Contacts of the helix formed by residues 135 - 149 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133C GLN* 3.4 8.0 + - + +
134C LYS* 1.3 86.0 - - + +
136C GLU* 1.3 65.3 + - - +
137C ALA* 3.8 8.8 + - - +
138C ALA* 3.1 25.3 + - - +
139C LYS* 3.2 26.8 + - - +
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Residues in contact with GLU 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ARG 5.8 1.1 - - - +
8C ILE* 3.6 35.0 + - + +
15C ARG* 2.9 25.8 + - - -
134C LYS 4.3 0.2 + - - -
135C THR* 1.3 73.9 - - - +
137C ALA* 1.3 57.4 + - - +
139C LYS* 3.2 8.1 + - + +
140C ILE* 2.9 37.4 + - + +
166C LEU* 4.5 13.9 - - + +
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Residues in contact with ALA 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LYS* 4.5 18.4 - - + -
6C ARG* 3.5 41.4 + - + +
135C THR* 3.3 8.6 - - - +
136C GLU* 1.3 79.3 - - - +
138C ALA* 1.3 61.5 + - - +
140C ILE* 3.5 3.2 + - - +
141C LEU* 3.2 21.3 + - - +
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Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C ALA* 3.3 31.5 - - + +
133C GLN* 3.6 26.7 - - + +
135C THR* 3.1 21.9 + - - +
137C ALA* 1.3 77.3 - - - +
139C LYS* 1.3 58.2 - - - +
141C LEU* 3.3 10.9 + - + +
142C ALA* 3.0 23.2 + - - +
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Residues in contact with LYS 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A CYS 5.1 3.0 + - - -
165A GLY* 4.5 21.2 - - - +
130C ALA 4.7 0.7 - - - -
131C LYS* 3.1 28.4 + - + +
132C LEU 5.0 0.4 - - - -
133C GLN 2.9 27.0 + - - +
134C LYS* 4.1 14.9 - - - +
135C THR 3.2 17.8 + - - +
136C GLU* 3.7 4.7 - - + +
138C ALA* 1.3 74.7 - - - +
140C ILE* 1.3 64.9 + - - +
142C ALA* 3.3 7.8 + - - +
143C ILE* 3.0 29.2 + - + +
166C LEU* 4.0 31.4 - - + -
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Residues in contact with ILE 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ARG* 3.9 13.7 - - + +
8C ILE* 3.8 32.8 - - + +
17C TYR* 3.6 47.1 - - + -
18C PHE* 4.4 11.3 - - + -
79C ASP* 5.0 0.2 - - - +
136C GLU* 2.9 26.2 + - + +
137C ALA* 3.8 7.9 - - - +
139C LYS* 1.3 76.6 - - - +
141C LEU* 1.3 57.3 + - - +
143C ILE* 3.2 6.4 + - - +
144C LEU* 2.9 27.9 + - + +
163C LEU* 5.5 2.2 - - + -
166C LEU* 3.8 17.5 - - + -
168C LEU* 4.4 6.3 - - + -
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Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ARG* 3.9 33.6 - - - +
107C ASP* 4.3 4.0 - - - +
108C LEU* 4.0 22.7 - - + -
126C MSE 4.7 15.3 - - + -
130C ALA* 4.4 15.3 - - + -
137C ALA 3.2 11.9 + - - +
138C ALA* 3.5 10.5 - - - +
140C ILE* 1.3 78.9 - - - +
142C ALA* 1.3 63.2 + - - +
144C LEU* 3.2 5.9 + - + +
145C ILE* 2.9 42.7 + - + +
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Residues in contact with ALA 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C GLY* 3.2 34.5 - - - +
130C ALA* 4.1 0.9 - - + +
131C LYS* 3.6 30.5 - - + +
138C ALA 3.0 9.3 + - - +
139C LYS 3.6 8.1 - - - +
140C ILE 3.3 0.2 - - - -
141C LEU* 1.3 76.6 - - - +
143C ILE* 1.3 59.4 + - + +
145C ILE* 3.3 1.7 + - - +
146C LYS* 3.0 39.3 + - - +
