Contacts of the helix formed by residues 135 - 149 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A LYS* 6.4 0.4 - - - +
133A GLN* 3.4 5.7 + - + +
134A LYS* 1.3 86.3 - - + +
136A GLU* 1.3 65.0 + - - +
137A ALA* 3.7 9.0 + - - +
138A ALA* 3.1 25.5 + - - +
139A LYS* 3.2 26.6 + - - +
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Residues in contact with GLU 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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6A ARG 5.6 1.8 - - - +
8A ILE* 3.7 34.8 + - + +
15A ARG* 2.9 24.7 + - - -
134A LYS 4.2 0.2 + - - -
135A THR* 1.3 73.7 - - - +
137A ALA* 1.3 62.7 + - - +
139A LYS* 3.2 8.5 + - + +
140A ILE* 2.9 31.7 + - + +
166A LEU* 4.6 15.0 - - + +
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Residues in contact with ALA 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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5A LYS* 4.2 19.7 - - + -
6A ARG* 3.4 40.9 + - + +
135A THR* 3.2 8.9 + - - +
136A GLU* 1.3 78.9 - - - +
138A ALA* 1.3 60.7 + - - +
140A ILE* 3.5 3.7 + - - +
141A LEU* 3.2 21.3 + - - +
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Residues in contact with ALA 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 ALA* 3.3 32.0 - - + +
133A GLN* 3.5 27.6 - - + +
135A THR* 3.1 21.2 + - - +
137A ALA* 1.3 78.0 - - - +
139A LYS* 1.3 58.1 + - - +
141A LEU* 3.3 9.9 + - - +
142A ALA* 3.0 23.4 + - - +
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Residues in contact with LYS 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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130A ALA 4.8 0.7 - - - -
131A LYS* 3.1 26.3 + - + +
132A LEU 4.9 0.6 - - - -
133A GLN 2.9 26.6 + - - +
134A LYS* 4.0 16.5 - - - +
135A THR 3.2 19.7 + - - +
136A GLU* 3.2 4.2 + - + +
138A ALA* 1.3 72.5 - - - +
140A ILE* 1.3 64.9 + - - +
142A ALA* 3.3 8.0 + - - +
143A ILE* 3.0 31.9 + - + +
166A LEU* 4.0 28.9 - - + -
164C CYS 5.0 3.6 + - - -
165C GLY* 4.5 20.9 - - - +
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Residues in contact with ILE 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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6A ARG* 4.0 20.4 - - + +
8A ILE* 3.8 30.3 - - + -
17A TYR* 3.7 45.8 - - + -
18A PHE* 4.2 12.9 - - + -
79A ASP* 5.2 0.2 - - - +
136A GLU* 2.9 24.8 + - + +
137A ALA* 3.8 4.7 - - - +
139A LYS* 1.3 74.2 - - - +
141A LEU* 1.3 64.3 + - - +
143A ILE* 3.2 6.5 + - - +
144A LEU* 2.9 23.8 + - + +
163A LEU* 5.4 1.3 - - + -
166A LEU* 3.8 19.1 - - + -
168A LEU* 4.4 6.1 - - + -
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Residues in contact with LEU 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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6A ARG* 3.8 34.5 - - - +
107A ASP* 4.5 4.5 - - - +
108A LEU* 4.0 22.9 - - + -
126A MSE 4.6 16.4 - - + -
130A ALA* 4.4 15.7 - - + -
137A ALA 3.2 12.1 + - - +
138A ALA* 3.3 10.7 + - - +
140A ILE* 1.3 79.5 - - - +
142A ALA* 1.3 61.2 + - - +
144A LEU* 3.3 5.4 + - + +
145A ILE* 2.9 43.5 + - + +
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Residues in contact with ALA 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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127A GLY* 3.3 33.0 - - - +
130A ALA* 4.2 1.1 - - + +
131A LYS* 3.6 26.2 - - + +
138A ALA 3.0 13.4 + - - +
139A LYS 3.6 7.9 - - - +
140A ILE 3.2 0.4 - - - -
141A LEU* 1.3 77.4 - - - +
143A ILE* 1.3 57.1 + - + +
145A ILE* 3.3 2.4 + - - +
146A LYS* 2.9 40.0 + - - +
