Contacts of the helix formed by residues 135 - 149 (chain B) in PDB entry 5W4A
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 135 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LYS* 6.4 1.6 - - - -
133B GLN* 3.3 7.4 + - + +
134B LYS* 1.3 87.3 - - + +
136B GLU* 1.3 64.3 + - - +
137B ALA* 3.8 8.3 + - - +
138B ALA* 3.1 26.0 + - - +
139B LYS* 3.2 26.0 + - - +
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Residues in contact with GLU 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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6B ARG 5.8 0.4 - - - +
8B ILE* 3.6 33.2 + - + +
15B ARG* 2.9 26.0 + - - -
134B LYS 4.2 0.2 + - - -
135B THR* 1.3 70.6 - - - +
137B ALA* 1.3 67.2 + - - +
139B LYS* 3.2 8.4 + - + +
140B ILE* 2.9 32.7 + - + +
166B LEU* 4.6 14.0 - - + +
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Residues in contact with ALA 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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5B LYS* 4.6 17.7 - - + -
6B ARG* 3.4 44.3 + - + +
135B THR* 3.3 8.1 + - - +
136B GLU* 1.3 78.9 - - - +
138B ALA* 1.3 60.6 + - - +
140B ILE* 3.5 3.6 + - - +
141B LEU* 3.2 22.3 + - - +
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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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130B ALA* 3.4 30.8 - - + +
133B GLN* 3.6 26.7 - - + +
135B THR* 3.1 21.7 + - - +
137B ALA* 1.3 77.1 - - - +
139B LYS* 1.3 60.6 + - - +
141B LEU* 3.3 9.9 + - - +
142B ALA* 3.0 23.4 + - - +
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Residues in contact with LYS 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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131B LYS* 3.1 29.7 + - + +
132B LEU 4.9 0.6 - - - -
133B GLN 2.8 27.3 + - - +
134B LYS* 4.1 17.7 - - - +
135B THR 3.2 18.7 + - - +
136B GLU* 3.2 4.4 + - + +
138B ALA* 1.3 74.5 - - - +
140B ILE* 1.3 64.4 + - - +
142B ALA* 3.2 8.4 + - - +
143B ILE* 3.0 29.3 + - + +
166B LEU* 3.9 31.6 - - + -
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Residues in contact with ILE 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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6B ARG* 4.0 15.7 - - + +
8B ILE* 3.8 31.4 - - + +
17B TYR* 3.6 46.9 - - + -
18B PHE* 4.4 11.0 - - + -
79B ASP* 5.1 0.2 - - - +
136B GLU* 2.9 25.9 + - + +
137B ALA* 3.8 7.2 - - - +
139B LYS* 1.3 74.2 - - - +
141B LEU* 1.3 58.3 + - - +
143B ILE* 3.2 6.6 + - - +
144B LEU* 2.9 29.1 + - + +
163B LEU* 5.4 1.8 - - + -
166B LEU* 3.8 18.4 - - + -
168B LEU* 4.4 6.1 - - + -
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Residues in contact with LEU 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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6B ARG* 3.8 38.8 - - - +
107B ASP* 4.4 1.3 - - - +
108B LEU* 4.1 18.6 - - + -
126B MSE 4.5 16.6 - - + -
130B ALA* 4.4 14.4 - - + -
137B ALA 3.2 14.7 + - - +
138B ALA* 3.5 10.1 - - - +
140B ILE* 1.3 77.5 - - - +
142B ALA* 1.3 56.0 + - - +
144B LEU* 3.2 5.9 + - + +
145B ILE* 2.9 49.9 + - + +
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Residues in contact with ALA 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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127B GLY* 3.3 33.6 - - - +
130B ALA* 4.3 0.4 - - + +
131B LYS* 3.6 28.5 - - + +
138B ALA 3.0 13.6 + - - +
139B LYS 3.5 8.1 - - - +
140B ILE 3.2 0.2 - - - -
141B LEU* 1.3 78.0 - - - +
143B ILE* 1.3 62.3 + - - +
145B ILE* 3.3 2.8 + - - +
146B LYS* 3.0 32.0 + - - +
