.3 67.4 + - - +
133B GLU* 2.8 31.1 + - - +
134B GLN* 3.0 37.7 + - + +
135B LEU 3.4 0.3 + - - -
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Residues in contact with ILE 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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125B GLU* 4.3 8.7 - - + +
128B PHE* 3.7 17.3 - - + -
130B GLY 3.1 6.0 + - - +
131B ASP* 1.3 77.3 + - - +
133B GLU* 1.3 73.8 + - + +
135B LEU* 3.4 12.1 + - + +
136B TYR* 3.0 26.7 + - + +
163B ARG* 3.7 57.9 - - + +
166B LEU* 5.6 4.7 - - + -
167B LEU* 4.5 19.5 - - + -
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Residues in contact with GLU 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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131B ASP* 2.8 18.4 + - - +
132B ILE* 1.3 85.7 - - + +
134B GLN* 1.3 57.4 + - - +
136B TYR* 3.8 16.6 - - + +
137B HIS* 3.1 27.0 + - - +
166B LEU* 3.5 27.2 - - - +
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Residues in contact with GLN 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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95B MET* 3.4 23.8 - - + +
98B HIS* 3.4 25.6 - - + -
128B PHE* 5.6 0.7 - - + -
131B ASP* 3.0 26.1 + - + +
133B GLU* 1.3 79.5 - - - +
135B LEU* 1.3 64.2 + - - +
137B HIS* 3.1 9.4 + - + +
138B MET* 3.0 18.7 + - - +
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Residues in contact with LEU 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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91B ALA* 3.8 24.9 - - + +
94B LEU* 6.3 1.3 - - + -
95B MET* 4.0 13.8 - - - +
123B ILE* 4.8 12.1 - - + -
125B GLU* 5.3 3.8 - - - -
128B PHE* 3.5 49.3 - - + -
131B ASP 3.4 2.6 + - - -
132B ILE* 3.4 14.3 + - + +
134B GLN* 1.3 78.6 - - - +
136B TYR* 1.3 58.1 + - - +
138B MET* 3.3 15.2 + - - +
139B LEU* 3.1 50.8 + - + +
167B LEU* 4.8 5.4 - - + -
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Residues in contact with TYR 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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132B ILE* 3.0 14.8 + - + +
133B GLU* 3.8 16.8 - - + +
135B LEU* 1.3 73.6 - - - +
137B HIS* 1.3 79.2 + + - +
139B LEU* 3.8 5.0 + - + +
140B ALA* 3.4 27.4 + - + +
166B LEU* 3.4 41.7 - - + -
167B LEU* 3.4 34.9 - - + +
168B SER* 5.7 1.8 - - - -
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Residues in contact with HIS 137 (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 GLU 3.1 16.7 + - - +
134B GLN* 3.1 16.1 + - + +
136B TYR* 1.3 89.1 - + - +
138B MET* 1.3 59.2 + - - +
140B ALA* 3.0 26.8 - - - +
141B TYR* 3.4 4.7 + - - +
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Residues in contact with MET 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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91B ALA 5.9 0.2 - - - +
94B LEU* 3.6 30.5 - - + +
95B MET* 3.9 27.1 - - + +
98B HIS* 3.9 26.0 - - + +
99B GLY* 4.0 3.6 - - - -
134B GLN 3.0 11.9 + - - +
135B LEU* 3.3 17.0 + - - +
137B HIS* 1.3 73.3 - - - +
139B LEU* 1.3 71.9 + - + +
141B TYR* 2.8 33.2 + - + +
142B TYR* 3.1 46.7 + - + +
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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
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94B LEU* 5.4 0.4 - - + -
121B LEU* 5.1 0.7 - - + -
123B ILE* 4.3 19.3 - - + -
135B LEU* 3.1 32.7 + - + +
136B TYR* 4.3 4.5 - - + +
137B HIS 3.4 0.2 - - - -
138B MET* 1.3 93.9 - - + +
140B ALA* 1.3 62.2 + - - +
142B TYR* 3.1 10.7 + - + +
143B ARG* 2.9 29.9 + - - +
149B ILE* 3.6 41.0 - - + +
167B LEU* 3.4 36.1 - - + +
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Residues in contact with ALA 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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136B TYR* 3.4 24.8 + - + +
137B HIS* 3.0 19.9 + - - +
139B LEU* 1.3 77.2 - - - +
141B TYR* 1.3 61.3 + - - +
143B ARG* 3.1 21.2 + - - +
144B THR* 3.1 19.4 + - + +
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Residues in contact with TYR 141 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B LEU* 3.9 17.0 - - + -
107B LYS* 5.5 0.2 + - - -
137B HIS 3.4 3.7 + - - +
138B MET* 2.8 19.6 + - + +
140B ALA* 1.3 73.6 - - - +
142B TYR* 1.3 69.6 + + + +
144B THR* 2.3 34.4 + - + -
145B TYR* 3.4 40.4 + + - -
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Residues in contact with TYR 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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94B LEU* 4.1 1.7 - - + +
98B HIS 4.9 1.1 - - - -
99B GLY* 2.7 36.7 + - - -
102B PHE* 3.6 18.6 - + - +
103B LEU* 3.5 29.4 + - + -
106B LEU* 4.9 0.4 - - + -
121B LEU* 3.5 35.0 - - + -
138B MET* 3.1 39.7 + - + +
139B LEU* 3.1 15.2 + - + +
141B TYR* 1.3 83.0 - + + +
143B ARG* 1.3 56.3 + - - +
145B TYR* 2.9 30.3 + - - +
147B ILE* 3.5 37.4 - - + +
149B ILE* 4.9 4.3 - - + -
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Residues in contact with ARG 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 LEU* 2.9 20.5 + - - +
140B ALA* 3.1 14.3 + - - +
142B TYR* 1.3 69.9 - - - +
144B THR* 1.3 55.3 + - + +
145B TYR 2.9 5.6 - - - -
146B GLY* 2.6 27.0 + - - -
147B ILE 3.6 20.6 + - - +
149B ILE* 4.2 14.3 - - + +
167B LEU 4.2 8.4 + - - -
168B SER* 2.6 31.4 + - - -
169B PRO* 3.2 3.2 - - - +
170B ASP* 2.8 50.6 + - - +
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Residues in contact with THR 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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140B ALA* 3.1 16.1 + - + +
141B TYR* 2.3 33.6 + - + -
143B ARG* 1.3 74.1 - - + +
145B TYR* 1.3 66.8 + - - +
146B GLY 3.5 0.2 - - - -
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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