Contacts of the helix formed by residues 133 - 156 (chain C) in PDB entry 5DQZ
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 SER 133 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LEU* 4.2 6.7 - - - -
132C ARG* 1.3 76.8 - - - +
134C VAL* 1.3 64.5 + - - +
135C GLU* 3.5 15.2 + - - +
136C GLN* 3.1 31.4 + - - +
137C LEU* 3.2 20.6 + - - +
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Residues in contact with VAL 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLU* 5.1 3.8 - - - +
112C ARG* 3.9 43.7 - - - +
113C LEU* 3.9 25.1 - - + +
116C VAL* 4.2 22.6 - - + +
133C SER* 1.3 75.5 - - - +
135C GLU* 1.3 58.6 + - - +
137C LEU* 3.3 7.4 + - - +
138C ARG* 2.9 38.3 + - - +
206C PHE 4.1 9.2 - - - +
207C VAL* 4.7 5.6 - - + -
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Residues in contact with GLU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C SER* 3.3 16.6 + - - +
134C VAL* 1.3 76.2 - - - +
136C GLN* 1.3 72.1 + - - +
138C ARG* 3.4 26.6 + - - +
139C GLY* 3.0 22.5 + - - -
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Residues in contact with GLN 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ARG 4.0 2.6 - - - +
132C ARG* 3.1 37.4 - - - +
133C SER* 3.1 33.3 + - - +
135C GLU* 1.3 92.0 + - - +
137C LEU* 1.3 64.7 + - - +
139C GLY* 3.1 3.9 + - - +
140C ILE* 3.0 28.4 + - - +
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Residues in contact with LEU 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C LEU* 4.1 16.8 - - + -
116C VAL* 3.8 28.3 - - + +
117C ARG* 4.2 17.7 - - + +
120C PHE* 4.5 16.9 - - + -
128C ALA* 3.6 27.1 - - + -
129C PRO 5.0 0.2 - - - +
132C ARG* 3.8 22.4 - - + +
133C SER 3.2 18.3 + - - +
134C VAL* 3.3 7.2 + - - +
136C GLN* 1.3 77.4 - - - +
138C ARG* 1.3 55.9 + - - +
140C ILE* 3.2 14.4 + - + +
141C GLU* 2.9 27.3 + - - +
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Residues in contact with ARG 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ARG* 4.4 6.9 - - - +
134C VAL* 2.9 30.8 + - - +
135C GLU* 3.6 27.3 - - - +
136C GLN 3.2 0.2 - - - -
137C LEU* 1.3 77.9 - - - +
139C GLY* 1.3 56.5 + - - +
141C GLU* 3.2 20.9 + - - +
142C GLY* 2.9 24.6 + - - -
207C VAL* 3.0 39.7 + - + +
209C THR* 5.6 1.4 + - - -
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Residues in contact with GLY 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C GLU 3.0 14.2 + - - -
136C GLN* 3.1 5.5 + - - -
138C ARG* 1.3 77.2 - - - +
140C ILE* 1.3 62.2 + - - +
142C GLY* 3.0 12.6 + - - -
143C SER* 3.1 12.3 + - - -
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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
----------------------------------------------------------
120C PHE* 3.9 23.3 - - + -
129C PRO* 3.7 33.0 - - + -
132C ARG* 3.9 17.7 - - - +
136C GLN 3.0 15.3 + - - +
137C LEU* 3.2 15.2 + - + +
139C GLY* 1.3 74.7 - - - +
141C GLU* 1.3 62.4 + - - +
143C SER* 3.3 8.6 + - - -
144C ARG* 3.0 40.5 + - + +
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Residues in contact with GLU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C PHE* 4.8 1.5 - - + -
123C ARG* 2.5 40.8 + - - +
124C PHE* 4.0 20.9 - - + -
137C LEU 2.9 13.2 + - - +
138C ARG* 3.4 25.7 - - - +
140C ILE* 1.3 73.9 - - - +
142C GLY* 1.3 67.9 + - - +
144C ARG* 3.9 0.7 - - - +
145C VAL* 2.9 35.0 + - + +
207C VAL* 4.1 14.0 - - - +
208C HIS* 4.8 5.7 + - - -
221C ASP* 3.7 11.3 - - - +
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Residues in contact with GLY 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ARG 2.9 14.0 + - - -
139C GLY* 3.0 4.9 + - - -
141C GLU* 1.3 76.5 - - - +
143C SER* 1.3 62.2 + - - +
145C VAL* 3.2 6.8 + - - +
146C ARG* 3.1 32.2 + - - +
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Residues in contact with SER 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 GLY 3.1 10.1 + - - -
140C ILE* 3.5 10.8 - - - -
142C GLY* 1.3 76.5 - - - +
144C ARG* 1.3 66.1 + - - +
146C ARG* 3.2 32.0 + - - +
147C ALA* 3.0 20.3 + - - +
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Residues in contact with ARG 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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120C PHE* 4.2 16.6 - - - -
124C PHE* 3.5 56.8 + - + +
126C GLU* 2.9 31.8 + - - +
127C PRO 5.8 0.6 + - - -
129C PRO* 5.8 3.8 - - - +
140C ILE* 3.0 31.1 + - + +
141C GLU 4.0 0.4 - - - +
143C SER* 1.3 78.1 - - - +
145C VAL* 1.3 57.6 + - - +
147C ALA* 3.2 10.7 + - - +
148C THR* 2.9 32.2 + - - +
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Residues in contact with VAL 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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123C ARG* 3.2 31.4 - - - +
