Contacts of the helix formed by residues 134 - 149 (chain C) in PDB entry 1SL0
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 GLU 134 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C THR* 5.6 1.6 + - - -
108C GLY* 5.8 1.6 - - - -
130C TYR* 3.4 43.3 + - + +
131C ARG* 4.3 7.4 - - - +
133C GLY* 1.3 70.2 - - - +
135C MET* 1.3 53.6 + - - +
136C LYS 2.8 16.2 + - - -
137C GLY* 2.8 17.2 + - - +
138C GLU* 3.4 7.0 + - - +
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Residues in contact with MET 135 (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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131C ARG* 3.6 41.2 - - - +
132C LEU* 3.6 14.5 - - - +
133C GLY 3.0 0.4 - - - -
134C GLU* 1.3 77.1 - - - +
136C LYS* 1.3 59.4 + - - +
137C GLY 3.4 0.2 - - - -
138C GLU* 3.5 10.0 - - + +
170C TYR* 3.4 52.6 - - + +
173C GLN* 4.3 7.9 - - + -
174C ASP* 3.2 47.3 - - - +
177C VAL* 4.4 16.2 - - - -
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Residues in contact with LYS 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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107C MET 5.7 2.2 - - - +
132C LEU 4.3 3.0 + - - +
133C GLY 3.3 13.9 + - - +
134C GLU 2.8 2.2 + - - -
135C MET* 1.3 78.8 - - - +
137C GLY* 1.3 61.2 + - - +
139C TYR* 3.1 23.8 + - - +
140C LYS* 3.3 5.5 + - - +
160C TRP* 4.8 16.6 - - + -
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Residues in contact with GLY 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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134C GLU* 2.8 10.0 + - - +
136C LYS* 1.3 74.8 - - - +
138C GLU* 1.3 65.0 + - - +
139C TYR 3.0 2.0 - - - -
140C LYS* 3.0 21.8 + - - +
141C ASP* 3.2 20.3 + - - +
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Residues in contact with GLU 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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131C ARG* 6.0 3.6 - - - +
134C GLU 3.4 4.0 + - - +
135C MET* 3.5 21.5 - - + +
136C LYS 3.2 0.4 - - - -
137C GLY* 1.3 78.1 - - - +
139C TYR* 1.3 55.6 + - - +
141C ASP* 4.7 1.6 - - - +
142C ASP* 3.0 21.8 + - - +
170C TYR* 2.5 28.2 + - + +
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Residues in contact with TYR 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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7C GLU* 6.0 1.1 - - - -
136C LYS* 3.1 11.1 + - - +
137C GLY 3.0 0.2 - - - -
138C GLU* 1.3 77.2 - - - +
140C LYS* 1.3 67.0 + - - +
142C ASP* 3.6 2.6 - - - +
143C PHE* 3.1 25.8 + - + +
159C GLU* 2.8 42.2 + - + -
160C TRP* 3.9 29.8 - + + -
164C ASN* 3.4 16.8 + - - -
166C GLU* 4.1 10.5 - - + -
167C MET* 3.3 44.9 - - + +
170C TYR* 3.1 47.4 + + + -
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Residues in contact with LYS 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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136C LYS 3.3 4.4 + - - +
137C GLY* 3.0 18.5 + - - +
139C TYR* 1.3 83.7 - - - +
141C ASP* 1.3 62.1 + - - +
143C PHE* 3.1 4.3 + - - +
144C LYS* 2.5 58.3 + - + +
154C TYR* 3.1 37.0 + - + +
156C ASP 4.5 2.4 + - - -
159C GLU* 3.4 25.0 + - + +
160C TRP* 6.2 0.2 - - - +
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Residues in contact with ASP 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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137C GLY* 3.2 13.3 + - - +
138C GLU* 4.9 1.8 - - - +
140C LYS* 1.3 84.0 - - - +
142C ASP* 1.3 59.3 + - - +
144C LYS* 3.6 27.0 + - - +
145C ARG* 2.7 49.6 + - + +
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Residues in contact with ASP 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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138C GLU 3.0 23.2 + - - +
139C TYR* 3.6 8.1 - - - +
140C LYS 3.2 0.2 - - - -
141C ASP* 1.3 77.6 - - - +
143C PHE* 1.3 60.2 + - - +
145C ARG* 4.6 2.9 - - - +
146C MET* 3.4 22.9 + - - +
166C GLU* 3.9 23.2 - - - +
170C TYR* 3.9 19.5 + - - +
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Residues in contact with PHE 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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139C TYR* 3.1 27.6 + - + +
140C LYS 3.1 3.2 + - - +
142C ASP* 1.3 81.5 - - - +
144C LYS* 1.3 68.9 + - - +
145C ARG 3.3 0.2 - - - -
146C MET* 3.4 5.1 + - - +
147C LEU* 3.3 23.2 + - - +
159C GLU* 4.5 17.9 - - + -
164C ASN* 6.0 1.8 - - - +
166C GLU* 5.7 3.1 - - + -
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Residues in contact with LYS 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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140C LYS* 2.5 50.1 + - + +
141C ASP* 3.6 23.4 + - - +
143C PHE* 1.3 74.8 - - - +
145C ARG* 1.3 54.1 + - - +
147C LEU* 3.3 2.3 - - - +
148C GLU* 2.4 43.9 + - + +
154C TYR* 3.3 55.9 - - + +
159C GLU* 5.9 0.2 - - - +
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Residues in contact with ARG 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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141C ASP* 2.7 37.6 + - + +
142C ASP* 4.6 3.6 - - - +
144C LYS* 1.3 67.9 - - + +
146C MET* 1.3 53.9 + - - +
147C LEU 2.4 19.3 + - - -
148C GLU* 2.7 14.5 + - + -
149C GLU* 2.7 35.3 + - - +
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Residues in contact with MET 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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142C ASP 3.4 19.0 + - - +
143C PHE* 3.4 6.8 + - - +
145C ARG* 1.3 74.9 - - - +
147C LEU* 1.3 57.8 + - - +
149C GLU* 4.7 0.7 - - - -
150C GLN* 3.7 21.0 + - - +
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Residues in contact with LEU 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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143C PHE 3.3 12.8 + - - +
144C LYS* 3.0 3.1 + - - +
145C ARG 2.4 17.2 + - - -
146C MET* 1.3 71.5 - - - +
148C GLU* 1.3 50.9 + - - +
149C GLU 3.0 9.7 + - - +
150C GLN* 3.5 15.2 + - - +
152C GLU* 2.6 47.3 + - + +
154C TYR* 6.5 0.7 - - - -
158C MET* 6.2 4.3 - - + -
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Residues in contact with GLU 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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144C LYS* 2.4 40.7 + - + +
145C ARG* 2.7 7.1 + - + +
147C LEU* 1.3 71.9 - - - +
149C GLU* 1.3 67.1 + - - +
151C GLY 4.9 1.7 + - - -
152C GLU 3.9 9.4 - - - -
153C GLU* 5.7 0.7 - - - +
154C TYR* 5.2 8.1 - - + +
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Residues in contact with GLU 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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145C ARG* 2.7 42.1 + - - +
146C MET* 4.7 0.3 - - - -
147C LEU 3.0 0.4 - - - -
148C GLU* 1.3 94.9 - - - +
150C GLN* 1.3 78.6 + - - +
151C GLY 3.0 10.6 + - - -
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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