Contacts of the helix formed by residues 153 - 167 (chain A) in PDB entry 1QTE
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 ASP 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A LYS* 5.5 8.7 + - - +
146A TRP* 5.0 2.2 - - + -
151A LYS 3.3 7.5 + - - +
152A GLN* 1.3 74.3 - - - +
154A PRO* 1.3 73.0 - - - +
155A LEU* 3.2 32.4 + - - +
156A ALA* 2.9 35.2 + - + +
157A TYR 3.3 3.8 + - - -
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Residues in contact with PRO 154 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A GLN* 3.2 9.4 - - + +
153A ASP* 1.3 90.3 - - - +
155A LEU* 1.3 62.7 + - + +
157A TYR* 3.1 12.7 + - + +
158A LEU 3.0 18.5 + - - -
181A PRO* 4.9 8.1 - - + -
183A ASP* 4.0 26.2 - - - +
184A TYR* 3.3 31.1 - - + +
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Residues in contact with LEU 155 (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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153A ASP* 3.1 21.2 + - - +
154A PRO* 1.3 79.5 - - + +
156A ALA* 1.3 59.1 + - - +
158A LEU* 3.5 6.4 + - + +
159A GLU* 2.9 28.8 + - - +
184A TYR* 3.4 17.2 + - + +
901A GOL 3.9 18.4 - - - +
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Residues in contact with ALA 156 (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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126A LYS* 4.7 16.2 - - + -
129A TRP* 3.1 23.7 + - + +
130A LEU* 4.0 13.5 - - + +
146A TRP* 4.8 10.3 - - + -
153A ASP* 2.9 25.4 + - + +
155A LEU* 1.3 76.6 - - - +
157A TYR* 1.3 65.8 + - - +
159A GLU* 3.3 8.4 + - - +
160A ARG 3.2 13.2 + - - -
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Residues in contact with TYR 157 (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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129A TRP* 3.6 33.6 - + - +
147A ARG* 3.7 17.0 - - - -
152A GLN* 3.6 23.0 - - - +
153A ASP 3.3 3.1 + - - +
154A PRO* 3.1 18.1 + - + +
156A ALA* 1.3 79.6 - - - +
158A LEU* 1.3 63.9 + - - +
160A ARG* 3.2 14.6 + - - +
161A ILE* 3.4 12.7 + - + +
176A LEU* 2.5 54.8 + - + +
179A GLN* 3.3 22.2 + - - +
180A MET* 4.1 11.2 - - - -
181A PRO* 3.4 28.5 - - + -
184A TYR* 5.5 0.7 - + - -
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Residues in contact with LEU 158 (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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154A PRO 3.0 14.3 + - - +
155A LEU* 3.9 7.6 - - + +
157A TYR* 1.3 78.8 - - - +
159A GLU* 1.3 61.6 + - - +
161A ILE* 3.2 18.9 + - + +
162A ARG 3.2 9.2 + - - -
180A MET* 4.2 17.7 - - + -
184A TYR* 4.0 31.4 - - + +
187A ILE* 4.8 1.6 - - + -
213A PHE* 3.6 45.6 - - + -
901A GOL 3.6 42.2 - - - +
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Residues in contact with GLU 159 (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 LEU* 3.8 20.0 - - + -
155A LEU 2.9 19.0 + - - +
156A ALA* 3.5 9.9 - - - +
157A TYR 3.2 0.2 - - - -
158A LEU* 1.3 77.9 - - - +
160A ARG* 1.3 57.7 + - - +
162A ARG* 2.8 46.9 + - - +
163A LEU* 3.0 38.8 + - + +
213A PHE* 5.9 0.2 - - - -
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Residues in contact with ARG 160 (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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129A TRP* 3.0 76.0 + - + +
130A LEU* 4.8 0.9 - - + +
131A THR 3.0 22.1 + - - +
133A LYS 3.0 24.7 + - - -
134A SER* 4.2 0.6 - - - +
135A GLN* 3.8 24.9 - - - +
143A PHE* 3.8 13.2 - - - -
156A ALA 3.2 4.6 + - - -
157A TYR 3.2 6.7 + - - +
159A GLU* 1.3 72.8 - - - +