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Residues in contact with ILE 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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18B PHE* 5.6 1.8 - - + -
131B LYS* 5.3 10.3 - - + +
139B LYS* 3.0 19.0 + - + +
140B ILE* 3.2 4.4 + - - +
142B ALA* 1.3 77.5 - - + +
144B LEU* 1.3 62.4 + - - +
146B LYS* 3.3 9.0 + - + +
147B THR* 2.9 34.5 + - - +
159B GLU 3.7 20.4 - - - +
160B LEU* 4.6 1.8 - - + -
162B GLU* 3.7 38.6 - - + +
163B LEU* 3.9 30.1 - - + +
166B LEU* 4.0 21.5 - - + -
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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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6B ARG* 4.1 7.4 - - - +
18B PHE* 4.2 15.6 - - + -
79B ASP* 3.3 58.6 - - + +
82B LEU* 4.4 1.1 - - + -
83B ALA* 4.0 19.3 - - + +
108B LEU* 3.8 19.3 - - + -
140B ILE* 2.9 17.6 + - + +
141B LEU* 3.5 6.3 - - + +
143B ILE* 1.3 76.2 - - - +
145B ILE* 1.3 59.5 + - - +
147B THR* 3.2 5.5 + - - -
148B ILE* 2.9 51.3 + - + +
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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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108B LEU* 4.5 11.0 - - + -
123B LEU* 3.3 49.6 - - + +
124B ASN* 4.1 3.8 - - - +
126B MSE 4.1 15.3 - - - -
127B GLY* 3.8 19.7 - - - +
141B LEU* 2.9 44.3 + - + +
142B ALA 3.7 4.3 - - - +
143B ILE 3.3 0.2 - - - -
144B LEU* 1.3 75.7 - - - +
146B LYS* 1.3 59.2 + - + +
148B ILE* 3.3 8.4 + - - +
149B ASN* 3.0 39.8 + - - +
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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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124B ASN* 5.1 8.3 + - - +
127B GLY 4.5 13.9 - - - -
128B ARG* 3.8 30.5 - - - +
131B LYS* 4.2 29.8 - - + +
142B ALA* 3.0 23.9 + - - +
143B ILE* 3.8 7.9 - - + +
145B ILE* 1.3 79.5 - - + +
147B THR* 1.3 60.2 + - - +
149B ASN* 3.5 6.6 + - - +
150B SER* 2.8 26.8 + - - -
155B GLU* 5.2 0.7 - - - +
159B GLU* 3.6 36.7 - - + +
162B GLU* 6.0 0.7 - - + -
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Residues in contact with THR 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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83B ALA* 4.1 17.0 - - + +
143B ILE* 2.9 19.9 + - - +
144B LEU* 3.5 7.4 - - - -
146B LYS* 1.3 73.9 - - - +
148B ILE* 1.3 65.1 + - - +
150B SER* 3.1 24.6 + - - +
156B LYS* 3.6 33.2 - - + -
159B GLU* 4.1 3.4 - - - +
160B LEU* 3.4 46.6 + - + +
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Residues in contact with ILE 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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82B LEU* 3.8 39.0 - - + +
83B ALA* 4.6 0.9 - - - +
108B LEU* 4.2 6.7 - - + -
111B LEU* 3.8 30.1 - - + -
120B LYS* 3.6 29.4 + - - +
123B LEU* 5.7 2.5 - - + -
144B LEU* 2.9 45.0 + - + +
145B ILE* 3.6 7.2 - - + +
147B THR* 1.3 76.9 - - - +
149B ASN* 1.3 66.3 + - - +
150B SER 3.4 6.2 + - - +
151B GLU* 5.7 0.2 - - - +
156B LYS* 5.9 0.4 - - - +
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Residues in contact with ASN 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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111B LEU* 5.4 0.2 - - - +
120B LYS* 3.1 59.8 + - + +
123B LEU* 4.5 2.3 - - - +
124B ASN* 3.8 15.1 - - - +
145B ILE* 3.0 35.4 + - - +
146B LYS* 3.8 7.3 - - - +
147B THR 3.2 0.2 - - - -
148B ILE* 1.3 79.7 - - - +
150B SER* 1.3 61.5 + - - +
151B GLU* 3.7 13.1 + - - +
155B GLU* 4.4 5.5 - - - +
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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