Contacts of the helix formed by residues 134 - 150 (chain C) in PDB entry 1QBJ
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 134 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135C ILE* 1.3 62.9 + - - +
136C TYR* 3.5 14.7 + - - +
137C GLN* 3.4 44.2 + - - +
138C ASP* 3.1 34.0 + - - +
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Residues in contact with ILE 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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134C SER* 1.3 73.4 + - - +
136C TYR* 1.3 60.9 + - - +
137C GLN 3.2 0.2 - - - -
138C ASP* 3.2 13.3 + - + +
139C GLN* 3.0 53.3 + - + +
171C GLU* 5.4 1.8 - - - +
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Residues in contact with TYR 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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134C SER* 3.4 8.1 + - - +
135C ILE* 1.3 76.8 - - - +
137C GLN* 1.3 62.1 + - - +
139C GLN* 3.3 3.6 + - - +
140C GLU* 3.0 55.1 + - + +
171C GLU* 3.9 23.8 - - + +
174C ARG* 4.2 20.8 + - + +
175C VAL* 3.6 37.3 - - + +
178C SER* 4.4 10.4 + - - -
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Residues in contact with GLN 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 SER* 3.4 37.8 + - - +
135C ILE 3.2 0.4 - - - -
136C TYR* 1.3 81.0 - - + +
138C ASP* 1.3 65.8 + - - +
140C GLU* 3.1 19.6 + - - +
141C GLN* 3.0 38.6 + - + +
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Residues in contact with ASP 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C SER 3.1 22.9 + - - +
135C ILE* 3.2 19.9 + - + +
137C GLN* 1.3 76.5 - - - +
139C GLN* 1.3 60.6 + - + +
141C GLN* 3.2 12.0 + - - +
142C ARG* 2.9 39.8 + - + +
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Residues in contact with GLN 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C ILE* 3.0 36.0 + - + +
136C TYR 3.6 3.6 - - - +
138C ASP* 1.3 75.6 - - - +
140C GLU* 1.3 61.6 + - - +
142C ARG* 2.9 36.4 + - - +
143C ILE* 3.0 35.6 + - + +
165C LEU* 5.1 1.4 - - - +
166C GLY 5.8 0.2 + - - -
167C THR* 3.0 24.6 + - + +
171C GLU* 3.3 31.0 + - + +
172C ILE* 5.8 0.6 - - + +
175C VAL* 5.3 3.6 - - + -
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Residues in contact with GLU 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 TYR* 3.0 45.9 + - + +
137C GLN* 3.1 23.4 + - - +
139C GLN* 1.3 77.9 - - - +
141C GLN* 1.3 59.5 + - + +
143C ILE* 3.2 3.5 + - - +
144C LEU* 2.9 39.1 + - + +
175C VAL* 3.8 26.1 - - + +
178C SER* 5.2 2.9 + - - -
179C LEU* 3.9 20.8 - - + +
182C LYS* 5.0 8.7 + - - -
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Residues in contact with GLN 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 GLN* 3.0 29.2 + - + +
138C ASP* 3.7 10.3 - - - +
140C GLU* 1.3 75.0 - - + +
142C ARG* 1.3 61.1 + - + +
143C ILE 3.2 0.2 - - - -
144C LEU* 3.9 7.2 - - - +
145C LYS* 2.9 31.1 + - - +
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Residues in contact with ARG 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 ASP* 2.9 30.8 + - + +
139C GLN* 2.9 36.5 + - - +
141C GLN* 1.3 75.8 - - + +
143C ILE* 1.3 61.2 + - - +
145C LYS* 3.9 9.1 - - + +
146C PHE* 3.0 28.4 + - - +
164C LYS 5.3 0.4 + - - -
165C LEU* 2.7 61.6 + - + +
166C GLY 5.0 0.2 - - - -
167C THR* 3.3 6.5 + - - -
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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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139C GLN* 3.0 20.5 + - + +
140C GLU* 3.2 7.2 + - - +
142C ARG* 1.3 75.8 - - - +
144C LEU* 1.3 64.4 + - + +
146C PHE* 3.3 4.3 + - - +
147C LEU* 3.0 34.3 + - + +
161C LEU* 4.5 7.6 - - + -
165C LEU* 3.9 21.3 - - + -
172C ILE* 3.7 29.4 - - + +
175C VAL* 3.5 35.4 - - + -
176C LEU* 3.7 23.8 - - + -
179C LEU* 4.8 8.7 - - + -
185C LEU* 4.8 0.4 - - + -
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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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140C GLU* 2.9 32.2 + - + +
141C GLN* 3.9 7.2 - - - +
142C ARG 3.4 0.2 - - - -
143C ILE* 1.3 77.5 - - + +
145C LYS* 1.3 56.5 + - - +
147C LEU* 3.4 5.6 + - - +
148C GLU* 2.9 46.8 + - - +
179C LEU* 3.5 33.9 - - + -
184C LYS* 4.5 24.9 - - + +
185C LEU* 4.3 11.9 - - + -
197C ILE* 3.9 24.5 - - + -
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Residues in contact with LYS 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 GLN 2.9 18.9 + - - +
142C ARG* 3.9 9.4 - - + +
144C LEU* 1.3 77.3 - - - +
146C PHE* 1.3 61.4 + - - +
148C GLU* 3.2 13.7 + - - +
149C GLU* 3.0 58.7 + - + +
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Residues in contact with PHE 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 ARG 3.0 20.5 + - - +
143C ILE* 3.6 4.3 - - - +
145C LYS* 1.3 76.9 - - - +
147C LEU* 1.3 63.5 + - + +
149C GLU* 3.3 12.2 + - - +
150C LEU* 3.0 42.7 + - + +
156C THR* 4.3 9.6 - - + -
160C ASP* 4.0 16.2 - - - -
161C LEU* 3.4 29.6 - - + -
164C LYS* 3.6 44.0 - - + -
165C LEU* 4.4 13.2 - - + -
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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 ILE* 3.0 30.9 + - + +
144C LEU* 3.9 2.5 - - - +
146C PHE* 1.3 81.2 - - + +
148C GLU* 1.3 57.2 + - - +
150C LEU* 3.5 15.8 - - + +
151C GLY 3.1 27.9 + - - +
154C LYS 4.6 1.0 - - - +
156C THR* 3.7 31.0 - - + -
161C LEU* 4.7 3.8 - - + -
176C LEU* 4.7 5.4 - - + -
185C LEU* 3.7 37.0 - - + -
195C TRP 3.8 13.7 - - - +
196C LYS* 4.5 9.6 - - - +
197C ILE* 3.7 20.7 - - + +
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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 LEU* 2.9 40.4 + - - +
145C LYS* 3.2 12.0 + - - +
147C LEU* 1.3 75.8 - - - +
149C GLU* 1.3 65.3 + - + +
151C GLY* 3.1 14.6 + - - -
152C GLU* 4.6 6.1 + - + +
197C ILE* 4.6 16.4 - - + +
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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 LYS* 3.0 51.7 + - + +
146C PHE* 3.8 8.3 - - - +
148C GLU* 1.3 75.9 - - + +
150C LEU* 1.3 66.6 + - - +
151C GLY* 3.3 0.7 + - - -
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Residues in contact with LEU 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 PHE* 3.0 28.1 + - + +
147C LEU* 3.5 25.6 - - + +
149C GLU* 1.3 77.9 - - - +
151C GLY* 1.3 57.7 + - - +
154C LYS* 3.6 52.2 - - + +
155C ALA 4.1 4.7 - - - +
156C THR* 4.0 21.5 - - + -
160C ASP* 6.0 0.4 - - - +
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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