124C PHE* 5.2 3.4 - - + -
141C GLU* 2.9 31.8 + - + +
142C GLY* 3.6 6.1 - - - +
143C SER 3.2 0.2 - - - -
144C ARG* 1.3 74.0 - - - +
146C ARG* 1.3 68.7 + - + +
148C THR* 3.0 8.8 + - - -
149C TYR* 3.0 47.3 + - + -
225C PHE* 3.8 13.0 - - + -
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Residues in contact with ARG 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C GLY 3.1 15.0 + - - +
143C SER* 3.4 35.6 + - - +
145C VAL* 1.3 78.8 - - + +
147C ALA* 1.3 64.4 + - - +
148C THR 3.3 0.2 + - - -
149C TYR* 3.3 9.7 + - + +
150C ALA* 3.0 23.8 + - - +
160C TRP* 5.5 0.3 + - - -
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Residues in contact with ALA 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 SER 3.0 12.9 + - - +
144C ARG* 3.3 13.5 - - - +
145C VAL 3.2 0.2 - - - -
146C ARG* 1.3 77.8 - - - +
148C THR* 1.3 57.2 + - - +
150C ALA* 3.4 6.6 + - - +
151C LEU* 3.0 29.5 + - - +
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Residues in contact with THR 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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124C PHE* 5.7 2.4 - - - -
144C ARG* 2.9 16.0 + - - +
145C VAL* 3.0 10.3 + - - -
147C ALA* 1.3 73.7 - - - +
149C TYR* 1.3 64.8 + - - +
151C LEU* 3.2 10.6 + - + +
152C LEU* 2.9 35.1 + - + +
225C PHE* 3.6 39.0 - - + +
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Residues in contact with TYR 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 VAL* 3.0 41.8 + - + -
146C ARG* 3.7 10.5 - - + +
148C THR* 1.3 76.5 - - - +
150C ALA* 1.3 55.9 + - - +
152C LEU* 3.9 3.9 - - + +
153C ALA* 2.9 31.3 + - - +
160C TRP* 3.5 41.2 - + - +
163C ARG* 4.1 24.8 + - + +
180C ILE* 3.9 26.4 - - + +
224C LYS* 5.0 7.6 + - - -
225C PHE* 3.8 25.4 - + - -
229C VAL* 4.2 7.7 - - + +
233C PHE* 4.1 15.6 - + - -
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Residues in contact with ALA 150 (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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146C ARG 3.0 13.6 + - - +
147C ALA* 3.6 9.2 - - - +
149C TYR* 1.3 76.0 - - - +
151C LEU* 1.3 63.7 + - - +
153C ALA* 3.2 7.8 + - - +
154C LYS* 3.0 25.1 + - - +
160C TRP* 4.7 7.5 - - + -
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Residues in contact with LEU 151 (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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147C ALA 3.0 18.6 + - - +
148C THR* 3.2 10.7 + - + +
150C ALA* 1.3 77.1 - - - +
152C LEU* 1.3 59.9 + - + +
154C LYS* 3.2 13.9 + - + +
155C GLN* 2.9 58.4 + - + +
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Residues in contact with LEU 152 (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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148C THR* 2.9 36.1 + - + +
149C TYR* 4.0 3.4 - - - +
151C LEU* 1.3 74.9 - - + +
153C ALA* 1.3 66.2 + - - +
155C GLN* 4.1 14.1 - - - +
156C TYR* 3.0 52.6 + - + +
225C PHE* 4.4 3.8 - - + +
229C VAL* 3.7 29.4 - - + -
230C PRO* 4.1 25.1 - - + -
233C PHE* 3.9 18.4 - - + -
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Residues in contact with ALA 153 (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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149C TYR 2.9 19.2 + - - +
150C ALA* 3.2 8.3 + - - +
152C LEU* 1.3 75.9 - - - +
154C LYS* 1.3 58.1 + - + +
157C GLY* 3.1 3.8 + - - -
158C VAL 2.7 45.3 + - - +
160C TRP* 3.5 22.0 - - + -
233C PHE* 3.5 15.8 - - + -
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Residues in contact with LYS 154 (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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150C ALA 3.0 15.4 + - - +
151C LEU* 4.0 11.7 - - + +
153C ALA* 1.3 78.4 - - - +
155C GLN* 1.3 67.8 + - + +
156C TYR 3.3 0.4 - - - -
157C GLY* 3.3 10.1 + - - +
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Residues in contact with GLN 155 (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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151C LEU* 2.9 48.4 + - + +
152C LEU* 3.3 20.5 + - - +
154C LYS* 1.3 80.5 - - + +
156C TYR* 1.3 69.0 + - + +
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Residues in contact with TYR 156 (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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152C LEU* 3.0 40.9 + - + +
155C GLN* 1.3 89.5 - - + +
157C GLY* 1.3 59.0 + - - +
158C VAL* 4.4 3.6 - - + -
230C PRO* 3.5 27.5 + - + +
231C LYS* 5.9 0.9 - - - +
233C PHE* 3.8 24.2 - - + +
234C GLU* 3.6 40.9 + - + +
237C ARG* 2.9 33.3 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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