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Residues in contact with ILE 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C PHE* 5.6 2.5 - - + -
131C LYS* 5.5 9.4 - - - +
139C LYS* 3.0 18.9 + - + +
140C ILE 3.8 3.6 - - - +
142C ALA* 1.3 76.2 - - + +
144C LEU* 1.3 57.7 + - - +
146C LYS* 3.3 9.9 + - + +
147C THR* 2.9 39.6 + - - +
159C GLU* 3.7 19.4 - - - +
160C LEU* 4.5 2.7 - - + -
162C GLU* 3.7 39.5 - - + +
163C LEU* 3.8 29.8 - - + +
166C LEU* 3.9 21.1 - - + -
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Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ARG* 4.1 7.6 - - - +
18C PHE* 4.1 15.7 - - + -
79C ASP* 3.3 58.8 - - + +
82C LEU* 4.4 2.2 - - + -
83C ALA* 4.0 19.7 - - + +
108C LEU* 3.8 19.3 - - + -
140C ILE* 2.9 17.2 + - + +
141C LEU* 3.2 6.3 + - + +
143C ILE* 1.3 77.2 - - - +
145C ILE* 1.3 58.0 + - - +
147C THR* 3.2 5.8 + - - -
148C ILE* 2.9 49.7 + - + +
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Residues in contact with ILE 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C LEU* 4.3 11.7 - - + -
123C LEU* 3.4 48.9 - - + +
124C ASN* 4.1 4.0 - - - +
126C MSE 4.1 15.9 - - - -
127C GLY* 3.8 20.0 - - - +
141C LEU* 2.9 43.0 + - + +
142C ALA 3.7 4.3 - - - +
144C LEU* 1.3 74.1 - - - +
146C LYS* 1.3 67.1 + - + +
148C ILE* 3.3 7.9 + - - +
149C ASN* 2.9 34.6 + - - +
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Residues in contact with LYS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A THR* 5.9 3.6 - - - +
124C ASN* 4.9 8.9 + - - +
127C GLY 4.5 13.0 - - - -
128C ARG* 3.8 31.0 - - - +
131C LYS* 4.1 31.6 - - + +
142C ALA* 3.0 23.9 + - - +
143C ILE* 3.8 8.1 - - + +
145C ILE* 1.3 79.9 - - + +
147C THR* 1.3 59.8 + - - +
149C ASN* 3.5 6.7 + - - +
150C SER* 2.8 26.8 + - - -
155C GLU* 5.2 0.9 - - - +
159C GLU* 3.5 36.5 - - + +
162C GLU* 6.0 0.4 - - + -
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Residues in contact with THR 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ALA* 4.2 17.0 - - + +
143C ILE* 2.9 20.1 + - - +
144C LEU* 3.2 8.2 + - - -
146C LYS* 1.3 73.5 - - - +
148C ILE* 1.3 65.0 + - - +
150C SER* 3.1 23.8 + - - +
156C LYS* 3.6 33.2 - - + +
159C GLU* 4.1 3.4 - - - +
160C LEU* 3.4 47.0 + - + +
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Residues in contact with ILE 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C LEU* 3.9 37.5 - - + +
83C ALA* 4.8 0.9 - - - +
108C LEU* 4.0 8.7 - - + -
111C LEU* 3.8 33.4 - - + -
120C LYS* 3.8 27.5 + - - -
123C LEU* 5.6 2.2 - - + -
144C LEU* 2.9 45.8 + - + +
145C ILE* 3.6 7.2 - - + +
147C THR* 1.3 76.5 - - - +
149C ASN* 1.3 63.4 + - - +
150C SER 3.4 5.9 + - - +
156C LYS* 5.9 0.9 - - - +
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Residues in contact with ASN 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C LYS* 3.1 60.7 + - - +
123C LEU* 4.5 2.1 - - - +
124C ASN* 3.8 14.6 - - - +
145C ILE* 2.9 35.0 + - - +
146C LYS* 3.8 6.5 - - - +
148C ILE* 1.3 78.5 - - - +
150C SER* 1.3 63.4 + - - +
151C GLU* 3.6 13.0 + - - +
155C GLU* 4.5 5.3 - - - +
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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