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Residues in contact with ILE 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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18A PHE* 5.6 2.2 - - + -
131A LYS* 5.7 6.1 - - - -
139A LYS* 3.0 20.3 + - + +
140A ILE* 3.7 4.0 - - - +
142A ALA* 1.3 76.6 - - + +
144A LEU* 1.3 64.4 + - - +
146A LYS* 3.3 9.2 + - + +
147A THR* 2.9 34.1 + - - +
159A GLU 3.7 18.2 - - - +
160A LEU* 4.5 4.0 - - + -
162A GLU* 3.8 39.7 - - + +
163A LEU* 3.8 36.1 - - + +
166A LEU* 4.0 16.2 - - + -
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Residues in contact with LEU 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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6A ARG* 4.2 7.9 - - - +
18A PHE* 4.3 12.5 - - + -
79A ASP* 3.3 57.9 - - + +
82A LEU* 4.2 2.2 - - + -
83A ALA* 3.8 25.1 - - + +
108A LEU* 3.9 18.8 - - + -
140A ILE* 2.9 17.2 + - + +
141A LEU* 3.3 5.6 + - + +
143A ILE* 1.3 78.8 - - - +
145A ILE* 1.3 55.9 + - - +
147A THR* 3.2 4.4 + - - -
148A ILE* 2.9 46.7 + - + +
160A LEU* 6.4 0.2 - - - -
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Residues in contact with ILE 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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108A LEU* 4.3 11.9 - - + -
123A LEU* 3.3 49.6 - - + +
124A ASN* 4.1 3.1 - - - +
126A MSE 4.0 16.8 - - + -
127A GLY* 3.8 20.9 - - - +
141A LEU* 2.9 43.6 + - + +
142A ALA 3.7 3.8 - - - +
144A LEU* 1.3 75.3 - - - +
146A LYS* 1.3 68.1 + - + +
148A ILE* 3.3 8.8 + - + +
149A ASN* 2.9 34.6 + - - +
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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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124A ASN* 5.0 7.5 + - - +
127A GLY 4.4 12.8 - - - -
128A ARG* 3.8 30.9 - - - +
131A LYS* 4.0 32.8 - - + +
142A ALA* 2.9 23.9 + - - +
143A ILE* 3.3 8.5 + - + +
145A ILE* 1.3 80.2 - - + +
147A THR* 1.3 58.8 - - - +
149A ASN* 3.5 7.9 + - - +
150A SER* 2.8 26.1 + - - -
155A GLU* 5.0 0.5 - - - +
159A GLU* 3.5 35.7 - - + +
162A GLU* 6.1 0.7 - - + -
158C THR* 6.0 2.4 - - - +
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Residues in contact with THR 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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83A ALA* 3.9 29.2 - - - +
143A ILE* 2.9 18.6 + - - +
144A LEU* 3.5 6.7 - - - -
146A LYS* 1.3 74.9 - - - +
148A ILE* 1.3 66.9 + - - +
150A SER* 3.0 25.0 + - - +
156A LYS* 4.1 14.5 - - + +
159A GLU* 4.0 10.2 - - - +
160A LEU* 3.4 45.3 + - + +
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Residues in contact with ILE 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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82A LEU* 3.8 41.3 - - + +
83A ALA* 5.0 0.2 - - - -
108A LEU* 4.1 7.2 - - + -
111A LEU* 3.8 42.4 - - + -
120A LYS* 3.8 18.5 + - - -
123A LEU* 5.5 2.2 - - + -
144A LEU* 2.9 36.9 + - + +
145A ILE* 3.5 6.7 - - + +
147A THR* 1.3 76.3 - - - +
149A ASN* 1.3 70.6 + - - +
150A SER 3.2 6.3 + - - +
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Residues in contact with ASN 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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111A LEU* 5.4 0.2 - - - +
120A LYS* 3.0 59.7 + - - +
123A LEU* 4.6 1.9 - - - +
124A ASN* 3.7 22.8 + - - +
145A ILE* 2.9 27.5 + - - +
146A LYS* 3.7 7.6 - - - +
147A THR 3.1 0.4 - - - -
148A ILE* 1.3 77.1 - - - +
150A SER* 1.3 60.1 + - - +
151A GLU* 3.8 4.4 + - - +
155A GLU* 4.3 7.1 - - - +
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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