161A ILE* 1.3 61.1 + - - +
163A LEU* 3.3 7.9 + - - +
164A ALA* 2.8 29.1 + - - +
172A LEU* 3.7 27.1 - - + +
176A LEU* 4.0 12.4 - - + +
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Residues in contact with ILE 161 (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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157A TYR* 3.7 15.3 - - + +
158A LEU* 3.3 13.2 - - + +
160A ARG* 1.3 78.0 - - - +
162A ARG* 1.3 56.5 + - - +
164A ALA* 3.4 3.8 + - - +
165A MET* 3.0 28.1 + - - +
173A VAL* 3.8 15.7 - - + +
176A LEU* 3.7 34.3 - - + -
177A ALA* 4.1 9.2 - - + +
180A MET* 3.8 36.8 - - + -
191A ILE* 4.3 4.0 - - + -
213A PHE* 3.9 9.2 - - + -
217A MET* 3.8 22.9 - - + -
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Residues in contact with ARG 162 (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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158A LEU 3.2 8.9 + - - +
159A GLU* 2.8 45.9 + - - +
161A ILE* 1.3 79.7 - - - +
163A LEU* 1.3 62.8 + - - +
165A MET* 3.3 3.1 + - - +
166A LYS* 3.0 50.9 + - + +
213A PHE* 4.0 21.3 - - + +
216A GLN* 2.6 61.3 + - + +
217A MET* 4.0 13.2 - - - +
713A SO4 3.0 41.1 + - - -
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Residues in contact with LEU 163 (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 LEU* 3.6 37.7 - - + +
131A THR* 3.6 4.7 - - - +
132A GLY* 3.5 15.7 - - - +
159A GLU* 3.0 36.3 + - + +
160A ARG* 3.7 6.1 - - - +
162A ARG* 1.3 99.8 - - - +
164A ALA* 1.3 61.9 + - - +
166A LYS* 3.4 11.1 + - + +
167A ALA* 3.0 24.6 + - - +
713A SO4 4.2 9.0 - - - +
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Residues in contact with ALA 164 (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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132A GLY* 3.5 12.9 - - - +
160A ARG 2.8 21.7 + - - +
161A ILE* 3.7 2.9 - - - +
163A LEU* 1.3 70.1 - - - +
165A MET* 1.3 64.1 + - - +
167A ALA 3.2 1.7 + - - -
168A GLY 3.2 3.1 + - - -
169A ASN* 2.8 34.0 + - - +
172A LEU* 3.8 29.6 - - + -
173A VAL* 3.6 18.8 - - + +
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Residues in contact with MET 165 (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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161A ILE 3.0 17.7 + - - +
162A ARG 3.6 4.9 - - - +
164A ALA* 1.3 76.5 - - - +
166A LYS* 1.3 62.4 + - - +
168A GLY* 3.0 14.6 + - - -
169A ASN 4.9 0.7 - - - +
170A THR* 4.4 16.8 - - + +
173A VAL* 3.3 19.9 - - + +
194A LEU* 3.9 41.7 - - + +
195A ALA* 4.8 3.4 - - - -
198A PRO* 6.1 0.4 - - + -
217A MET* 3.6 33.2 - - - +
220A VAL* 3.4 33.4 - - + +
221A ALA* 4.0 17.0 - - + +
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Residues in contact with LYS 166 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A ARG* 3.0 46.2 + - + +
163A LEU* 3.8 11.0 - - - +
164A ALA 3.3 0.2 - - - -
165A MET* 1.3 77.8 - - + +
167A ALA* 1.3 60.0 + - - +
168A GLY 3.2 0.9 + - - -
216A GLN* 4.2 7.6 + - + +
220A VAL* 3.9 24.8 - - + +
713A SO4 3.4 33.9 + - - -
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Residues in contact with ALA 167 (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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132A GLY* 4.2 20.2 - - - +
133A LYS* 4.9 0.7 - - - +
163A LEU 3.0 16.9 + - - +
164A ALA 3.7 4.7 - - - +
165A MET 3.2 0.6 - - - -
166A LYS* 1.3 76.2 - - - +
168A GLY* 1.3 60.4 + - - +
169A ASN* 3.1 3.3 + - + +
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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